InteractiveFly: GeneBrief

maternal expression at 31B: Biological Overview | References

Gene name - maternal expression at 31B

Synonyms -

Cytological map position- 31B1-31B1

Function - post-transcriptional regulation

Keywords - oogenesis, CNS, post-transcriptional regulation, P-bodies

Symbol - me31B

FlyBase ID: FBgn0004419

Genetic map position - 2L: 10,239,326..10,242,175 [+]

Classification - DEAD-box helicase

Cellular location - cytoplasmic

NCBI links: EntrezGene

Me31b orthologs: Biolitmine
Recent literature
Wang, M., Ly, M., Lugowski, A., Laver, J. D., Lipshitz, H. D., Smibert, C. A. and Rissland, O. S. (2017). ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. Elife 6. PubMed ID: 28875934
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). An RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. It is proposed that ME31B is a global repressor whose regulatory impact changes based on its biological context.
Ren, L., Mo, D., Li, Y., Liu, T., Yin, H., Jiang, N. and Zhang, J. (2018). A genetic mosaic screen identifies genes modulating Notch signaling in Drosophila. PLoS One 13(9): e0203781. PubMed ID: 30235233
Notch signaling is conserved in most multicellular organisms and plays critical roles during animal development. The core components and major signal transduction mechanism of Notch signaling have been extensively studied. However, understanding of how Notch signaling activity is regulated in diverse developmental processes still remains incomplete. This study reports a genetic mosaic screen in Drosophila melanogaster that leads to identification of Notch signaling modulators during wing development. A group of genes was discovered required for the formation of the fly wing margin, a developmental process that is strictly dependent on the balanced Notch signaling activity. These genes encode transcription factors, protein phosphatases, vacuolar ATPases and factors required for RNA transport, stability, and translation. These data support the view that Notch signaling is controlled through a wide range of molecular processes. These results also provide foundations for further study by showing that Me31B and Wdr62 function as two novel modulators of Notch signaling activity.
Jensen, L., Venkei, Z. G., Watase, G. J., Bisai, B., Pletcher, S., Lee, C. Y. and Yamashita, Y. M. (2021). me31B regulates stem cell homeostasis by preventing excess dedifferentiation in the Drosophila male germline. Jensen, L., Venkei, Z. G., Watase, G. J., Bisai, B., Pletcher, S., Lee, C. Y. and Yamashita, Y. M. (2021). J. Cell Sci. 134(14):jcs258757. PubMed ID: 34164657
Tissue-specific stem cells maintain tissue homeostasis by providing a continuous supply of differentiated cells throughout the life of organisms. Differentiated/differentiating cells can revert back to a stem cell identity via dedifferentiation to help maintain the stem cell pool beyond the lifetime of individual stem cells. Although dedifferentiation is important for maintaining the stem cell population, it is speculated that it underlies tumorigenesis. Therefore, this process must be tightly controlled. This study shows that a translational regulator, me31B, plays a critical role in preventing excess dedifferentiation in the Drosophila male germline: in the absence of me31B, spermatogonia dedifferentiate into germline stem cells (GSCs) at a dramatically elevated frequency. These results show that the excess dedifferentiation is likely due to misregulation of nos, a key regulator of germ cell identity and GSC maintenance. Taken together, the data reveal negative regulation of dedifferentiation to balance stem cell maintenance with differentiation.
Sankaranarayanan, M., Emenecker, R. J., Wilby, E. L., Jahnel, M., Trussina, I., Wayland, M., Alberti, S., Holehouse, A. S. and Weil, T. T. (2021). Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development. Dev Cell. PubMed ID: 34655524
Ribonucleoprotein condensates can exhibit diverse physical states in vitro and in vivo. Despite considerable progress, the relevance of condensate physical states for in vivo biological function remains limited. This study investigated the physical properties of processing bodies (P bodies) and their impact on mRNA storage in mature Drosophila oocytes. The conserved DEAD-box RNA helicase Me31B forms viscous P body condensates, which adopt an arrested physical state. Structurally distinct proteins and protein-protein interactions, together with RNA, regulate the physical properties of P bodies. Using live imaging and in situ hybridization, this study shows that the arrested state and integrity of P bodies support the storage of bicoid (bcd) mRNA and that egg activation modulates P body properties, leading to the release of bcd for translation in the early embryo. Together, this work provides an example of how physical states of condensates regulate cellular function in development.
Sankaranarayanan, M., Emenecker, R. J., Wilby, E. L., Jahnel, M., Trussina, I., Wayland, M., Alberti, S., Holehouse, A. S. and Weil, T. T. (2021). Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development. Dev Cell. PubMed ID: 34655524
Ribonucleoprotein condensates can exhibit diverse physical states in vitro and in vivo. Despite considerable progress, the relevance of condensate physical states for in vivo biological function remains limited. This study investigated the physical properties of processing bodies (P bodies) and their impact on mRNA storage in mature Drosophila oocytes. This study shows that the conserved DEAD-box RNA helicase Me31B forms viscous P body condensates, which adopt an arrested physical state. This study demonstrates that structurally distinct proteins and protein-protein interactions, together with RNA, regulate the physical properties of P bodies. Using live imaging and in situ hybridization, this study shows that the arrested state and integrity of P bodies support the storage of bicoid (bcd) mRNA and that egg activation modulates P body properties, leading to the release of bcd for translation in the early embryo. Together, this work provides an example of how physical states of condensates regulate cellular function in development (Sankaranarayanan, 2021).
Pushpalatha, K. V., Solyga, M., Nakamura, A. and Besse, F. (2022). RNP components condense into repressive RNP granules in the aging brain. Nat Commun 13(1): 2782. PubMed ID: 35589695
Cytoplasmic RNP condensates enriched in mRNAs and proteins are found in various cell types and associated with both buffering and regulatory functions. While a clear link has been established between accumulation of aberrant RNP aggregates and progression of aging-related neurodegenerative diseases, the impact of physiological aging on neuronal RNP condensates has never been explored. Through high-resolution imaging, this study uncover that RNP components progressively cluster into large yet dynamic granules in the aging Drosophila brain. It was further shown that age-dependent clustering is caused by an increase in the stoichiometry of the conserved helicase Me31B/DDX6, and requires PKA kinase activity. Finally, this functional analysis reveals that mRNA species recruited to RNP condensates upon aging exhibit age-dependent translational repression, indicating that co-clustering of selected mRNAs and translation regulators into repressive condensates may contribute to the specific post-transcriptional changes in gene expression observed in the course of aging.
Zhu, Y., Liu, L., Zhang, C., Zhang, C., Han, T., Duan, R., Jin, Y., Guo, H., She, K., Xiao, Y., Goto, A., Cai, Q. and Ji, S. (2022). Endoplasmic reticulum-associated protein degradation contributes to Toll innate immune defense in Drosophila melanogaster. Front Immunol 13: 1099637. PubMed ID: 36741393
In Drosophila, the endoplasmic reticulum-associated protein degradation (ERAD) is engaged in regulating pleiotropic biological processes, with regard to retinal degeneration, intestinal homeostasis, and organismal development. The extent to which it functions in controlling the fly innate immune defense, however, remains largely unknown. This study shows that blockade of the ERAD in fat bodies antagonizes the Toll but not the IMD innate immune defense in Drosophila. Genetic approaches further suggest a functional role of Me31B in the ERAD-mediated fly innate immunity. Moreover, evidence is provided that silence of Xbp1 other than PERK or Atf6 partially rescues the immune defects by the dysregulated ERAD in fat bodies. Collectively, this study uncovers an essential function of the ERAD in mediating the Toll innate immune reaction in Drosophila.
Layana, C., Vilardo, E. S., Corujo, G., Hernandez, G. and Rivera-Pomar, R. (2023). Drosophila Me31B is a Dual eIF4E-Interacting Protein. J Mol Biol 435(5): 167949. PubMed ID: 36638908
Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). This study showed that Drosophila eIF4E-1 and eIF4E-3 occur in PBs along the DEAD-box RNA helicase Me31B. This study shows that Me31B interacts with eIF4E-1 and eIF4E-3 by means of yeast two-hybrid system, FRET in D. melanogaster S2 cells and coimmunoprecipitation in testis. Truncation and point mutations of Me31B proteins show two eIF4E-binding sites located in different protein domains. Residues Y401-L407 (at the carboxy-terminus) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminus) are critical for interaction with eIF4E-3. The residue W117 in eIF4E-1 and the homolog position F103 in eIF4E-3 are necessary for Me31B-eIF4E interaction suggesting that the change of tryptophan to phenylalanine provides specificity. Me31B represents a novel type of eIF4E-interacting protein with dual and specific interaction domains that might be recognized by different eIF4E isoforms in different tissues, adding complexity to the control of gene expression in eukaryotes.
Zhu, Y., Liu, L., Zhang, C., Zhang, C., Han, T., Duan, R., Jin, Y., Guo, H., She, K., Xiao, Y., Goto, A., Cai, Q. and Ji, S. (2022). Endoplasmic reticulum-associated protein degradation contributes to Toll innate immune defense in Drosophila melanogaster. Front Immunol 13: 1099637. PubMed ID: 36741393

In Drosophila, the endoplasmic reticulum-associated protein degradation (ERAD) is engaged in regulating pleiotropic biological processes, with regard to retinal degeneration, intestinal homeostasis, and organismal development. The extent to which it functions in controlling the fly innate immune defense, however, remains largely unknown. This study shows that blockade of the ERAD in fat bodies antagonizes the Toll but not the IMD innate immune defense in Drosophila. Genetic approaches further suggest a functional role of Me31B in the ERAD-mediated fly innate immunity. Moreover, evidence is provided that silence of Xbp1 other than PERK or Atf6 partially rescues the immune defects by the dysregulated ERAD in fat bodies. Collectively, this study uncovers an essential function of the ERAD in mediating the Toll innate immune reaction in Drosophila (Zhu, 2022).

Kara, E., McCambridge, A., Proffer, M., Dilts, C., Pumnea, B., Eshak, J., Smith, K. A., Fielder, I., Doyle, D. A., Ortega, B. M., Mukatash, Y., Malik, N., Mohammed, A. R., Govani, D., Niepielko, M. G. and Gao, M. (2023). Mutational analysis of the functional motifs of the DEAD-box RNA helicase Me31B/DDX6 in Drosophila germline development. FEBS Lett 597(14): 1848-1867. PubMed ID: 37235728
Me31B/DDX6 is a DEAD-box family RNA helicase playing roles in post-transcriptional RNA regulation in different cell types and species. Despite the known motifs/domains of Me31B, the in vivo functions of the motifs remain unclear. This study used the Drosophila germline as a model and used CRISPR to mutate the key Me31B motifs/domains: helicase domain, N-terminal domain, C-terminal domain and FDF-binding motif. Then, screening characterization was performed on the mutants, and the effects of the mutations on the Drosophila germline, on processes such as fertility, oogenesis, embryo patterning, germline mRNA regulation and Me31B protein expression were reported. The study indicates that the Me31B motifs contribute different functions to the protein and are needed for proper germline development, providing insights into the in vivo working mechanism of the helicase.

A DEAD-box protein, Me31B, forms a cytoplasmic RNP complex with oocyte-localizing RNAs. During early oogenesis, loss of Me31B causes premature translation of oocyte-localizing RNAs within nurse cells, without affecting their transport to the oocyte. In early egg chambers that lack Me31B, at least two mRNAs in particles, OSK and Bicaudal-D mRNAs, are prematurely translated in nurse cells, though the transport of these RNAs to the oocyte is Me31B independent. These results suggest that Me31B mediates translational silencing of RNAs during their transport to the oocyte. These data provide evidence that RNA transport and translational control are linked through the assembly of RNP complex (Nakamura, 2001).

A visual screen was conducted with an ovarian GFP-cDNA library, in which fusion genes are expressed in germline cells during oogenesis. Transgenic flies were generated with this library and proteins were identified that distribute in a granular pattern during oogenesis. Screening ~3000 independent lines, one was isolated in which GFP signals were detected as cytoplasmic particles during oogenesis. The particles were dispersed in the cytoplasm of both nurse cells and oocytes but never detected within nuclei. The particles were frequently observed passing through ring canals, suggesting that the particles are assembled in nurse cell cytoplasm and transported to the oocyte (Nakamura, 2001).

The cDNA from this line was identified as me31B. In the cDNA fusion, almost the entire coding region of me31B, which lacks only the first four codons, was fused in frame with that of gfp. Me31B, a DEAD-box protein and therefore a putative ATP-dependent RNA helicase, was isolated as a gene expressed extensively during oogenesis. Me31B is a part of an evolutionally conserved DEAD-box protein group, which includes human RCK/p54 (71% identical), Xenopus Xp54 (73%), Caenorhabditis elegans C07H6.5 (76%), Schizosaccharomyces pombe Ste13 (68%) and Saccharomyces cerevisiae Dhh1 (68%). Furthermore, Me31B is phylogenetically close to two evolutionally conserved proteins, eIF4A and Dbp5/Rat8p but far from Vasa, which functions in germline development (Nakamura, 2001).

To examine distribution of the endogenous Me31B, antibodies were generated that specifically recognized Me31B. The distribution pattern of endogenous Me31B is identical to that of GFP-Me31B. No detectable signal in somatic follicle cells is observed at any stage of oogenesis. Me31B is first detected at a low level in germarium region 2B, where the signal is concentrated in the pro-oocytes. The signal remains concentrated in the oocyte until mid-oogenesis. In early egg chambers, a low level Me31B signal is detected in nurse cell cytoplasm. In both nurse cells and oocytes, the signal appears to be granular. Me31B signals in nurse cell cytoplasm become more evident from stage 5-6, when Me31B expression is drastically increased. In addition, Me31B is frequently enriched around nurse cell nuclei. Later, Me31B accumulates at the posterior pole of stage 10 oocytes. However, this posterior accumulation is transient, as revealed by uniform distribution of the signal in cleavage embryos. By cellular blastoderm stage, Me31B becomes undetectable in the entire embryonic region. No zygotic expression of Me31B was detected during embryogenesis (Nakamura, 2001).

Because Me31B is probably an RNA-binding protein that is transported to the oocyte, it was asked whether Me31B forms a complex with oocyte-localizing RNAs. Colocalization of OSK mRNA with Me31B was examined. OSK mRNA starts to accumulate in oocytes from germarium region 2B, with the concentration of OSK increasing over time. Posterior accumulation of OSK mRNA in the oocyte begins from stage 8 onwards. By fluorescent in situ hybridization, OSK mRNA exhibits particulate signals in the cytoplasm of both nurse cells and oocytes, and is frequently concentrated around nurse cell nuclei. This distribution pattern of OSK mRNA is essentially identical to that of Me31B, with colocalization present until OSK mRNA localizes to the posterior pole of stage 10 oocytes (Nakamura, 2001).

Colocalization of Me31B with other RNAs was also examined. Ovaries were doublestained for Me31B and BicD mRNA. In early egg chambers, BicD mRNA also produces particulate signals, and appears to localize in Me31B-containing particles. This colocalization becomes apparent from stage 5-6, when BicD mRNA expression is elevated. The oocyte-localizing RNAs examined [BCD, NOS, Oo18 RNA-binding (ORB), Polar granule component (PGC) and Germ cell-less (GCL)] all produce particulate signals in the cytoplasm of both nurse cells and oocytes, and colocalize with Me31B. In contrast, Vasa mRNA, which is not specifically transported to the oocyte, does not appear to be colocalized with Me31B. These results indicate that Me31B forms cytoplasmic particles that contain oocyte-localizing RNAs (Nakamura, 2001).

The complicated and redundant phenotypes observed in me31B- egg chambers in mid-oogenesis are unlikely to be the primary effect of loss of me31B function. Earlier phenotypes of me31B- egg chambers were examined using a FLP/FRT system to generate homozygous germline clones that are marked by the loss of Vas-GFP fusion protein. Based on Hoechst and phalloidin staining, me31B- egg chambers are morphologically normal until stage 4-5. From stage 6 onwards, oocytes in me31B- egg chambers fail to grow normally. At this stage, these egg chambers begin to degenerate. In early me31B- egg chambers, Exu signal is concentrated to the oocytes. Distributions of OSK and BicD mRNAs in me31B- egg chambers were examined. Both OSK and BicD mRNAs also accumulate in the oocytes of me31B- egg chambers until the chambers degenerate. Particulate signals for these RNAs are detectable in nurse cell cytoplasm in these egg chambers. These results indicate that Exu, OSK and BicD mRNAs can be transported to the oocyte even in the absence of Me31B. It is concluded that in early egg chambers, Me31B is dispensable for the transport of the molecules that form a complex with Me31B (Nakamura, 2001).

Whether loss of Me31B affects translation of OSK and BicD mRNAs was examined. Ovaries were immunostained with an anti-Osk antiserum. Although OSK mRNA is expressed during almost all stages of oogenesis, its translation is repressed to keep Osk protein level very low during early oogenesis. In me31B- egg chambers, Osk signal is significantly increased compared with that in the neighboring me31B+ egg chambers (Nakamura, 2001).

A similar increase of BicD signal in me31B- egg chambers is more evident. In wild-type egg chambers, BicD protein, like BicD mRNA, is highly concentrated in the oocytes starting from germarium region 2B. In the egg chambers lacking me31B, increased BicD signal is detected in nurse cell cytoplasm. These results suggest that loss of Me31B in germline cells causes derepression of OSK and BicD mRNA translation during their transport to the oocyte (Nakamura, 2001).

Me31B silences translation of oocyte-localizing RNAs through the formation of cytoplasmic RNP complex during Drosophila oogenesis

Translational control is a critical process in the spatio-temporal restriction of protein production. In Drosophila oogenesis, translational repression of oskar1 (osk) RNA during its localization to the posterior pole of the oocyte is essential for embryonic patterning and germ cell formation. This repression is mediated by the osk 3' UTR binding protein Bruno (Bru), but the underlying mechanism has remained elusive. An ovarian protein, Cup, is required to repress precocious osk translation. Cup binds the 5'-cap binding translation initiation factor eIF4E through a sequence conserved among eIF4E binding proteins. A mutant Cup protein lacking this sequence fails to repress osk translation in vivo. Furthermore, Cup interacts with Bru in a yeast two-hybrid assay, and the Cup-eIF4E complex associates with Bru in an RNA-independent manner. These results suggest that translational repression of osk RNA is achieved through a 5'/3' interaction mediated by an eIF4E-Cup-Bru complex (Nakamura, 2004).

In a search for new components of the oskar RNP complex, this study identified the 147-kD protein of this complex as the product of the female sterile gene cup. Surprisingly, cup is required both for translational repression and localization of oskar mRNA. Cup was found to bind to eukaryotic initiation factor 4E (eIF4E) and is necessary to recruit the localization factor Barentsz to the complex. Thus, Cup is a translational repressor of oskar that is required to assemble the oskar mRNA localization machinery. Because of its interactions with both the localization and translational control complexes, it is proposed that Cup is a likely regulatory target for the coupling machinery (Nakamura, 2004).

During localization, osk RNA forms cytoplasmic granules in both nurse cells and the oocyte. The granules contain several proteins, including the DEAD-box protein Maternal expression at 31B (Me31B), the Y-box protein Ypsilon schachtel (Yps), and Exuperantia (Exu). Genetic evidence has shown that Exu is involved in the proper localization of bcd and osk RNAs in oogenesis, although the molecular function of Exu remains unknown. Both Yps and Me31B are involved, directly or indirectly, in the translational silencing of osk RNA in oogenesis. Yps antagonizes Orb, a positive regulator of osk RNA localization and translation. In egg chambers lacking me31B, osk RNA is prematurely translated in early oogenesis (Nakamura, 2001). These data indicate that the granules are maternal ribonucleoprotein (RNP) complexes containing proteins required for both RNA localization and translational control. The complex is highly enriched in eIF4E and a germline protein, Cup. Cup is required to repress osk translation. Evidence is provided that Cup-mediated translational repression is achieved by preventing the assembly of the eIF4F complex at the 5' end of osk RNA, and that Cup acts together with Bru to repress osk translation (Nakamura, 2004).

To identify new proteins in the Me31B complex, ovarian extracts from wild-type females were immunoprecipitated on a preparative scale using an affinity-purified anti-Me31B antibody (α-Me31B). α-Me31B specifically coprecipitatesmany proteins from the extracts. Mass spectrometric analyses of these proteins revealed that both Exu and Yps, the known components in the Me31B complex (Nakamura, 2001), are present in the immunoprecipitates. The analyses also revealed that the 35 kDa protein was eIF4E and the 150 kDa protein is Cup, a germline-specific protein required for oogenesis. Cup is expressed from early oogenesis and present until the blastoderm stage of embryogenesis. Numerous cup alleles have been isolated as female sterile mutants, which show a wide range of phenotypes. However, the biochemical function of Cup has remained elusive (Nakamura, 2004).

To examine the association among Me31B, eIF4E and Cup in vivo, ovaries expressing a GFP-Me31B fusion protein were stained for eIF4E and Cup. The GFP-Me31B form cytoplasmic particles in the germline, and the distribution patterns of the fusion protein are indistinguishable from those of endogenous Me31B (Nakamura, 2001). α-eIF4E stains cytoplasmic particles that are positive for GFP-Me31B. This colocalization is observed throughout oogenesis. Cup colocalized with GFP-Me31B is also found throughout oogenesis. Thus, eIF4E, Cup, and Me31B all form a complex during oogenesis (Nakamura, 2004).

To better understand the interactions between Me31B, eIF4E, and Cup, ovarian extracts were immunoprecipitated by α-Me31B and α-eIF4E, and the precipitates were analyzed by Western blotting. α-Me31B coprecipitates eIF4E and Cup, and α-eIF4E coprecipitates Me31B and Cup, indicating that they all form a complex. However, in the presence of RNase during immunoprecipitation, α-Me31B fails to coprecipitate eIF4E or Cup. Thus, the Me31B-eIF4E and the Me31B-Cup interactions are indirect and probably mediated through RNA in the complex. In contrast, α-eIF4E coprecipitates Cup even in the presence of RNases, suggesting a direct interaction between eIF4E and Cup in vivo (Nakamura, 2004).

The interaction of Cup and eIF4E in vitro was studied using a GST pull-down assay. GST-eIF4E pulls down Cup synthesized in vitro. The association is unaffected by RNase. These results indicate that Cup associates with eIF4E in vitro and that the interaction is RNA independent (Nakamura, 2004).

The results show that Cup is an eIF4E binding protein that is involved in translational repression of osk RNA during oogenesis. The conserved YxxxxLφ motif in Cup is important for eIF4E binding and Cup and eIF4G are likely to bind the same surface of eIF4E. These results suggest that Cup competes with eIF4G for eIF4E binding, and hence inhibits translation initiation. CupΔ212 protein, which lacks the conserved eIF4E binding sequence, is unable to bind eIF4E in vivo, and fails to repress osk translation. These results strongly suggest that the Cup-eIF4E interaction is essential for the Cup-mediated repression of osk translation, although it is possible that other of Cup's functions are also affected in the cupΔ212 mutant. Furthermore, Cup was found to interact with Bru in a yeast two-hybrid assay and that the Cup-eIF4E complex associates with Bru in an RNA-independent manner. Based on these results, it is speculated that the Bru-mediated repression of osk translation is operated, at least in part, through the interaction with Cup, which binds eIF4E and prevents the eIF4E-eIF4G interaction at the 5' end of osk RNA (Nakamura, 2004).

Staufen- and FMRP-containing neuronal RNPs are structurally and functionally related to somatic P bodies

Local control of mRNA translation modulates neuronal development, synaptic plasticity, and memory formation. A poorly understood aspect of this control is the role and composition of ribonucleoprotein (RNP) particles that mediate transport and translation of neuronal RNAs. This study shows that staufen- and FMRP-containing RNPs in Drosophila neurons contain proteins also present in somatic 'P bodies,' including the RNA-degradative enzymes Decapping protein 1 (Dcp1p) and Xrn1p/Pacman and crucial components of miRNA (Argonaute), NMD (Upf1p), and general translational repression (Dhh1p/Me31B) pathways. Drosophila Me31B, a DEAD-box helicases, is shown to participate (1) with an FMRP-associated, P body protein (Scd6p/Trailer hitch) in FMRP-driven, Argonaute-dependent translational repression in developing eye imaginal discs; (2) in dendritic elaboration of larval sensory neurons; and (3) in bantam miRNA-mediated translational repression in wing imaginal discs. These results argue for a conserved mechanism of translational control critical to neuronal function and open up new experimental avenues for understanding the regulation of mRNA function within neurons (Barbee, 2006).

Several observations now indicate that P bodies, maternal granules, and a major subclass of neuronal RNP are similar in underlying composition and represent a conserved system for the regulation of cytoplasmic mRNAs. Known RNA transport and translational repressors shared between maternal and neuronal staufen granules now include, Stau, Btz, dFMR1, Pum, Nos, Yps, Me31B, Tral, Cup, eIF4E, Ago-2, and Imp. Strikingly, in human cells, the Me31B homolog RCK/p54, the Tral homolog RAP55, the four human argonaute proteins, eIF4E, and a eIF4E-binding protein analogous to Cup, 4E-T, are all found in P bodies. In yeast, homologs of Me31B (Dhh1p) and Tral (Scd6p) are also known to be in P bodies, and Dhh1p in particular plays a role in recruiting RNA-decapping proteins and exonucleases to these RNPs. Consistent with the above observations in yeast, the enzymes involved in mRNA hydrolysis including the 5′ to 3′ RNA exonuclease Xrn1p/Pcm and the RNA-decapping enzyme DCP1 are present on Drosophila neuronal staufen RNPs and maternal RNA granules. These data unequivocally demonstrate tight spatial proximity of components mediating various RNA regulatory processes in Drosophila neurons (Barbee, 2006).

The large collection of proteins and processes common to P bodies, staufen granules, and likely maternal RNA granules suggests that they share an underlying core biochemical composition and function, which would then be elaborated in different biological contexts. For example, one anticipates that proteins involved in mRNA transport will be more prevalent in maternal and neuronal RNPs, which need to be transported for their biological function (Barbee, 2006).

An interesting aspect of neuronal staufen RNPs described in this study is the diversity of translational repression systems that are present within them. (1) In Me31B, these RNPs contain a protein that works in general translation repression of a wide variety of mRNAs and can also affect miRNA-based repression. (2) In Ago-2, they contain a component specific to miRNA/RNAi-dependent repression. (3) Neuronal staufen granules also contain UPF1, which was originally thought to be solely involved in mRNA degradation. However, because UPF1 can act as a translation repressor and physically interacts with Stau, a reasonable hypothesis is that UPF1 might work in neuronal granules, in conjunction with Stau, to repress the translation of a subset of mRNAs. The presence of multiple mechanisms for translation repression colocalizing in granules in Drosophila neurons may allow for differential translation control of subclasses of mRNA in response to different stimuli (Barbee, 2006).

Evidence accumulating in the literature suggests that there is a potential diversity of RNA granule types in neurons. Observations in Drosophila neurons are most consistent with a model in which a major subclass of neuronal RNP, in which various translational repressor and mRNA turnover proteins colocalize, is related to other compositionally distinct, diverse RNPs. A major subclass of staufen-containing RNP is indicated by data showing substantial colocalization among various proteins analyzed. Diversity is indicated by the lack of 100% colocalization: for instance, 55% of staufen-positive particles in wild-type neurons do not contain detectable dFMR1 (Barbee, 2006).

Two types of observations suggest that the apparent subclasses of particles containing Stau or dFMR1, but not both, are related to the particles in which they colocalize: (1) these two types of RNPs are clearly compositionally related to particles that contain both proteins; (2) this is supported by the observation that colocalization can be substantially increased under some conditions. Overexpression of either dFMR1 or Stau:GFP increases colocalization between Stau and dFMR1 from 45% in wild-type neurons to more than 80%. Concurrent with increased frequency of colocalization, Stau:GFP or dFMR1 induction increases apparent particle size (or brightness) and reduces the total number of particles. The increase in colocalization and brightness, as well as reduction in particle number, is most easily explained by growth and/or fusion of related RNPs. Significantly, similar effects on mammalian neuronal granule size and number have been reported following overexpression of Stau or another granule protein, RNG105. Thus, the underlying regulatory processes appear conserved between Drosophila and mammalian neurons (Barbee, 2006).

While it remains unclear how FMRP, Stau, or RNG105 enhance granule growth or fusion, it is conceivable that individual mRNAs first form small RNPs whose compositions reflect specific requirements for translational repression of the mRNAs they contain. These small RNPs exist in dynamic equilibrium with larger RNPs in which multiple, diverse translational repression complexes are sequestered. Induction of factors that promote granule assembly could push the equilibrium toward mRNP sequestration within large granules. A requirement of this dynamic model, which postulates interactions among different types of RNP, is that the RNPs themselves can change in composition during transport to synaptic domains. This is supported by FRAP analyses showing rapid exchange of Stau:GFP between cytosol and granule (Barbee, 2006).

Additional types of RNPs have also been described in neurons. For example, polysomes apparently arrested in translation have been observed near dendritic spines, and these RNPs show no obvious similarity to large, ribosome-containing particles, termed neuronal RNA granules. In addition, a potentially distinct RNP containing Stau, kinesin, and translationally repressed RNAs, but not ribosomes, has been purified from the mammalian brain. More recently, it has been shown that RNPs containing stress-granule markers TIA-1 and TIA-R as well as pumilio2 are induced by arsenate-treatment of mammalian cultured neurons. Interestingly, as previously shown for somatic cells, these large stress granules appear tightly apposed to domains containing DCP1 and Lsm1, markers of P bodies. Determining the temporal and compositional relatedness of such varied RNPs, their pathways of assembly as well as their functions, is a broad area of future research not only in neuroscience but also in cell biology (Barbee, 2006).

These diverse types of biochemical compartments for individual mRNAs suggest that neural activity or other developmental signaling events would influence translation in two steps: first, by desequestering mRNPs held within large granules and, then, by derepressing quiescent mRNAs in individual mRNPs. Thus, RNPs described in this study could have a complex precursor-product relationship with other RNPs, including polysomes discovered by now-classical studies at dendritic spines (Barbee, 2006).

Despite the complexity revealed by the diversity of neuronal RNPs, the importance and significance of the observed colocalization of Me31B, Tral, argonaute, and dFMR1 in staufen-positive neuronal RNPs is most clearly demonstrated by functional analyses revealing biological pathways in which these proteins function together (Barbee, 2006).

Several independent lines of evidence are consistent with a function for Me31B in neuronal translational repression as part of a biochemical complex that includes dFMR1. (1) Subcellular localization studies indicate that Me31B and Tral localize to dFMR1-containing RNPs especially prominent at neurite branch points in cultured Drosophila neurons. (2) Me31B, Tral, and dFMR1 coimmunoprecipitate from Drosophila head extract, thus confirming the physical association of three proteins. (3) Loss-of-function alleles of either Me31B or Tral suppress the rough eye phenotype seen when dFMR1 is overexpressed in the sev-positive photoreceptors. (4) Overexpression of Me31B in sensory neurons leads to altered branching of terminal dendrites, a phenotype also seen with overexpression analyses of Nos, Pum, and dFMR1. (5) Reduction of Me31B expression in sensory neurons by RNAi results in abnormal dendrite morphogenesis and tiling defects, phenotypes similar to that observed following loss of nanos, pum, or dFmr1 function. Significantly, the effect of Me31B on dendritic growth is correlated with its ability to function in translational repression. These five independent lines of evidence provide considerable support for Me31B (and Tral) function in neuronal translation control processes. While the site of functional interaction between dFMR1, Me31B, and Tral (soma or neuronal processes) is not identified here, the importance of the physical interactions is clearly demonstrated (Barbee, 2006).

Several observations also argue that Me31B acts, at least in part, within neurons to promote translation repression and/or mRNA degradation in response to miRNAs. This possibility was first suggested by the physical and genetic interactions of Me31B with dFMR1, a protein that has been implicated in the miRNA-mediated repression. Using direct assays for miRNA-mediated function in vivo, this study shows that Me31B is required for efficient repression by the bantam miRNA in developing wing imaginal discs. This identifies Me31B as a protein required for efficient miRNA-based repression (Barbee, 2006).

Recently, miRNA-based regulation has been shown to be important for the control of spine growth in hippocampal neurons and to be a target of protein-degradative pathways involved in long-term memory formation in Drosophila. Thus, the data predict that Me31B will be important in modulating miRNA function pertinent to development of functional neuronal plasticity. More generally, because Me31B homologs in yeast and mammals have been shown to function in P body formation in somatic cells, the requirement for Me31B in miRNA function provides evidence to support a model in which formation of P bodies is required for efficient miRNA-based repression in varied cell types and biological contexts (Barbee, 2006).

The conclusion that staufen- and dFMR1-containing neuronal RNPs are similar in organization and function to P bodies has several implications for neuronal translational control. (1) The presence of diverse translational repression systems on these RNPs suggests that, like in P bodies, different classes of mRNAs will be repressed by different mechanisms. This may allow specific RNA classes to be released for new translation in response to different stimuli. Such diversity of control may allow synapses to remodel themselves differently, depending on the frequency and strength of stimulation (e.g., LTD or LTP). (2) FRAP experiments indicate that both P bodies and staufen granules are dynamic structures. This argues that, like P bodies, staufen granules are in a state of dynamic flux, perhaps in activity-regulated equilibrium with the surrounding translational pool. (3) The presence of mRNA-degradative enzymes on staufen granules suggests regulation of mRNA turnover may play an important role in local synaptic events. For example, if synaptic signaling were to induce turnover of specific mRNAs at a synapse, then stimulated synapses could acquire properties different from unstimulated ones that retain a 'naive' pool of stored synaptic mRNAs. Finally, these observations imply that the proteins known to function in translation repression within P bodies will play important roles in modulating translation in neurons. Thus, it is anticipated that proteins of mammalian or yeast P bodies such as Edc3p, Pat1p, the Lsm1-7p complex, GW182, and FAST will be present on and influence assembly and function of neuronal granules (Barbee, 2006).

The Me31B DEAD-box helicase localizes to postsynaptic foci and regulates expression of a CaMKII reporter mRNA in dendrites of Drosophila olfactory projection neurons

mRNP granules at adult central synapses are postulated to regulate local mRNA translation and synapse plasticity. However, they are very poorly characterized in vivo. This study presents early observations and characterization of candidate synaptic mRNP particles in Drosophila olfactory synapses; one of these particles contains a widely conserved, DEAD-box helicase, Me31B. In Drosophila, Me31B is required for translational repression of maternal and miRNA-target mRNAs. A role in neuronal translational control is primarily suggested by Me31B's localization, in cultured primary neurons, to neuritic mRNP granules that contain: (1) various translational regulators; (2) CaMKII mRNA; and (3) several P-body markers including the mRNA hydrolases, Dcp1, and Pcm/Xrn-1. In adult neurons, Me31B localizes to P-body like cytoplasmic foci/particles in neuronal soma. In addition it is present to synaptic foci that may lack RNA degradative enzymes and localize predominantly to dendritic elements of olfactory sensory and projection neurons (PNs). MARCM clones of PNs mutant for Me31B show loss of both Me31B and Dcp1-positive dendritic puncta, suggesting potential interactions between these granule types. In PNs, expression of validated hairpin-RNAi constructs against Me31B causes visible knockdown of endogenous protein, as assessed by the brightness and number of Me31B puncta. Knockdown of Me31B also causes a substantial elevation in observed levels of a translational reporter of CaMKII, a postsynaptic protein whose mRNA has been shown to be localized to PN dendrites and to be translationally regulated, at least in part through the miRNA pathway. Thus, neuronal Me31B is present in dendritic particles in vivo and is required for repression of a translationally regulated synaptic mRNA (Hillebrand, 2010).

The Me31B/Dhh1p/DDX6/CGH-1 class of DEAD box helicases is associated with many different kinds of mRNP aggregates, including maternal RNA storage granules, P-bodies, stress granules, as well as various granule subtypes observed during C. elegans germline development. In addition it is required for the assembly of P-bodies in yeast, Drosophila and mammalian cells and as well for the formation of stress granules in mammals. For these reasons, the punctate distribution of Me31B in postsynaptic dendrites is likely to indicate its presence in a specific type of synaptic mRNP particle. However, unlike Me31B-positive particles described in neurites of cultured Drosophila neurons, synaptic Me31B foci do not appear to contain the RNA hydrolases Dcp1 and Pcm/Xrn-1. Thus, they may be a distinct class of particle, which localize preferentially to postsynaptic dendrites. These represent early images of candidate mRNA storage particles at synapses in vivo. A paucity of antibodies and the challenging nature of such high-resolution immunocytochemistry in whole brain tissue has so far made it difficult to more completely characterize other components of synaptic Me31B particles as well as to establish whether Dcp1, Pcm, and Stau coexist on the same or different particle in the adult brain. Indeed even the conclusion that Me31B particles constitute a separate class must be qualified by the possibility that the visualization of two apparently distinct particle types arises from an artifact of incomplete antibody penetration into the neuropil (Hillebrand, 2010).

It is possible that synaptic Me31B particles could be analogous to recently described granules in the C. elegans germline, which contain translationally controlled mRNAs and CGH-1/Me31B but exclude decapping enzymes and the P-body protein PATR1/PAT1. Immunoprecipitation and further colocalization studies suggest that these granules can also contain PAB-1, ATX-2, or TIA-1, markers of stress granules, which in other systems, contain translation initiation factors together with mRNAs stalled in translational initiation. Thus, it is conceivable that Me31B/CGH-1-containing storage particles contain mRNAs stored in a stress-granule like state, in which the resident mRNAs are available for rapid activation (Hillebrand, 2010).

The potential separation of storage and degradative particles leads to an attractive model in which individual mRNAs may transition from being available for translational activation in a storage granule, to being targeted for degradation in a P-body like particle. This is supported as well by observations in dendrites of cultured mammalian neurons where a distinct class of RNPs contain the degradative enzyme Xrn1, which is excluded from RNPs supposedly involved in storage (Hillebrand, 2010).

At synapses, a transition between storage and degradation particles may occur by three, non-exclusive, candidate mechanisms: (1) by the remodeling of a storage mRNP to a degradative one through protein exchange; (2) by the initial exit of mRNA from the storage RNP to a translating pool, followed by its subsequent targeting to a degradative particle; or (3) the fusion of the two particles. Recent studies in Drosophila provide a possible mechanism by which a change of proteins in RNP complexes could alter its function. Two related proteins of the Lsm-family, Enhancer of Decapping 3 (EDC3), which is implicated to play a role in mRNA decay, and Trailer Hitch (Tral), which supposedly is involved in mRNA repression, interact at the same domain with the Me31B protein. This suggests that the function of Me31B complexes might be determined by the interaction with specific binding partners. Some support for the second model is provided by the observation that the synaptically localized Arc mRNA is targeted for degradation after its translation is induced by synaptic activity and also by the observation that RCK-positive particles in dendrites of cultured hippocampal neurons are transiently disassembled following BDNF stimulation. Further studies are required to understand how, when, and even whether these transitions of mRNA state occur in synapses and other biological contexts (Hillebrand, 2010).

Together with many analogous studies in yeast and mammalian cells, previous observations in Drosophila that Me31B is a repressor of maternal mRNA translation, a component of a repression pathway mediated by the bantam microRNA, and a repressor of growth of terminal dendrites, has led to a strong model that Me31B is a translational repressor protein. In contrast, recent studies in C. elegans and P. falciparum have shown that Me31B orthologs, CGH-1 and DOZI, associate with specific mRNAs and protects them from degradation (Hillebrand, 2010).

The observations in neurons indicate a function for Me31B in repressing translation of a miRNA regulated, dendritically localized reporter mRNA in vivo. This is consistent with two related lines of data. First, it is consistent with the known function for Me31B in repression of miRNA-target genes in Drosophila wing imaginal cells as well as for its human homolog RCK in mammalian cultured cells. Second, the correlation observed between loss of synaptic Dcp1 puncta and upregulation of the CaMKII reporter, is consistent with observations in hippocampal cultured cells, where observed disassembly of 'dendritic P-bodies' induced by synaptic stimulation has been proposed to underlie the temporally coincident translation of localized mRNAs (Hillebrand, 2010).

Thus, this study suggestd a simple model in which neuronal Me31B, as well as its homologs in other metazoa, mediates the formation of synaptic mRNP particles that contain locally repressed mRNAs. And that synaptic stimulation-induced disassembly of these particles is one aspect of the mechanism of local translational control (Hillebrand, 2010).

One key goal of future studies will be to understand the composition and dynamics of dendritic mRNPs in vivo. This will be aided by genetic techniques to replace endogenous translational control molecules with genetically encoded, fluorescently tagged variants that retain functional and localization patterns of the endogenous proteins. When coupled with procedures to induce local protein synthesis in dendrites, such reagents will allow analysis of functionally relevant particle dynamics in vivo. In addition, by eliminating the need for antibodies whose use may be associated with artifacts of inclusion and exclusion, such reagents may provide more direct insight into the real nature of synaptic mRNPs in vivo (Hillebrand, 2010).

A second goal is to understand the mechanism by which Me31B regulates the expression of CaMKII reporter levels in vivo. Although Me31B has been shown to be required for the miRNA pathway it is also required for other forms of translational repression, for example in S. cerevisiae that does not have miRNAs. Similarly, although the reporter used in this study is miRNA regulated, the same UTR also has binding sites for translational regulators that may operate independently of miRNAs. Thus, important and linked goals of future studies are to understand mechanisms by which the CaMKII UTR is regulated in dendrites and how Me31B engages with these mechanisms of neuronal translational control (Hillebrand, 2010).

The Ataxin-2 protein is required for microRNA function and synapse-specific long-term olfactory habituation: Atx2 protein regulates Ago1- and Me31B-dependent miRNA-mediated translational repression

Spinocerebellar ataxia type 2 (SCA-2) is an autosomal dominantly inherited neurodegenerative disease caused by trinucleotide (CAG) expansion in the ATXN2 gene resulting in the lengthening of polyglutamine stretch in the encoded protein ataxin-2. Ataxin-2 is a large conserved protein that carries an Sm-domain and a PAM-2 motif on the C-terminal side of the Sm-domain. The PAM-2 motif mediates interaction with the C-terminal helical domain of the poly(A) binding protein (PABP; see Drosophila pAbp) and is present in several PABP-interacting proteins. Levels of mutant ataxin-2 (with expanded polyglutamine stretch) are higher in brain tissue of patients with SCA-2 compared with that of wild-type ataxin-2 in normal individuals. Further, abnormal expression of Ataxin-2 has been shown to be deleterious in Drosophila (Satterfield, 2002). However, the biological function of ataxin-2 and the mechanism by which lengthening of the polyglutamine stretch in ataxin-2 leads to the disease are not clear (Tharun, 2008 and references therein).

Several studies implicate ataxin-2 in mRNA decay and regulation of translation suggesting that deregulation of these processes could be related to the disease. Ataxin-2 homologs from multiple organisms have been shown to interact with PABP consistent with the presence of PAM-2 motif in Ataxin-2. Depletion of Ataxin-2 homolog in C. elegans affects germline development and this seems to be due to the deregulation of translational repression by GLD-1 and MEX-3 of their mRNA targets. Reducing the expression of ATXN2 in mammalian cells using siRNAs impairs the formation of stress granules which are the sites where untranslated mRNAs are localized during stress. Finally, both in human cells and in Drosophila, Ataxin-2 is associated with the polysomes (Satterfield, 2006). These observations suggest that Ataxin-2 may have a role in translational repression in vivo. Interestingly, enhancement and suppression of Ataxin-2 expression in human cells leads to decrease and increase in the levels of PABP, respectively, without affecting the levels of PABP mRNA. Given that PABP is a key translation factor, it remains to be seen if the effects on translation caused by alterations in Ataxin-2 expression are related to the changes in the levels of PABP. Ataxin-2 overexpression also leads to decrease in the number of P-bodies in human cells. This seems to be related to the ability of Ataxin-2 to interact with Dhh1/RCK/p54, which is one of the decay factors important for P-body assembly in human cells. Importantly, reduction in P-bodies was caused by overexpression of Ataxin-2 irrespective of whether the polyglutamine stretch in Ataxin-2 was normal or long. These observations together suggest that deregulation of mRNA decay and/or translational repression resulting from abnormal expression of Ataxin-2 may be one of the reasons for the disease phenotype and the expanded polyglutamine stretch could contribute to increased expression of the mutant Ataxin-2 in the diseased individuals (Tharun, 2008 and references therein).

Studies in Drosophila suggest that Ataxin-2 is required for microRNA function and synapse-specific long-term olfactory habituation. Local control of mRNA translation has been proposed as a mechanism for regulating synapse-specific plasticity associated with long-term memory. Glomerulus-selective plasticity of Drosophila multiglomerular local interneurons observed during long-term olfactory habituation (LTH) requires the Ataxin-2 protein (Atx2) to function in uniglomerular projection neurons (PNs) postsynaptic to local interneurons (LNs). PN-selective knockdown of Atx2 selectively blocks LTH to odorants to which the PN responds and in addition selectively blocks LTH-associated structural and functional plasticity in odorant-responsive glomeruli. Atx2 has been shown previously to bind DEAD box helicases of the Me31B family, proteins associated with Argonaute (Ago) and microRNA (miRNA) function. Robust transdominant interactions of atx2 with me31B and ago1 indicate that Atx2 functions with miRNA-pathway components for LTH and associated synaptic plasticity. Further direct experiments show that Atx2 is required for miRNA-mediated repression of several translational reporters in vivo. Together, these observations (1) show that Atx2 and miRNA components regulate synapse-specific long-term plasticity in vivo; (2) identify Atx2 as a component of the miRNA pathway; and (3) provide insight into the biological function of Atx2 that is of potential relevance to spinocerebellar ataxia and neurodegenerative disease (McCann, 2011).

In the mammalian brain, single neurons form up to 100,000 different synapses whose weights may be regulated independently during learning. In principle, the synapse-specificity of short-term plasticity may be explained simply by the restriction of signaling events to active synapses. However, synapse-specific long-term plasticity, which depends on products of nuclear gene expression that would be available in a cell-wide manner, clearly depends on distinct synaptic tags that mark only active synapses (McCann, 2011).

Several lines of evidence suggest that activity-regulated local translation of synaptic mRNAs normally stored in a repressed state contributes to the synapse-specificity of long-term plasticity. Consistent with this idea, several translational control molecules, such as fragile X mental retardation 1 protein, Staufen, cytoplasmic polyadenylation element binding protein/Orb2, and the Gld2 polyA polymerase, are required in Drosophila for long-term but not short-term memory. In the context of identified synapses, local protein synthesis is required for cAMP response element-binding protein (CREB)-dependent, synapse-specific long-term plasticity in cultured Aplysia sensorimotor synapses: In this system, postsynaptic translation may trigger a retrograde signal, which in turn stimulates local translation at presynaptic terminals. However, in vivo, the requirement for and regulation of local protein synthesis at synapses remains poorly understood, in part because of the paucity of preparations in which behavioral learning arises from plasticity within a defined, experimentally convenient, neural circuit (McCann, 2011).

Recent work has shown that long-term olfactory habituation (LTH), a phenomenon in which sustained exposure to an odorant results in a decreased behavioral response, arises through plasticity of synapses between local interneurons (LNs) and projection neurons (PNs) in the Drosophila antennal lobe (Das, 2011; Sachse, 2007). Although LTH requires the transcription factor CREB2 to function (globally) in a multiglomerular class of LNs, LTH is odorant selective and associated with glomerulus-selective (and hence local) structural and physiological plasticity. In screening candidate RNA-binding proteins for potential roles in PNs during LTH, Ataxin-2 (Atx2), a molecule of considerable interest for its known involvement in the human neurodegenerative disease spinocerebellar ataxia-2 (SCA2), was identified. Expansion of a polyglutamine tract in human Atx2 from about 22 (normal) to >32 (pathogenic) glutamines causes degeneration of cerebellar Purkinje cells. While Atx2 has been implicated in many different biological functions, it is generally believed to function in RNA regulation. Evidence for this role comes from biochemical and cell biological studies of the protein or its evolutionarily conserved orthologs in Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster (McCann, 2011).

In C. elegans, Atx2 is required in postembryonic germline cells for appropriate translational control of GLD-1- and MEX-3-target mRNAs. Atx2 binds the RNA regulatory proteins, polyA-binding protein (PABP) and Me31B/RCK/ Dhh1p/CGH-1, through domains also required for its observed assembly with polyribosomes. At a cell biological level, Atx2 function has been shown to regulate the assembly of P-bodies and stress granules, distinct cytoplasmic messenger ribonucleoprotein particles that contain translationally repressed mRNAs, together with the translational repressor Me31B/RCK/Dhh1p (McCann, 2011 and references therein).

Significantly, both the proteins and cytoplasmic structures with which Atx2 associates have been linked to translation repression by microRNAs (miRNAs), a class of small, noncoding RNAs that bind complementary sequences in mRNA 3'UTRs and repress translation via the RNA-induced silencing complex (RISC). Furthermore, miRNAs and miRNA components have been linked either to long-term memory in Drosophila or to sensorimotor synapses (McCann, 2011).

This study shows that (1) Atx2 functions in olfactory projection neurons for LTH as well as associated glomerulus-selective physiological and structural plasticity; (2) Atx2 functions in LTH with the known miRNA-pathway proteins Argonaute 1 (Ago1) and Me31B; and (3) Atx2 is part of a general machinery required for efficient miRNA-mediated translational repression (McCann, 2011).

When tested in a Y-maze apparatus, flies exposed to either 15% CO2 or 5% ethyl butyrate (EB) for 30 min show a reduced aversive response that lasts less than 1 h (short-term habituation, STH). In contrast, flies exposed to 5% CO2 or 20% EB for 4 d show reduced aversion for days (LTH) and reduced odor-evoked responses in respective odor-responsive PNs, together with CREB-dependent growth of odor-responsive glomeruli (V and DM2/DM5, respectively). In this well-defined behavioral and synaptic context, it was asked whether PNs require Atx2 for LTH and associated synapse-specific structural plasticity. Expression of a UAS-Atx2RNAi construct in GH146-expressing neurons responsive to EB but not to CO2 (GH146Gal4/UASAtx2RNAi) completely blocked LTH to EB without altering LTH to CO2. Atx2 knockdown in GH146-expressing PNs blocked LTH to EB but had no effect on either STH to EB or the EB-avoidance response. Similarly, knockdown of Atx2 in the CO2-responsive VPN (VPNGal4;UASAtx2RNAi/+) selectively blocked LTH to CO2 without altering either STH to CO2 or the naive olfactory response to CO2. Thus, Atx2 is selectively required in glomerulus-specific PNs for odorant-selective LTH (McCann, 2011).

Two observations argue that Atx2 functions in adult neurons for LTH. First, both baseline behavioral responses to odorants and STH are normal in animals after Atx2 knockdown in PNs, indicating relatively normal development of the olfactory system. Second and more direct evidence is the selective block in LTH to EB seen following adult-specific knockdown of Atx2 in EB-responsive PNs using the TubGal80ts system (McCann, 2011).

Atx2 knockdown in odor-responsive PNs blocks not only olfactory LTH but also the LTH-associated increase in the volume of behaviorally relevant glomeruli. Thus, following 4 d of EB exposure, GH146Gal4/UAS-Atx2RNAi flies, which do not show LTH, also show no increase in the volume of either the DM5 glomerulus, previously shown to mediate the aversive response to this odorant, or the EB-responsive DM2 glomerulus. In contrast, the same GH146Gal4/UAS-Atx2RNAi flies show normal LTH to CO2 and robust increases in the volume of the VPN glomerulus in response to 4-d CO2 exposure as observed in control flies. Similarly, VPNGal4;UAS-Atx2RNAi/+ flies do not show LTH to CO2 or associated growth of the V glomerulus but display normal EB-induced LTH and EB-associated growth of DM5. Thus, Atx2 is required in specific PNs for the glomerulus-selective structural plasticity that accompanies odorant-selective LTH (McCann, 2011).

Normal LTH to EB is associated with an experience-dependent reduction in the EB-evoked physiological response of DM2 and DM5 PNs. This reduction can be measured in vivo by imaging odor-evoked calcium transients in PNs of flies expressing the genetically encoded calcium sensor, GCaMP3 (McCann, 2011).

To test whether this LTH-associated physiological plasticity requires Atx2 function in PNs, EB-evoked calcium fluxes were imaged and quantified in PN dendrites of 4-d EB-exposed and mock-exposed GH146Gal4, UAS-GCaMP3/UAS-Atx2RNAi flies (which do not show LTH to EB), and these results were compared with normally habituating GH146Gal4,UAS-GCaMP3/+ controls. In DM2 and DM5 of GH146Gal4, UAS-GCaMP3/UAS-Atx2RNAi flies, 4-d EB exposure caused significantly less change in EB (McCann, 2011).

Biochemical interactions of Atx2 orthologs in Drosophila and other organisms point to an interesting potential mechanism through which Atx2 regulates synapse-specific long-term plasticity required for LTH. In particular, Atx2 binding to Me31B and PABP orthologs, which in turn interact with other core miRNA-pathway proteins, GW182 and Argonaute, suggests that Atx2 may regulate miRNA-mediated translational repression directly. Could the function of Atx2 in LTH reflect a role in the miRNA pathway (McCann, 2011)?

To address this question, the possibility of strong dominant genetic interactions between atx2X1 and mutations affecting core components of the miRNA pathway was examined. First, LTH and STH were examined in ago1K08121/+; atx2X1/+ double-heterozygote animals, and these behaviors were compared with those of single-heterozygote controls. The results were striking. Although STH to EB and CO2 was normal in double heterozygote ago1K08121/+; atx2X1/+ animals, LTH to both EB and CO2 was completely abolished. In contrast, control +/+; atx2X1/+ and ago1K08121/P[atx2+]; atx2X1/+ animals showed normal LTH to both odorants (McCann, 2011).

The observation that the atx2 genomic rescue construct P[atx2+] restored normal LTH to ago1K08121/+; atx2X1/+ flies also shows that altered LTH in the double-heterozygote flies is caused specifically by a defect in atx2. In a similar experiment LTH and STH were examined in me31Bδ2/+; atx2X1/+ double-heterozygote animals exposed to EB or CO2. Again, these double heterozygotes showed no LTH but normal STH. The defects in LTH were not observed in +/+; atx2X1/+ or me31Bδ2 /P[atx2+]; atx2X1/+ animals, further confirming the involvement of atx2. LTH-associated structural plasticity also was blocked in ago1K08121/+; atx2X1/+ and me31Bδ2/+; atx2X1/+ double heterozygotes. Thus, although the V and DM5 glomeruli of +/+; atx2X1/+ flies showed the expected growth following 4 d of CO2 or EB exposure, respectively, both the EB-evoked increase in DM5 volume and the CO2-induced increase in V was abolished in ago1K08121/+; atx2X1/+ and me31Bδ2/+; atx2X1/+ double heterozygotes. In every instance, the defect in structural plasticity was restored by a wild-type genomic atx2+ transgene: Both ago1K08121/ P[atx2+]; atx2X1/+ flies and me31Bδ2/P[atx2+]; atx2X1/+ flies showed normal odor-induced structural plasticity (McCann, 2011).

These data indicate that Atx2 functions in odorant-selective LTHas well as in glomerulus-selective structural plasticity through a pathway that depends on Ago1 and on Me31B, two proteins previously linked with miRNA-driven translational control. Consistent with this hypothesis, RNAi-based knockdown of Me31B in EB-responsive PNs mimics the effects of Atx2 knockdown, causing a specific defect in LTH to EB (McCann, 2011).

The observed genetic interactions of atx2 mutations with me31B and ago1 mutations point to a likely role for the Atx2 protein in regulating Ago1- and Me31B-dependent, miRNA-mediated translational repression in vivo. To examine this possibility, it was asked if Drosophila Atx2 is required for miRNA-mediated translational repression in wing imaginal discs, a tissue in which the function and activities of endogenous miRNAs can be analyzed conveniently (McCann, 2011).

To reduce levels of endogenous Atx2 in identified subpopulations of wing imaginal disc cells, either a patched Gal4-driven RNAi construct (UAS-Atx2RNAi) was used against atx2 or the Flippase recognition target-Flippase (FRT-FLP) recombinase system to generate genetic-mosaic animals carrying clusters of homozygous atx2X1/atx2X1 mutant cells in the wing imaginal discs of hs-flp;+/+; FRT82B, atx2X1/FRT82B, arm-lacZ. Homozygous mutant atx2X1/atx2X1 cells were identified using either an Atx2 antibody or a surrogate, anti-lacZ staining, which here labels all cells except the atx2X1/atx2X1 mutant clones generated by mitotic recombination (McCann, 2011).

To examine Atx2 function in the miRNA pathway, such clones were generated in a genetic background that included any one of a number of transgenically encoded, miRNA-dependent translational reporters, and how loss of Atx2 affected GFP expression of these reporters was assessed. Reporters for head involution defective (hid), bantam, mir-12, costal-2, and sickle were used. The hid, sickle, and costal-2 reporters consist of the 3' UTR of hid, sickle, or costal-2, respectively, placed downstream of GFP-coding sequences under the control of a tubulin promoter (McCann, 2011).

The 3' UTR of hid is repressed by endogenous bantam miRNA and that of sickle by miR-2b. The bantam and miR-12 reporters consist of two copies of the bantam target recognition sequence or four copies of the miR-12 target recognition sequence, respectively, also downstream of GFP-coding sequences (McCann, 2011).

Atx2-deficient cells had a noticeable reduction in the intensity of Me31B and Ago1 staining, suggesting that in vivo Drosophila Atx2 is necessary for maintaining Me31B particles potentially involved in miRNA-mediated translational repression. In addition, and consistent with a defect in miRNA function in vivo, cells lacking Atx2 showed distinctly elevated expression of specific miRNA reporters (McCann, 2011).

Clones of atx2X1/atx2X1 mutant cells showed clear up-regulation of the hid reporter compared with flanking atx2X1/+ or +/+ cells. The increased hid reporter levels in atx2X1/atx2X1 mutant cells were not observed if similar clones also expressed a wild-type atx2 genomic transgene). This observed genetic rescue confirms that the increase in hid-reporter expression in atx2X1/atx2X1 cells is caused by the absence of atx2 and not by any other unknown potential mutation on the FRT82B,atx2X1 chromosome. Thus, as predicted by its biochemical and genetic interactions with various miRNA-pathway components, Atx2 is required for optimal repression of a miRNA reporter in vivo (McCann, 2011).

Further experiments confirmed that this requirement reflects a broad requirement for Atx2 function for the repression of many different miRNA-target genes. Clones of atx2X1/atx2X1 cells also show increased expression of the sickle, bantam BandBŒ), and miR12 reporters. Given that the latter two reporters are regulated by artificial UTRs engineered to be repressed solely through the miRNA pathway, these data strongly argue that Atx2 is broadly required for miRNA function. In contrast to the other four miRNA reporters, costal-2 reporter expression was not increased detectably in atx2X1/atx2X1 cells. This result was surprising, because the costal-2 reporter is similar to the other reporters in being repressed by miRNAs through a mechanism that requires Dicer-1 (Dcr-1), the endonuclease involved in miRNA biogenesis. Therefore, Atx2 is required only for repression of a subset of miRNA targets (McCann, 2011).

A model is considered in which Atx2 functions in only one of two miRNA-repression pathways recently distinguished in Drosophila. Although produced by Dcr-1, miRNAs may repress translation by one of two alternative pathways: either through an Ago1-RISC that requires GW182 or through an Ago2 RISC via a poorly understood GW182-independent mechanism. To test the possibility that Atx2 would be required exclusively for the Ago1/GW182-dependent pathway, previously shown to be required for bantam miRNA function, how the various reporters were affected by knockdown of GW182 was examined (McCann, 2011).

To knock down GW182 in identified groups of cells, the FLP-out technique was used to overexpress a transgenic RNAi construct against GW182 in wing imaginal discs expressing hid, miR12, or costal-2 reporters. Cells expressing a GW182RNAi construct (labeled by anti-lacZ staining) showed visibly increased expression of the Atx2-sensitive hid and miR12 reporters but no up-regulation of the Atx2-insenstive costal-2 reporter (McCann, 2011).

To understand why the costal-2 reporter could be insensitive to GW182 (or Atx2) knockdown, the sequence of its 3' UTR was examined and it was found to contain not only target sites for miR12 and miR283, but also two binding sites for miR277. This finding is significant because, unlike the majority of Dcr1-dependent miRNAs, miR277 is loaded preferentially onto Ago2-RISC complexes because of the extensive base-pairing between its miRNA and miRNA* strands. Thus, these observations suggest that Atx2, although necessary for GW182-dependent repression through Ago1-RISC, may not be necessary for Ago2-RISC.dependent repression (McCann, 2011).

This tentative model is supported by the observation that RNAi-induced, Ago-2-dependent eye phenotypes also are not sensitive to knockdown of Atx2. Knockdown of the caspase inhibitor Drosophila inhibitor of apoptosis (DIAP) by GMRGal4- driven expression of UAS-DIAPRNAi results in significantly smaller eyes because of increased apoptosis. The cell-death phenotype is suppressed if Ago2 levels are reduced by simultaneous expression of UAS-Ago2RNAi. However, similar coexpression of a functional UAS-Atx2RNAi (or UAS-GFPRNAi) does not alter phenotypes of GMRGal4;UASDIAPRNAi flies (McCann, 2011).

Taken together with prior evidence that Atx2 associates physically with Me31B and PABP, two proteins required for the Ago1-RISC pathway, these data indicate that Atx2 is part of a core pathway required for miRNA-mediated translational repression. However, Atx2 may be dispensable for repression by the Ago2-RISC pathway (McCann, 2011).

The circuit that underlies LTH has allowed experience-induced, synapse-specific plasticity to be examined in the context of behavioral memory. Previous pioneering work in cultured Aplysia sensorimotor synapses has led to a model in which CREB-dependent nuclear gene expression provides global (cell-wide) control of long-term facilitation. This facilitation can be restricted to specific synapses, in part through the synapse-specific local translation of stored mRNAs, which also is required for long-term plasticity. In the context of olfactory LTH, which is driven by the plasticity of inhibitory LN-PN synapses in the antennal lobe, previous work has shown that CREB function is required globally in a multiglomerular class of LNs for LTH to CO2 and EB. This study now shows that LTH additionally requires Atx2 in postsynaptic PNs for the glomerulus-restricted plasticity necessary for odorant-selective LTH. Knockdown of Atx2 in adult-stage PNs selectively blocks LTH without affecting either basal odorant response or STH. This distinctive phenotype also is shown following Me31B knockdown in PNs or in animals doubly heterozygote for atx2 and ago1 or atx2 and me31B. When taken together with independent observations that Atx2 is required for efficient miRNA function, these very strong genetic interactions point to a role for Atx2 in miRNA-mediated translational control in the regulation of long-term memory (McCann, 2011).

It is hypothesized that, under appropriate circumstances, NMDA receptor activation in PN dendrites may trigger local protein synthesis, perhaps through RISC degradation, giving rise to a retrograde signal from PNs to LNs that in turn stimulates or synergizes with the cell biological changes required for glomerulus- limited, long-term plasticity. The data do not demonstrate that Atx2 and Me31B function in local translation of synaptic mRNAs, but they do show a specific requirement for Atx2 and Me31B for miRNA function and synapse-specific LTH (but not STH) and thus provide a strong argument for local translation of synaptic mRNAs being the underlying mechanism by which these proteins regulate synapse-specific long-term plasticity in vivo (McCann, 2011).

The proposed need for postsynaptic translation and postulate of retrograde signaling are consistent with recent observations and models explaining long-term synaptic facilitation in Aplysia (Wang, 2009; Cai, 2008). In Drosophila, these models may be tested and elaborated through further genetic and in vivo studies and may lead to an understanding of the local and global mechanisms and their interactions that regulate long-term synaptic plasticity (McCann, 2011).

An important finding is that Atx2 is required for translational repression of four different miRNA reporters. Taken together with prior evidence, in particular that Atx2 binds two known components of the miRNA pathway, this finding indicates a wide and general requirement for Atx2 in miRNA-mediated translational repression (McCann, 2011).

However, Atx2 is not required for silencing of the costal-2 reporter, an observation that may be may be explained by costal-2 reporter's repression by a possibly Atx2-independent RISC complex. Previous work has shown that miRNAs partition between two different silencing complexes, Ago1-RISC and Ago2-RISC; in contrast, siRNAs associate almost exclusively with Ago2-RISC. Ago1-RISC and Ago2-RISC silence mRNAs by different mechanisms: Ago1-RISC is characterized by its dependence on GW182. The specific pathway that produces an miRNA or siRNA does not require that small RNA to associate with a particular Ago protein. Thus, although bantam and miR-277 miRNAs are produced by Dcr1, bantam associates exclusively with Ago1-RISC, whereas miR-277 is loaded into the Ago2 pathway. This loading of miR-227 occurs because, in contrast to the bantam microRNA, which has several bulges and mismatches, the duplex precursor to miR-277 strongly resembles an siRNA precursor with a high degree of perfect matching. By demonstrating that loss of Atx2 causes up-regulation of GW182- or Ago1-dependent miRNA reporters, the results identify Atx2 as a frequently used component of the Ago1-GW182 RISC pathway. Loss of Atx2 does not affect repression of the GW182-insensitive costal-2 reporter, possibly repressed via the Ago2-RISC pathway. This observation, combined with the insensitivity of the RNAi pathway to Atx2 knockdown in the Drosophila eye, suggests that Atx2 may not be required for Ago2-RISC function (McCann, 2011).

Atx2's role in the Ago1-miRNA pathway raises the question as to how Atx2 influences miRNA-mediated translational repression. Uncovering Atx2's molecular mechanism of action is complicated by lack of consensus as to how miRNAs regulate gene expression. However, Atx2 is likely to function through its interactions with PABP [mediated by its PABP-interacting motif 2 (PAM2) domain] or Me31B [via its Like Sm (Lsm) and Like-Sm-associated domain (LsmAD) domains] (McCann, 2011).

Three possible models for Atx2 actions are considered. Under appropriate conditions, Atx2 interactions with PABP could help break eukaryotic initiation factor (eIF) 4G eIF4g-PABP interactions required for efficient translational initiation. In addition, directly or through interactions with Me31B, Atx2 may help recruit either of two deadenylase complexes that promote mRNA deadenylation and consequent repression (McCann, 2011).

The identification of Atx2 as a core component of the neuronal and nonneuronal miRNA repression machinery has implications for understanding spinocerebellar ataxias and some forms of amyotrophic lateral sclerosis. Several studies underline the importance of functional components of the miRNA repression machinery in the mammalian brain. It has been demonstrated that miRNA-regulated activities play a role in polyglutamine-induced neurodegeneration. In addition, other work has shown that Atx2 is required for pathogenic forms of Atx1 and Atx3 to induce neurodegeneration in Drosophila, suggesting a potentially common pathway for neuronal loss in different ataxias. Loss of Dcr1 function results in microcephaly and progressive neurodegeneration, consistent with a model in which miRNA function is required for maintaining the adult nervous system (Saba, 2010). Given Atx2's involvement in human neurodegenerative disease, the current findings may help illuminate some of the phenotypes and symptoms of SCA2 patients and also may illuminate possibly common pathways for neuronal loss in different neurodegenerative conditions. If altered miRNA function contributes to neurodegeneration in SCA2 or related diseases, then it is possible that these diseases arise because of altered regulation of a subset of Atx2-target mRNAs in neurons. The identification and study of such target mRNAs may contribute to further understanding and potential therapeutic strategies (McCann, 2011).

miRISC recruits decapping factors to miRNA targets to enhance their degradation

MicroRNA (miRNA)-induced silencing complexes (miRISCs) repress translation and promote degradation of miRNA targets. Target degradation occurs through the 5'-to-3' messenger RNA (mRNA) decay pathway, wherein, after shortening of the mRNA poly(A) tail, the removal of the 5' cap structure by decapping triggers irreversible decay of the mRNA body. This study, carried out in Drosophila S2 cells, demonstrates that miRISC enhances the association of the decapping activators DCP1, Me31B and HPat with deadenylated miRNA targets that accumulate when decapping is blocked. DCP1 and Me31B recruitment by miRISC occurs before the completion of deadenylation. Remarkably, miRISC recruits DCP1, Me31B and HPat to engineered miRNA targets transcribed by RNA polymerase III, which lack a cap structure, a protein-coding region and a poly(A) tail. Furthermore, miRISC can trigger decapping and the subsequent degradation of mRNA targets independently of ongoing deadenylation. Thus, miRISC increases the local concentration of the decapping machinery on miRNA targets to facilitate decapping and irreversibly shut down their translation (Nishihara, 2013).

This study demonstrates that miRISCs enhance the association of DCP1, Me31B and HPat with miRNA targets in a miRNA-dependent manner. This association occurs even when the miRNA target lacks a 5' cap structure, an ORF and a poly(A) tail. Furthermore, mRNA reporters that are immune to deadenylation are degraded through decapping in the presence of the miRNA, indicating that miRISCs can promote decapping independently of deadenylation (Nishihara, 2013).

It is known that miRNAs promote the degradation of partially complementary targets through the 5'-to-3' decay pathway. In this pathway, decapping is coupled to deadenylation and does not occur on polyadenylated and fully functional mRNAs. This study investigated whether the decapping of miRNA targets occurs by default, as a consequence of this coupling, or whether miRISCs can also recruit decapping factors independently of deadenylation. miRISCs was shown to enhance the association of DCP1, Me31B and HPat with unadenylated 7SL-derived miRNA targets that have been transcribed by Pol III, indicating that the cap, a poly(A) tail and ongoing deadenylation are not required for the recruitment of decapping factors to miRNA targets. DCP1 association with the Alu-miRNA target reporterers, termed EvAluator reporters, was strictly miRNA dependent and stimulated by GW182. miRNAs and GW182 also stimulated the association of HPat and Me13B with the EvAluator reporters, indicating that these decapping factors interact with miRISC components that are bound to EvAluator RNA. However, DCP1 and Me31B did not interact with isolated AGO1 or GW182 in co-immunoprecipitation assays, suggesting that the interaction of decapping factors with miRISC is indirect or that DCP1 and Me31B recognize AGO1 and GW182 as a complex. Indeed, it is possible that the decapping factors are recruited by the PAN2-PAN3 or CCR4-NOT deadenylase complexes, which interact with GW182 proteins directly. Alternatively, DCP1 and Me31B might recognize AGO1 or GW182 only in a certain conformation that is adopted on target binding. Although HPat did interact with AGO1 and GW182 in co-immunoprecipitation assays, these interactions were apparently not sufficient to enhance the association of HPat and a polyadenylated miRNA target. Nevertheless, it is possible that these interactions contribute to the recruitment of HPat to deadenylated or oligoadenylated targets (Nishihara, 2013).

A previous study in human cells reported that EDC4 co-localized with a specific miRNA target in a miRNA-dependent manner, whereas DCP1 and RCK (the human ortholog of Dm Me31B) associated with the target, regardless of the presence of the miRNA. In agreement with that study, this study observed that decapping factors associate with miRNA targets in the absence of the miRNA; however, it was found that their binding is enhanced by the cognate miRNA. This enhancement was observed for targets that are not degraded or when degradation of the target was partially inhibited and may have escaped detection in co-localization studies (Nishihara, 2013).

A functional implication for the association of decapping factors with miRNA-targets is that miRNA targets can be decapped and degraded even in the absence of a poly(A) tail or ongoing deadenylation. In combination with previously published data, the current results suggest that miRISC has multiple and redundant activities to ensure robust gene regulation: it induces translational repression, deadenylation and decapping, the latter in both a deadenylation-dependent and -independent manner (Nishihara, 2013).

Under which circumstances can deadenylation-independent decapping contribute to silencing? Decapping might play a role in silencing specific miRNA targets when deadenylation is blocked or when decapping is blocked and targets that have undergone deadenylation accumulate. Indeed, deadenylation and decapping can be uncoupled on specific mRNAs, in different cell types and under various cellular conditions, leading to the accumulation of deadenylated repressed mRNAs. These mRNAs can re-enter the translational pool on polyadenylation or might be degraded in a deadenylation-independent manner once decapping resumes. For example, in immature mouse oocytes, DCP2 and DCP1 are not detectable, but their expression increases during oocyte maturation. Consequently, in immature oocytes, many maternal mRNAs (most likely including miRNA targets) accumulate in a deadenylated silenced form. These mRNAs may be polyadenylated and translated at later stages of oogenesis or embryogenesis. However, a fraction of these deadenylated targets may be degraded through decapping when DCP2 and DCP1 are expressed. Additionally, DCP1 and DCP2 are phosphorylated under cellular stress conditions, and DCP1 is hyperphosphorylated during mitosis. Under these conditions, a subset of mRNAs is stabilized, suggesting that DCP1 and DCP2 phosphorylation inhibits decapping. Thus, it is possible that under various stress conditions, miRNA targets accumulate in a deadenylated form because decapping is inhibited and that deadenylation-independent decapping is required for the clearance of these targets on return to normal cellular conditions (Nishihara, 2013).

Notably, in addition to their role in target degradation, decapping activators act as general repressors of translation even in the absence of decapping. Therefore, these factors could play a more direct role in the translational repression of miRNA targets in the absence of mRNA degradation (Nishihara, 2013).

In contrast to translational repression and deadenylation, decapping irreversibly shuts down translation initiation and commits mRNA to full degradation. Thus, decapping prevents the reversal of miRNA-mediated silencing. However, some miRNA targets have been shown to be released from miRNA-mediated repression in response to extracellular signals, suggesting that decapping is somehow blocked for these targets to allow for a fast reversal of their repression. How decapping is prevented in a target-specific manner remains unclear, but it can reasonable be expected that proteins associated with these targets block decapping in cis by preventing DCP2 access to the cap structure. These proteins may bind the cap structure directly or may act indirectly, for example, by stabilizing binding of the cap-binding protein eIF4E to the mRNA. Proteins that act as inhibitors of DCP2-mediated decapping have been described and include Variable Charged X chromosome VCX-A protein, YB-1, Y14 and Dm CUP. Thus, it is possible that additional proteins that prevent the decapping of specific mRNAs are present in eukaryotic cells. Such mRNA-specific decapping regulators would be likely to play an important role in controlling the reversibility of silencing. Alternatively, mRNAs can be recapped in the cytoplasm; however, how recapping is regulated remains unknown (Nishihara, 2013).

In addition to the aforementioned sequence-specific decapping regulators, the cap-binding protein eIF4E acts as a general inhibitor of decapping by limiting DCP2 access to the cap structure. Therefore, for decapping to occur, eIF4E needs to dissociate from the 5' end of the mRNA. This study shows that eIF4E remains bound to at least a fraction of silenced miRNA targets in cells in which decapping is blocked. Furthermore, the DCP2 catalytic mutant did not detectably associate with the mRNA target, even though its overexpression inhibited decapping. These observations suggest that DCP2 does not stably associate with miRNA targets. Similarly, DCP2 did not co-localize with miRNA targets in human cells, although in these cells, EDC4 co-localized with the target in a miRNA-dependent manner. Thus, the process of decapping may involve multiple consecutive steps, including the association of decapping activators with the target mRNA in the absence of DCP2, eIF4E dissociation, DCP2 recruitment and cap hydrolysis. The current results suggest that miRISC facilitates an early decapping step by increasing the local concentration of decapping factors on mRNA targets, promoting decapping independently of deadenylation. Further studies are necessary to determine whether, in addition to recruiting decapping factors, miRISC plays a more direct role in accelerating the chemical catalysis step of decapping (Nishihara, 2013).

FMRP and Ataxin-2 function together in long-term olfactory habituation and neuronal translational control

Fragile X mental retardation protein (FMRP) and Ataxin-2 (Atx2) are triplet expansion disease- and stress granule-associated proteins implicated in neuronal translational control and microRNA function. This study shows that Drosophila FMRP (dFMR1) is required for long-term olfactory habituation (LTH), a phenomenon dependent on Atx2-dependent potentiation of inhibitory transmission from local interneurons (LNs) to projection neurons (PNs) in the antennal lobe. dFMR1 is also required for LTH-associated depression of odor-evoked calcium transients in PNs. Strong transdominant genetic interactions among dFMR1, atx2, the deadbox helicase me31B, and argonaute1 (ago1) mutants, as well as coimmunoprecitation of dFMR1 with Atx2, indicate that dFMR1 and Atx2 function together in a microRNA-dependent process necessary for LTH. Consistently, PN or LN knockdown of dFMR1, Atx2, Me31B, or the miRNA-pathway protein GW182 increases expression of a Ca2+/calmodulin-dependent protein kinase II (CaMKII) translational reporter. Moreover, brain immunoprecipitates of dFMR1 and Atx2 proteins include CaMKII mRNA, indicating respective physical interactions with this mRNA. Because CaMKII is necessary for LTH, these data indicate that fragile X mental retardation protein and Atx2 act via at least one common target RNA for memory-associated long-term synaptic plasticity. The observed requirement in LNs and PNs supports an emerging view that both presynaptic and postsynaptic translation are necessary for long-term synaptic plasticity. However, whereas Atx2 is necessary for the integrity of dendritic and somatic Me31B-containing particles, dFmr1 is not. Together, these data indicate that dFmr1 and Atx2 function in long-term but not short-term memory, regulating translation of at least some common presynaptic and postsynaptic target mRNAs in the same cells (Sudhakaran, 2013).

Observations presented in this study lead to three significant insights into the endogenous functions of dFmr1 and Atx2 in the nervous system and their contribution to long-term synaptic plasticity. First, the data strongly indicate that both proteins function in the same pathway, namely translational control, to mediate the form of long-term memory analyzed in this study. Second, the remarkably similar effects of knocking down these proteins in LNs and PNs provide in vivo support for an emerging idea that translational control of mRNAs in both presynaptic and postsynaptic compartments of participating synapses is necessary for long-term synaptic plasticity. Finally, although both dFmr1 and Atx2 have isoforms containing prion-like, Q/N domains, the different effects of loss of Atx2 and dFmr1 on neuronal Me31B aggregates indicate important differences in the mechanisms by which the two proteins function in translational control (Sudhakaran, 2013).

The different molecular and clinical consequence of pathogenic mutations in FMRP and Atx2 encoding genes has led to largely different perspectives on their functions. Fragile X causative mutations cause reduced levels of the encoding mRNA and lower levels of FMRP, leading to increased protein synthesis and a range of pathologies evident in children and young adults. These pathologies importantly do not include the formation of inclusion bodies. In contrast, SCA-2 and amyotrophic laterosclerosis causative mutations in Atx2 result in the dominant formation of inclusion body pathologies and age-dependent degeneration of the affected neuronal types. Observations made in this article indicate that the distinctive pathologies of the two diseases have obscured common molecular functions for the two proteins in vivo (Sudhakaran, 2013).

The genetic, behavioral, and biochemical observations show (1) shared roles of the two proteins in olfactory neurons for long-term but not short-term habituation, and (2) striking transdominant genetic interactions of dfrm1 and atx2 mutations with each other as well as with miRNA pathway proteins, which is not only consistent with prior genetic and behavioral studies of the two respective proteins but also strongly indicative of a common role for the two proteins in translational repression of neuronal mRNAs. This conclusion is supported at a mechanistic level by (3) the finding that both proteins are required for efficient repression mediated by the 3' UTR of CaMKII, a 3' UTR that this study shows to be repressed by the miRNA pathway, and (4) strong evidence for in vivo biochemical interaction among dFmr1 and Atx2 and for binding of these regulatory proteins with the UTR of the CaMKII transcript that they jointly regulate. Thus, dFMR1 and Atx2 function with miRNA pathway proteins for the regulation of a dendritically localized mRNA in identified olfactory neurons (Sudhakaran, 2013).

An unexpected observation was that dFMR1 and Atx2 seemed to be necessary for LTH as well as for CaMKII reporter regulation in both inhibitory LNs and excitatory PNs of the antennal lobe (Sudhakaran, 2013).

Until recently mammalian FMRP was regarded as a postsynaptic protein, consistent with the view that translational control of mRNAs essential for long-term plasticity occurs exclusively in postsynaptic dendrites. In contrast, work in Aplysia indicated that translational control of mRNAs is required in presynaptic terminals for long-term synaptic plasticity. This conflict between vertebrate and invertebrate perspectives is beginning to be resolved by findings that (1) mammalian FMRP is present in axons and presynaptic terminals; and that (2) translational control of both presynaptic and postsynaptic mRNAs is essential for long-term plasticity of cultured Aplysia sensorimotor synapses (Sudhakaran, 2013 and references therein).

Prior studies at the Drosophila neuromuscular junction have strongly indicated presynaptic functions for dFmr1 and translational control but have also pointed to their significant postsynaptic involvement in neuromuscular junction maturation, growth, and plasticity. More direct studies of experience-induced long-term plasticity have been performed in the context of Drosophila olfactory associative memory, wherein a specific dFmr1 isoform in particular and translational control in general are necessary for long-term forms of memory. However, the incomplete understanding of the underlying circuit mechanism has made it difficult to conclude presynaptic, postsynaptic, or dual locations for dFmr1 function in long-term memory. In contrast, recent work showing an essential role for Atx2 and Me31B in PNs for LTH more strongly indicate a postsynaptic requirement for translational control mediated by these proteins; however, this did not address a potential additional presynaptic function (Sudhakaran, 2013).

The finding that dFmr1 and Atx2 are necessary in both LNs and PNs for LTH, a process driven by changes in the strength of LN–PN synapses, provides powerful in vivo support for a consensus model in which translational control on both sides of the synapse is necessary for long-term plasticity. A formal caveat is that the anatomy of LN–PN synapses in Drosophila antennal lobes remains to be clarified at the EM level. If it emerges that these are reciprocal, dendrodendritic synapses, similar to those between granule and mitral cells in the mammalian olfactory bulb, then a clear assignment of the terms 'presynaptic' and 'postsynaptic' to the deduced activities of dFmr1 and Atx2 in this context may require further experiments (Sudhakaran, 2013).

Previous studies in Drosophila have indicated a broader role for Atx2 than dFmr1 in miRNA function in nonneuronal cells. Although Atx2 is necessary for optimal repression of four miRNA sensors examined in wing imaginal disk cells, dFmr1 is not necessary for repression of any of these sensors. The resulting conclusion that dFmr1 is required only for a subset of miRNAs to function in context of specific UTRs is consistent with the observation that only a subset of neuronal miRNAs associate with mammalian FMRP and that the protein shows poor colocalization with miRNA pathway and P-body components in mammalian cells. Parallel studies have shown that Atx2 in cells from yeast to man is required for the formation of mRNP aggregates termed stress granules, which in mammalian cells also contain Me31B/RCK and FMRP. In addition, biochemical interactions between these proteins and their mammalian homologs with each other as well as with other components of the miRNA pathway have been reported. However, neither the mechanisms of Atx2-driven mRNP assembly, nor the potential role for FMRP in such assembly, have been tested in molecular detail (Sudhakaran, 2013).

The demonstration that loss of Atx2 in neurons results in a substantial depletion of Me31B-positive foci in PN cell bodies and in dendrites is consistent with Atx2 being required for the assembly of these two different (somatic and synaptic) in vivo mRNP assemblies. Thus, the mechanisms that govern their assembly, particularly of synaptic mRNPs in vivo, overlap with mechanisms used in P-body and stress granule assembly in nonneuronal cells (Sudhakaran, 2013).

The finding that loss of dFmr1 has no visible effect on these Me31B-positive foci can be explained using either of two models. A simple model is that dFmr1 is not required for mRNP assembly, a function mediated exclusively by Atx2. This would suggest that Atx2 contains one or more functional domains missing in dFmr1 that allow the multivalent interactions necessary for mRNP assembly. This is most consistent with the observation that that although dFMR1 is a component of stress granules in Drosophila nonneuronal cells, it is not required for their assembly. An alternative model would allow both dFmr1 and Atx2 to mediate mRNP assembly but posit that dFmr1 is only present on a small subset of mRNPs, in contrast to Atx2, which is present on the majority. In such a scenario, loss of dFmr1 would only affect a very small number of mRNPs, too low to detect using the microscopic methods used in this study. In the context of these models, it is interesting that both dFmr1 and Atx2 contain prion-like Q/N domains, potentially capable of mediating mRNP assembly. It is to be noted here that the dFmr1 Q/N domain, although lacking prion-forming properties, is capable of serving as a protein interaction domain enabling the assembly of dFmr1 into RNP complexes. This observation would support the view that dFmr1 may be involved in the formation of only a subset of cellular mRNP complexes. Future studies that probe the potential distinctive properties of these assembly domains may help discriminate between these models. In addition, potential interaction of Atx2 with other proteins that are involved in mRNP formation across species, like Staufen, could help to understand the mechanisms behind Atx2-dependent function in mRNP assembly (Sudhakaran, 2013).

However, the observations presented in this study clearly show that despite the remarkable similarities in the roles of dFmr1 and Atx2 for repression of CaMKII expression at synapses and the control of synaptic plasticity that underlies long-term olfactory habituation, both proteins also have distinctive molecular functions in vivo (Sudhakaran, 2013).

Mutations that affect neuronal translational control are frequently associated with neurological disease, particularly with autism and neurodegeneration. Although these clinical conditions differ substantially in their presentation, a broadly common element is the reduced ability to adapt dynamically to changing environments, a process that may require activity-regulated translational control at synapses. Taken together with others, the observations of this study suggest that there may be two routes to defective activity-regulated translation. First, as in dFmr1 mutants, the key mRNAs are no longer sequestered and repressed, leading to a reduced ability to induce a necessary activity-induced increase in their translation. Second, it is suggested that increased aggregation of neuronal mRNPs (indicated by the frequent occurrence of TDP-43 and Atx2-positive mRNP aggregates in neurodegenerative disease) may result in a pathologically hyperrepressed state from which key mRNAs cannot be recruited for activity-induced translation. Thus, altered activity-regulated translation may provide a partial explanation not only for defects in memory consolidation associated with early-stage neurodegenerative disease but also for defects in adaptive ability seen in autism spectrum disorders (Sudhakaran, 2013).

An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules

Drosophila Me31B is a conserved protein of germ granules, ribonucleoprotein complexes essential for germ cell development. Me31B post-transcriptionally regulates mRNAs by interacting with other germ granule proteins. However, a Me31B interactome is lacking. This study used an in vivo proteomics approach to show that the Me31B interactome contains polypeptides from four functional groups: RNA regulatory proteins, glycolytic enzymes, cytoskeleton/motor proteins, and germ plasm components. It was further shown that Me31B likely colocalizes with the germ plasm components Tudor, Vasa, and Aubergine in the nuage and germ plasm and provide evidence that Me31B may directly bind to Tudor in a symmetrically dimethylated arginine-dependent manner. This study supports the role of Me31B in RNA regulation and suggests its novel roles in germ granule assembly and function (DeHaan, 2017).

Comparative Proteomics Reveal Me31B's Interactome Dynamics, Expression Regulation, and Assembly Mechanism into Germ Granules during Drosophila Germline Development

Me31B is a protein component of Drosophila germ granules and plays an important role in germline development by interacting with other proteins and RNAs. To understand the dynamic changes that the Me31B interactome undergoes from oogenesis to early embryogenesis, this study characterized the early embryo Me31B interactome and compared it to the known ovary interactome. The two interactomes shared RNA regulation proteins, glycolytic enzymes, and cytoskeleton/motor proteins, but the core germ plasm proteins Vas, Tud, and Aub were significantly decreased in the embryo interactome. Follow-up on two RNA regulations proteins present in both interactomes, Tral and Cup, revealed that they colocalize with Me31B in nuage granules, P-bodies/sponge bodies, and possibly in germ plasm granules. It was further shown that Tral and Cup are both needed for maintaining Me31B protein level and mRNA stability, with Tral's effect being more specific. In addition, evidence is provided that Me31B likely colocalizes and interacts with germ plasm marker Vas in the ovaries and early embryo germ granules. Finally, it was shown that Me31B's localization in germ plasm is likely independent of the Osk-Vas-Tud-Aub germ plasm assembly pathway although its proper enrichment in the germ plasm may still rely on certain conserved germ plasm proteins (McCambridge, 2020).

To summarize, although Me31B's localization to the posterior of an oocyte is likely independent of Osk, Aub, and Dart5, its proper enrichment at the site may still rely on Aub. Together with a previous report that Me31B's localization pattern is not affected in vas and tud mutants, it is speculated that Me31B's localization in a developing oocyte may be independent of the Osk-Vas-Tud-Aub assembly pathway, but its proper enrichment at the posterior germ plasm may still depend on certain conserved germ plasm proteins like Aub. (McCambridge, 2020).

This speculation, together with earlier conclusions in this study, led to the proposal of a hypothetical model for Me31B localization and enrichment process in the germline cells (see Hypothetical model of Me31B localization and enrichment into germ plasm). In this model, Me31B and conserved germ plasm proteins, Osk-Vas-Tud-Aub, exist in distinct granules in the germ plasm, Osk-Vas-Tud-Aub in germ plasm granules and Me31B (possibly associated with Tral and Cup) in separate granules but in close proximity. Me31B granules use an Osk-Vas-Tud-Aub-independent mechanism to localize to the cortex and the posterior of a developing oocyte, then the posteriorly localized Me31B granules interact with the germ plasm granules, which is necessary for proper Me31B granule enrichment in the germ plasm. In the early embryos, Me31B proteins begin to degrade rapidly and become dispersed in the cytoplasm (McCambridge, 2020).

Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition

In animal embryos, the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. The maternal proteome represents more than half of the protein-coding capacity of Drosophila melanogaster's genome, and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). Although the ubiquitin-proteasome system is necessary for clearance of these repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL, and ME31B for degradation early in the MZT and the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG abrogates F-box protein interaction and confers immunity to degradation. Persistent SMG downregulates zygotic re-expression of mRNAs whose maternal contribution is degraded by SMG. Thus, clearance of SMG permits an orderly MZT (Cao, 2020).

This study has shown that, in Drosophila, an extremely small subset of its maternal proteome is cleared during the MZT. This contrasts with the massive degradation of the maternal mRNA transcriptome that occurs during the MZT of all animals. Previous studies in other animals have suggested that the maternal proteome may behave very differently from the maternal transcriptome during the MZT. For example, in C. elegans, a quarter of the transcriptome is downregulated, whereas only 5% of the proteome shows a similar decrease. In frog embryos, there is also a discordance between the temporal patterns of protein and mRNA (Cao, 2020).

The set of proteins cleared during the Drosophila MZT is enriched for RNP granule components. This is consistent with the importance of post-transcriptional processes during the first ('maternal') phase of the MZT and the possible need to downregulate these processes upon ZGA and the switch to zygotic control of development. By focusing on a subset of these RNP components, which function as post-transcriptional repressors, this study has uncovered precise temporal control of their clearance by two distinct E3 ubiquitin ligase complexes: the SCF E3 ligase governs the degradation of SMG, whereas the CTLH E3 ligase is responsible for the degradation of Cup, TRAL, and ME31B. Intriguingly, SMG is degraded later during the MZT compared with its co-repressors Cup, TRAL, and ME31B. This study also showed that clearance of SMG is essential for appropriate levels of re-expression of a subset of its targets during ZGA. The results raise questions about how temporal specificity of protein degradation is regulated, as well as why at least two temporally distinct mechanisms of protein degradation exist during the MZT (Cao, 2020).

Expression data support the hypothesis that timing of E3 ligase function might, at least in part, be determined by the timing of expression of one or more of their component subunits, notably Muskelin for CTLH and CG14317 for SCF. During the Drosophila MZT, most components of the CTLH complex display constant expression levels, but Muskelin protein is degraded with a similar profile to its target repressors. Mammalian Muskelin has been shown to be auto-ubiquitinated and targeted for degradation. Detection of a ubiquitinated peptide in Muskelin supports the possibility that the Drosophila CTLH complex may be negatively autoregulated through its Muskelin subunit during the MZT. In contrast, activation of CTLH function at the beginning of the MZT may not depend on changes in complex composition: previous studies have shown that going from stage 14 oocytes to activated eggs or early (0-1 h) embryos, there are no significant changes in either the levels of CTLH subunit proteins (including Muskelin) or the ribosome association of their cognate transcripts. Thus, it is speculated that post-translational modification of one or more CTLH subunits may activate CTLH function (Cao, 2020).

Modification of substrates may also play a role: the degradation of Cup, TRAL, and ME31B depends on the PNG kinase, which itself has temporally restricted activity coinciding with degradation of these repressors. PNG-dependent phosphorylation of Cup, TRAL, and ME31B may make them ubiquitination substrates. Furthermore, evidence suggests that temporal regulation of the E2 ubiquitin-conjugating enzyme, UBC-E2H, at this stage depends on the PNG kinase and may also contribute to the timing of ubiquitin ligase complex function during the MZT. Concomitant PNG-dependent activation of the CTLH complex, its cognate E2, and its substrates, coupled with subsequent self-inactivation of the complex through Muskelin degradation, would provide a precise time window for CTLH function and, therefore, for degradation of Cup, TRAL, and ME31B early in the MZT (Cao, 2020).

In contrast with these three co-repressors, degradation of SMG occurs near the end of the MZT and depends on zygotic gene expression. Although the levels of most SCF complex subunits are constant during the MZT, the F-box protein CG14317 displays a unique expression pattern: CG14317 protein and mRNA are absent at the beginning of the MZT, are zygotically synthesized, peak in NC14 embryos, and sharply decline shortly thereafter. Thus, CG14317 expression coincides with the timing of SMG protein degradation and, coupled with the zygotic nature of its accumulation, makes it a strong candidate to be a timer for SCF function. The fact that knockdown of SLMB stabilizes SMG protein suggests that both F-box proteins may be necessary for SMG degradation, with CG14317 serving as the timer. At present there are no forward or reverse genetic reagents available to test this hypothesis. Additionally, the function of SLMB in directing SMG-protein ubiquitination may itself be temporally restricted. Both Drosophila SLMB and its mammalian homolog are known to bind phosphorylated motifs. Phosphorylated residues have been detected in SMG in the embryo, including residues within its C terminus; one of these, S967, resides close to a ubiquitinated lysine, K965. In summary, despite the stable expression of SLMB during the MZT, temporal regulation of phosphorylation of its target proteins, including SMG, through yet uncharacterized mechanisms, may also contribute to temporal control of SMG protein degradation (Cao, 2020).

Because Cup, TRAL, and ME31B are known to function as co-repressors in a complex with SMG, why are the timing of degradation of Cup-TRAL-ME31B and SMG differentially regulated? Although the SMG-Cup-TRAL-ME31B-mRNA complex has been characterized to be extremely stable in vitro, it would be disrupted in vivo by the degradation of Cup, TRAL, and ME31B (or by the degradation of nos and other SMG-target mRNAs). SMG directs translational repression both through AGO1 and through Cup-TRAL-ME31B, as well as transcript degradation through recruitment of the CCR4-NOT deadenylase. CTLH-driven degradation of Cup, TRAL, and ME31B would abrogate SMG-Cup-TRAL-ME31B-dependent translational repression, but not AGO1-dependent repression, because AGO1 levels increase during the MZT. However, the relative contributions of AGO1 versus Cup-TRAL-ME31B to translational repression by SMG are unknown. That said, the CCR4-NOT deadenylase is present both during and after the MZT (Temme et al., 2004); thus, SMG-dependent transcript degradation would occur both before and after clearance of Cup, TRAL, and ME31B. 12% of SMG-associated transcripts are degraded, but not repressed, by SMG. Perhaps this subset is bound and degraded by SMG late in the MZT, after the drop in Cup, TRAL, and ME31B levels (Cao, 2020).

Another possible role for clearance of ME31B and TRAL derives from studies in budding yeast, where it has been shown that their orthologs, respectively, Dhh1p and Scd6p, have a potent inhibitory effect on 'general' translation. If this is also true in Drosophila, then degradation of ME31B and TRAL, which are present at exceedingly high concentrations in embryos, might also serve to permit high-level translation during the second phase of the MZT (Cao, 2020).

Previous work has shown that SMG has both direct and indirect roles in the MZT. SMG's direct role is to bind to a large number of maternal mRNA species and target them for repression and/or degradation. Two indirect effects have been shown in smg mutants. First, if maternal transcripts fail to be degraded and/or repressed, ZGA fails or is significantly delayed, likely because mRNAs encoding transcriptional repressors persist. Second, because zygotically synthesized microRNAs direct a second wave of maternal mRNA decay during the late MZT, in smg mutants, failure to produce those microRNAs results in failure to eliminate a second set of maternal transcripts late in the MZT (Cao, 2020).

This study has uncovered a role for rapid clearance of the SMG protein itself late in the MZT: to permit normal levels of zygotic re-expression of a subset of it targets. Notably, stabilized SMG (SMG767Δ999) rescues both clearance of its maternal targets and ZGA, excluding the possibility that lower-than-normal levels of re-expressed targets are a result of defective SMG function upon deletion of its C terminus. Indeed, in control experiments, SMG's exclusively maternal targets actually dropped to lower levels than normal, likely because SMG767Δ999 continues to direct their decay beyond when SMG normally disappears from embryos. Furthermore, in another control, strictly zygotic transcripts that lack SMG binding sites were expressed at higher levels in SMG767Δ999-rescued mutants than in full-length SMG-rescued mutants. This result is consistent with the hypothesis that clearance of transcriptional repressors by SMG permits ZGA; persistent SMG would clear these repressors to lower levels than normal, hence resulting in higher zygotic expression. The higher-than-normal expression of zygotic transcripts that lack SMG binding sites makes the lower-than-normal levels of SMG's zygotically re-expressed target transcripts by SMG767Δ999 even more striking. Together, these data support a model in which the timing of both SMG synthesis and clearance are important for orderly progression of the MZT (Cao, 2020).

WD40 protein Wuho controls germline homeostasis via TRIM-NHL tumor suppressor Mei-p26 in Drosophila

WD40 proteins control many cellular processes via protein interactions. Drosophila Wuho controls fertility, although the involved mechanisms are unclear. This study shows that Wh promotion of Mei-p26 (a human TRIM32 ortholog) function maintains ovarian germ cell homeostasis. Wh and Mei-p26 are epistatically linked, with wh and mei-p26 mutants showing nearly identical phenotypes, including germline stem cell (GSC) loss, stem-cyst formation due to incomplete cytokinesis between GSCs and daughter cells, and overproliferation of GSC progeny. Mechanistically, Wh interacts with Mei-p26 in different cellular contexts to induce cell type-specific effects. In GSCs, Wh and Mei-p26 promote BMP stemness signaling for proper GSC division and maintenance. In GSC progeny, Wh and Mei-p26 silence nanos translation, downregulate a subset of microRNAs involved in germ cell differentiation and suppress ribosomal biogenesis via dMyc to limit germ cell mitosis. This study also found that the human ortholog of Wh (WDR4) interacts with TRIM32 in human cells. These results show that Wh is a regulator of Mei-p26 in Drosophila germ cells and suggest that the WD40-TRIM interaction may also control tissue homeostasis in other stem cell systems (Rastegari, 2020).

Stem cell self-renewal and differentiation must be balanced for proper tissue homeostasis. This balance is known to be coordinated by transcriptional and post-transcriptional mechanisms, which have not been fully described at a molecular level. An excellent model for studying genetic regulation of the cell fate transition from stem cell to differentiated progeny is the Drosophila ovary, as its germline stem cells (GSCs) and differentiated progeny are well characterized in cell biology. Although the physiology of Drosophila egg production is well described at a cellular level, the molecular regulatory mechanisms are still an area of active investigation (Rastegari, 2020).

Wuho (Wh; meaning 'no progeny' in Chinese) is an evolutionarily conserved protein comprising five WD40 domains (Cheng, 2016; Wu, 2006), which mediate protein-protein interactions. Homologs of Wh have been shown to exert a wide variety of functions via interactions with m7G46 tRNA methyltransferase, Flap endonuclease 1 (FEN1) and Culin-Ring ubiquitin ligase 4. Interestingly, wh mutant males are sterile because their spermatids are not properly elongated to make functional spermatozoa, and female flies are semi-sterile for unknown reasons (Wu, 2006), suggesting that Wh may potentially play an important role in the molecular regulatory circuitry of the GSC lineage (Rastegari, 2020).

Interestingly, the ovarian phenotypes reported in Wh mutants are strikingly similar to those in Mei-p26 mutants. Mei-p26 is a member of the tripartite motif and Ncl-1, HT2A and Lin-41 domain (TRIM- NHL) family of proteins, which is highly conserved among metazoans. TRIM-NHL proteins are known to control developmental transitions through mechanisms such as the promotion of stem cell differentiation by suppressing proliferation. The molecular action of TRIM-NHL proteins is typically ubiquitination and translation silencing via E3 ligase RING domains; meanwhile, the NHL domains mediate protein-protein interactions. In the Drosophila germline, Mei-p26 controls GSC maintenance and differentiation depending on its expression level. However, the regulators of Mei-p26 in the GSC lineage are not known. This study shows that Wh is a key regulator of Mei-p26 and that these proteins function together in multiple contexts to control GSC maintenance and differentiation for germline homeostasis. These results document a potentially generalizable role for WD40 proteins as a bridge between TRIM-NHL proteins and other cellular components, a function that is necessary to balance self-renewal and differentiation in the GSC lineage (Rastegari, 2020).

Homeostatic regulation of stem cells, the very foundation of tissue homeostasis, remains poorly understood at a molecular level. Using the Drosophila GSC lineage as an in vivo model to study stem cell biology, this study found that Wh, a WD40 protein, controls GSC self- renewal and differentiation via Mei-p26, a TRIM-NHL protein. An interaction between the proteins was identified in the ovary, and striking similarities between wh7 and mei-p26 mutants were observed at both phenotypic and molecular levels. Based on these findings and published results regarding Mei-p26 function, it is proposed that, in wild-type GSCs, Wh, Mei-p26 and Nos form a complex to inhibit brat translation, allowing Mad to be stabilized and phosphorylated by BMP signaling. pMad then translocates to the nucleus, where it suppresses transcription of bam, a master regulator of differentiation. On the other hand, Wh also promotes differentiation of GSC progeny by multiple mechanisms. First, Wh, Mei-p26, Bgcn, Sxl and Bam form a complex that binds to the 3' UTR of nos to silence its translation, possibly helping to turn off BMP signaling in the differentiating GSC progeny. Second, Wh interacts with Mei-p26, an E3 ubquitin ligase, to control dMyc protein levels and allow proper ribosomal biogenesis. Third, the interaction between Wh and Mei-p26 also limits expression of a subset of microRNAs, which may contribute to differentiation. These functions of Wh appear to be especially important for the last step of cytokinesis (abscission), which is completed between the GSC and its daughter cell after early G2 phase, as revealed by closure of the ring canal (Rastegari, 2020).

In wh mutant GSCs, brat translation is not suppressed, decreasing the level of pMad and increasing the expression of the differentiation factor Bam. This sequence of events causes premature differentiation of GSCs and leads to GSC loss, consistent with the known roles of Brat and Bam in germ cell differentiation. Mutation of brat or bam increases GSC number, whereas overexpression of brat or bam in germ cells causes germ cell depletion by forcing GSC differentiation. Mutation of wh in germ cells also results in incomplete abscission between GSCs and daughter cells, leaving open ring canals that create stem-cysts. Although this study did not determine the molecular mechanism by which Wh controls GSC abscission, removing a copy of bam significantly reduced stem-cyst number in wh mutant germaria, which suggests a role for Bam in Wh control of GSC abscission. In wh mutant germaria, stem-cysts simultaneously express Nos (a GSC maintenance factor) and Bam; thus, the growths display characteristics of both GSCs and daughter cells. In addition, ribosomal biogenesis is promoted via upregulated dMyc and drives germ cell overproliferation. Lastly, some differentiation-associated microRNAs are increased in the mutant ovaries, although their functions are not yet clear. It is not known whether a defect in meiosis is a consequence of overproliferative wh mutant germ cells, or whether Wh has a separate role in meiosis (Rastegari, 2020).

The results show that Wh is required for Mei-p26 function in germ cell homeostasis. However, it is unclear whether Wh directly interacts with Mei-p26 and which domains in the two proteins mediate the interaction. It is possible that Wh serves as a bridge for Mei-p26 to interact with its known partners. This study observed an interaction between human orthologs of Wh (WDR4) and Mei-p26 (TRIM32), suggesting that the interaction is evolutionarily conserved. Thus, the interaction between WD40 and TRIM-NHL proteins may be crucial for stem cell regulation in other organisms (Rastegari, 2020).

The last step in cell division, cytokinesis, is completed by abscission, which physically separates the two daughter cells. Cytokinesis starts by ingression of the cleavage furrow, constricting the plasma membrane onto the spindle midzone to form an electron- dense structure, the midbody, which comprises a thin membrane channel bridging two nascent daughter cells. The stem-cyst forms owing to a failure of GSCs to separate from daughter cells. Two possible mechanisms may produce such an abscission failure. First, a stem-cell-specific defect may prevent GSC-CB abscission. Second, GSCs may exhibit characteristics of differentiating cells that cause them to adopt incomplete cell cytokinesis programs. In addition to controlling chromosome orientation and segmentation, Aurora B is known to intrinsically regulate the timing of cell abscission, including in Drosophila female GSCs. During abscission, Aurora B in GSCs is targeted to the midbody and triggers membrane abscission via Endosomal sorting complex required for transport III (ESCRT-III) machinery. Aurora B negatively controls ESCRT-III, i.e. when Aurora B is active, ESCRT-III activity is low and abscission is delayed, and vice versa. It has also been shown that ribosomal biogenesis coordinates with ESCRT-III in GSCs to promote GSC abscission. Increasing Aurora B activity or disrupting ESCRT-III generates stem-cysts with germ cells that undergo synchronous division, yielding 32 germ cells in most egg chambers. However, wh mutant germ cells within stem-cysts divide asynchronously with elevated ribosomal biogenesis, and wh mutant egg chambers carry various numbers of germ cells. In addition, in wh mutant stem-cysts, decreased pMad expression, upregulated Bam expression and branched fusomes are all hallmarks of differentiating cysts. These results suggest that wh mutant stem-cysts may adopt the abscission program of differentiating cysts. Interestingly, removing a copy of bam from wh mutants or from shrub (a subunit of ESCRT-III) mutants partially rescues stem-cysts, suggesting that GSC abscission is coupled with cell fate. Further studies will be required to understand the molecular targets of Wh that control GSC abscission, and how GSCs and differentiating cysts acquire different abscission programs. Nevertheless, this study has shown that Wh participates with Mei-p26 to regulate fate determination in stem cells and daughter cells. This novel interaction may be conserved in other species and introduces the idea that WD40 proteins may participate with TRIM-NHL proteins in cell fate decision (Rastegari, 2020).

A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing

CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. It is recruited to miRNA targets through interactions with tryptophan (W)-containing motifs in TNRC6/GW182 proteins and is required for both translational repression and degradation of miRNA targets. This study elucidated the structural basis for the repressive activity of CCR4-NOT and its interaction with TNRC6/GW182s. The conserved CNOT9 subunit attaches to a domain of unknown function (DUF3819) in the CNOT1 scaffold. The resulting complex provides binding sites for TNRC6/GW182, and its crystal structure reveals tandem W-binding pockets located in CNOT9. It was further shown that the CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6, a translational repressor and decapping activator. The crystal structure of this complex demonstrates striking similarity to the eIF4G-eIF4A complex. Together, these data provide the missing physical links in a molecular pathway that connects miRNA target recognition with translational repression, deadenylation, and decapping (Chen, 2014).

Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B

The DEAD box helicase DDX6/Me31B functions in translational repression and mRNA decapping. How particular RNA helicases are recruited specifically to distinct functional complexes is poorly understood. This paper presents the crystal structure of the human DDX6 C-terminal RecA-like domain bound to a highly conserved FDF sequence motif in the decapping activator EDC3. The FDF peptide adopts an alpha-helical conformation upon binding to DDX6, occupying a shallow groove opposite to the DDX6 surface involved in RNA binding and ATP hydrolysis. Mutagenesis of Me31B shows the relevance of the FDF interaction surface both for Me31B's accumulation in P bodies and for its ability to repress the expression of bound mRNAs. The translational repressor Tral contains a similar FDF motif. Together with mutational and competition studies, the structure reveals why the interactions of Me31B with EDC3 and Tral are mutually exclusive and how the respective decapping and translational repressor complexes might hook onto an mRNA substrate (Tritschler, 2009).

Functions of me31B orthologs in other species

ELAVL2-directed RNA regulatory network drives the formation of quiescent primordial follicles

Formation of primordial follicles is a fundamental, early process in mammalian oogenesis. However, little is known about the underlying mechanisms. This study reports that the RNA-binding proteins ELAVL2 and DDX6 (homolog of Drosophila Me31B) are indispensable for the formation of quiescent primordial follicles in mouse ovaries. Elavl2 knockout females are infertile due to defective primordial follicle formation. ELAVL2 associates with mRNAs encoding components of P-bodies (cytoplasmic RNP granules involved in the decay and storage of RNA) and directs the assembly of P-body-like granules by promoting the translation of DDX6 in oocytes prior to the formation of primordial follicles. Deletion of Ddx6 disturbs the assembly of P-body-like granules and severely impairs the formation of primordial follicles, indicating the potential importance of P-body-like granules in the formation of primordial follicles. Furthermore, Ddx6-deficient oocytes are abnormally enlarged due to misregulated PI3K-AKT signaling. These data reveal that an ELAVL2-directed post-transcriptional network is essential for the formation of quiescent primordial follicles (Kato, 2019).


Search PubMed for articles about Drosophila maternal expression at 31B

Barbee, S. A., et al. (2006). Staufen- and FMRP-containing neuronal RNPs are structurally and functionally related to somatic P bodies. Neuron 52(6): 997-1009. PubMed ID: 17178403

Chen, Y., Boland, A., Kuzuoglu-Ozturk, D., Bawankar, P., Loh, B., Chang, C. T., Weichenrieder, O. and Izaurralde, E. (2014). A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol Cell 54: 737-750. PubMed ID: 24768540

Cao, W. X., Kabelitz, S., Gupta, M., Yeung, E., Lin, S., Rammelt, C., Ihling, C., Pekovic, F., Low, T. C. H., Siddiqui, N. U., Cheng, M. H. K., Angers, S., Smibert, C. A., Wuhr, M., Wahle, E. and Lipshitz, H. D. (2020). Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition. Cell Rep 31(12): 107783. PubMed ID: 32579915

DeHaan, H., McCambridge, A., Armstrong, B., Cruse, C., Solanki, D., Trinidad, J. C., Arkov, A. L. and Gao, M. (2017). An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules. FEBS Lett [Epub ahead of print]. PubMed ID: 28945271

Fragkouli, A., Koukouraki, P., Vlachos, I. S., Paraskevopoulou, M. D., Hatzigeorgiou, A. G. and Doxakis, E. (2017). Neuronal ELAVL proteins utilize AUF-1 as a co-partner to induce neuron-specific alternative splicing of APP. Sci Rep 7: 44507. PubMed ID: 28291226

Hillebrand, J., et al. (2010). The Me31B DEAD-box helicase localizes to postsynaptic foci and regulates expression of a CaMKII reporter mRNA in dendrites of Drosophila olfactory projection neurons. Front Neural Circuits 4: 121. PubMed ID: 21267420

Kato, Y., Iwamori, T., Ninomiya, Y., Kohda, T., Miyashita, J., Sato, M. and Saga, Y. (2019). ELAVL2-directed RNA regulatory network drives the formation of quiescent primordial follicles. EMBO Rep 20(12): e48251. PubMed ID: 31657143

McCambridge, A., Solanki, D., Olchawa, N., Govani, N., Trinidad, J. C. and Gao, M. (2020). Comparative Proteomics Reveal Me31B's Interactome Dynamics, Expression Regulation, and Assembly Mechanism into Germ Granules during Drosophila Germline Development. Sci Rep 10(1): 564. PubMed ID: 31953495

McCann, C., et al. (2011). The Ataxin-2 protein is required for microRNA function and synapse-specific long-term olfactory habituation. Proc. Natl. Acad. Sci. 108(36):vE655-62. PubMed ID: 21795609

Nakamura, A., Amikura, R., Hanyu, K. and Kobayashi, S. (2001). Me31B silences translation of oocyte-localizing RNAs through the formation of cytoplasmic RNP complex during Drosophila oogenesis. Development 128(17): 3233-42. PubMed ID: 11546740

Nakamura, A., Sato, K. and Hanyu-Nakamura, K. (2004). Drosophila Cup is an eIF4E binding protein that associates with Bruno and regulates oskar mRNA translation in oogenesis. Dev. Cell 6: 69-78. 14723848

Nishihara, T., Zekri, L., Braun, J. E. and Izaurralde, E. (2013). miRISC recruits decapping factors to miRNA targets to enhance their degradation. Nucleic Acids Res 41: 8692-8705. PubMed ID: 23863838

Rastegari, E., Kajal, K., Tan, B. S., Huang, F., Chen, R. H., Hsieh, T. S. and Hsu, H. J. (2020). WD40 protein Wuho controls germline homeostasis via TRIM-NHL tumor suppressor Mei-p26 in Drosophila. Development 147(2). PubMed ID: 31941704

Satterfield, T. F., Jackson, S. M. and Pallanck, L. J. (2002). A Drosophila homolog of the polyglutamine disease gene SCA2 is a dosage-sensitive regulator of actin filament formation. Genetics 162: 1687-1702. PubMed ID: 12524342

Satterfield, T. F. and Pallanck, L. J. (2006). Ataxin-2 and its Drosophila homolog, ATX2, physically assemble with polyribosomes. Hum. Mol. Genet. 15: 2523-2532. PubMed ID: 16835262

Sudhakaran, I. P., Hillebrand, J., Dervan, A., Das, S., Holohan, E. E., Hulsmeier, J., Sarov, M., Parker, R., Vijayraghavan, K. and Ramaswami, M. (2013). FMRP and Ataxin-2 function together in long-term olfactory habituation and neuronal translational control. Proc Natl Acad Sci U S A. PubMed ID: 24344294

Tharun, S. (2008). Roles of Eukaryotic Lsm Proteins in the Regulation of mRNA Function. Int. Rev. Cell and Molec. Biol. 272: 149-189. PubMed ID: 19121818

Tritschler, F., Braun, J. E., Eulalio, A., Truffault, V., Izaurralde, E. and Weichenrieder, O. (2009). Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. Mol. Cell 33: 661-668. PubMed ID: 19285948

Biological Overview

date revised: 5 August 2023

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