Gene name - Mothers against dpp
Cytological map position - 23D
Function - TGF beta signal transduction
Key words - BMP signaling
Symbol - Mad
Genetic map position - 2-
Classification - novel signaling protein
Cellular location - cytoplasmic
|Recent literature||Dolezal, D., Liu, Z., Zhou, Q. and Pignoni, F. (2015). Fly LMBR1/LIMR-type protein Lilipod promotes germ-line stem cell self-renewal by enhancing BMP signaling. Proc Natl Acad Sci U S A 112: 13928-13933. PubMed ID: 26512105
Limb development membrane protein-1 (LMBR1)/lipocalin-interacting membrane receptor (LIMR)-type proteins are putative nine-transmembrane receptors that are evolutionarily conserved across metazoans. However, their biological function is unknown. This study shows that the fly family member Lilipod (Lili; CG5807) is required for germ-line stem cell (GSC) self-renewal in the Drosophila ovary where it enhances bone morphogenetic protein (BMP) signaling. lili mutant GSCs are lost through differentiation, and display reduced levels of the Dpp transducer pMad and precocious activation of the master differentiation factor bam. Conversely, overexpressed Lili induces supernumerary pMad-positive bamP-GFP-negative GSCs. Interestingly, differentiation of lili mutant GSCs is bam-dependent; however, its effect on pMad is not. Thus, although it promotes stem cell self-renewal by repressing a bam-dependent process, Lilipod enhances transduction of the Dpp signal independently of its suppression of differentiation. In addition, because Lili is still required by a ligand-independent BMP receptor, its function likely occurs between receptor activation and pMad phosphorylation within the signaling cascade. This first in vivo characterization of a LMBR1/LIMR-type protein in a genetic model reveals an important role in modulating BMP signaling during the asymmetric division of an adult stem cell population and in other BMP signaling contexts.
|Urrutia, H., Aleman, A. and Eivers, E. (2016).
Dullard functions as a Mad phosphatase to terminate BMP signaling.
Sci Rep 6: 32269. PubMed ID: 27578171
Bone morphogenetic proteins (BMPs) are growth factors that provide essential signals for normal embryonic development and adult tissue homeostasis. A key step in initiating BMP signaling is ligand induced phosphorylation of receptor Smads (R-Smads) by type I receptor kinases, while linker phosphorylation of R-Smads has been shown to cause BMP signal termination. This study demonstrates that the phosphatase Dullard is involved in dephosphorylating the Drosophila R-Smad, Mad, and is integral in controlling BMP signal duration. A hypomorphic Dullard allele or Dullard knockdown leads to increased Mad phosphorylation levels, while Dullard overexpression results in reduced Mad phosphorylations. Co-immunoprecipitation binding assays demonstrate phosphorylated Mad and Dullard physically interact, while mutation of Dullard's phosphatase domain still allows Mad-Dullard interactions but abolishes its ability to regulate Mad phosphorylations. Finally, linker and C-terminally phosphorylated Mad can be regulated by one of two terminating mechanisms, degradation by proteasomes or dephosphorylation by the phosphatase Dullard.
|Jordan-Alvarez, S., Santana, E., Casas-Tinto, S., Acebes, A. and Ferrus, A. (2017). The equilibrium between antagonistic signaling pathways determines the number of synapses in Drosophila. PLoS One 12(9): e0184238. PubMed ID: 28892511
Using the Drosophila larval neuromuscular junction, this study shows a PI3K-dependent pathway for synaptogenesis which is functionally connected with other previously known elements including the Wit receptor, its ligand Gbb, and the MAPkinases cascade. Based on epistasis assays, the functional hierarchy within the pathway was determined. Wit seems to trigger signaling through PI3K, and Ras85D also contributes to the initiation of synaptogenesis. However, contrary to other signaling pathways, PI3K does not require Ras85D binding in the context of synaptogenesis. In addition to the MAPK cascade, Bsk/JNK undergoes regulation by Puc and Ras85D which results in a narrow range of activity of this kinase to determine normalcy of synapse number. The transcriptional readout of the synaptogenesis pathway involves the Fos/Jun complex and the repressor Cic. In addition, an antagonistic pathway was identified that uses the transcription factors Mad and Medea and the microRNA bantam to down-regulate key elements of the pro-synaptogenesis pathway. Like its counterpart, the anti-synaptogenesis signaling uses small GTPases and MAPKs including Ras64B, Ras-like-a, p38a and Licorne. Bantam downregulates the pro-synaptogenesis factors PI3K, Hiw, Ras85D and Bsk, but not AKT. AKT, however, can suppress Mad which, in conjunction with the reported suppression of Mad by Hiw, closes the mutual regulation between both pathways. Thus, the number of synapses seems to result from the balanced output from these two pathways.
Kim, A. R., Choi, E. B., Kim, M. Y. and Choi, K. W. (2017). Angiotensin-converting enzyme Ance is cooperatively regulated by Mad and Pannier in Drosophila imaginal discs. Sci Rep 7(1): 13174. PubMed ID: 29030610
Angiotensin-converting enzyme (ACE) is an evolutionarily conserved peptidyl dipeptidase. Mammalian ACE converts angiotensin I to the active vasoconstrictor angiotensin II, thus playing a critical role for homeostasis of the renin-angiotensin system. In Drosophila, the ACE homolog Ance is expressed in specific regions of developing organs, but its regulatory mechanism has not been identified. This study provides evidence that Ance expression is regulated by a combination of Mad and Pannier (Pnr) in imaginal discs. Ance expression in eye and wing discs depends on Dpp signaling. The Mad binding site of Ance regulatory region is essential for Ance expression. Ance expression in imaginal discs is also regulated by the GATA family transcription factor Pnr. Pnr directly regulates Ance expression by binding to a GATA site of Ance enhancer. In addition, Pnr and Mad physically and genetically interact. Ance null mutants are morphologically normal but show genetic interaction with dpp mutants. Furthermore, human SMAD2 and GATA4 were shown to physically interact, and ACE expression in HEK293 cells is regulated by SMAD2 and GATA4. Taken together, this study reveals a cooperative mechanism of Ance regulation by Mad and Pnr. The data also suggest a conserved transcriptional regulation of human ACE.
|Patrnogic, J., Heryanto, C. and Eleftherianos, I. (2018). Wounding-induced upregulation of the Bone Morphogenic Protein signaling pathway in Drosophila promotes survival against parasitic nematode infection. Gene [Epub ahead of print]. PubMed ID: 29920363
The common fruit fly, Drosophila melanogaster is an outstanding model to analyze the regulation of conserved signaling pathways. This study examined whether signaling components in the Bone Morphogenic Protein (BMP) branch of the TGF-beta signaling pathway are involved in the response to wounding caused by either sterile injury or infection by parasitic nematodes in D. melanogaster adult flies. Following sterile injury, the BMP pathway Type I receptor sax and intracellular transcription factor Mad were found to be substantially upregulated. Also, inactivation of Mad or dpp promoted fly survival and increased antimicrobial peptide gene transcript levels upon sterile injury or H. bacteriophora nematode infection, respectively, but not against the bacterial pathogen Photorhabdus luminescens. These findings indicate the roles of certain BMP signaling components in the regulation of the fly immune response against sterile injury or nematode infection. In conclusion, this study highlights the ability of D. melanogaster to activate the BMP branch of TGF-beta signaling in order to modulate the response to injury in the absence or presence of pathogenic infection.
|Vuilleumier, R., Lian, T., Flibotte, S., Khan, Z. N., Fuchs, A., Pyrowolakis, G. and Allan, D. W. (2018). Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element. Nucleic Acids Res. PubMed ID: 30476189
Retrograde Bone Morphogenetic Protein (BMP) signaling in neurons is essential for the differentiation and synaptic function of many neuronal subtypes. BMP signaling regulates these processes via Smad transcription factor activity, yet the scope and nature of Smad-dependent gene regulation in neurons are mostly unknown. This study applied a computational approach to predict Smad-binding cis-regulatory BMP-Activating Elements (BMP-AEs) in Drosophila, followed by transgenic in vivo reporter analysis to test their neuronal subtype enhancer activity in the larval central nervous system (CNS). 34 BMP-AE-containing genomic fragments were identifed that are responsive to BMP signaling in neurons; the embedded BMP-AEs are required for this activity. RNA-seq analysis identified BMP-responsive genes in the CNS and revealed that BMP-AEs selectively enrich near BMP-activated genes. These data suggest that functional BMP-AEs control nearby BMP-activated genes, which were validated experimentally. Finally, it was demonstrated that the BMP-AE motif mediates a conserved Smad-responsive function in the Drosophila and vertebrate CNS. The results provide evidence that BMP signaling controls neuronal function by directly coordinating the expression of a battery of genes through widespread deployment of a conserved Smad-responsive cis-regulatory motif.
Mothers against dpp was discovered (Raftery, 1995) in a search for elements of the decapentaplegic signaling pathway in Drosophila (for review, see Raftery, 1999). When given the problem of identifying elements in a biochemical pathway, a geneticist will usually take a genetic approach, one that has worked in previous attempts in other systems. The tactic is to disclose enhancers which exacerbate known mutations. An enhancer is a mutation in the sought-for gene that engenders a more severe phenotype than that caused by the mutation of a single, already characterized gene. Thus a search was carried out for mutations that produce a more severe phenotype (an "enhancement") when combined with known dpp mutations. Mad mutations can be placed in an allelic series based on the relative severity of the maternal effect enhancement of weak dpp alleles, thus explaining the name Mothers against dpp.
Two types of experiments were carried out. The first was designed to reveal mutations in genes expressed in zygotes that exacerbate the phenotype of embryos that have a limiting amount of DPP. Mutations that act as enhancers of such DPP limited embryos cause embryonic lethality. The possibility that some of the gene products involved in DPP signaling might be supplied during oogenesis necessitated a second experiment looking for failure to recover progeny (that is, embryonic lethals) from mothers exhibiting a limiting amount of DPP. The two experiments yielded several kinds of enhancers: 1) new dpp alleles, which along with an already limited quantity of DPP cause embryonic lethality; 2) mutations in tolloid, a gene whose product is involved in DPP processing; 3) mutations in screw whose protein product is a ubiquitously expressed member of the TGF-beta family required for specification of dorsal cell fates in the Drosophila embryo; 4) mutations in Media, another gene involved in DPP signaling, and 5) mutations in Mad. Mutations in Mad, when interacting with limiting DPP levels, produce a defective amnioserosa (see also [Image]), the extra-embryonic membrane comprising the dorsal-most cells in early embryos (Raftery, 1995).
Mad mutations are also enhancers of mutant dpp appendage phenotypes. Thus Mad mutants produce a further reduction in wing blade size, a slight reduction in the eye, and loss of tarsal claws. These Mad mutant phenotypes exhibit a close correspondence to dpp mutant phenotypes. Homozygous Mad mutant larvae also show midgut defects and a greatly reduced gastric caecae. DPP signaling from visceral mesoderm to midgut endoderm is required for proper extension of the gastric caecae in parasegment 4 and for the induction of the homeotic gene labial in the adjacent endoderm of parasegment 7. Homozygous Mad mutant embryos lack labial expression and have defects in midgut constriction engendered by labial expression. Other imaginal disc derived structural defects are evident in homozygous Mad mutants, including heldout wings, split notum, loss of distal leg segments, duplications of the third antennal segment and defects in female genitalia (Sekelsky, 1995).
To date there is no indication that the Drosophila MAD protein is nuclear: antibody staining experiments indicate a cytoplasmic localization. Neverless there is clear indication that a human MAD homolog enters the nucleus upon BMP2 signaling (Hoodless, 1996).
A simple experiment was carried out to see if MAD acts upstream or downstream of DPP. DPP was ubiquitously expressed in Mad mutants. If Mad acts upstream of DPP, then ubiquitous expression of DPP should result in labial induction in the midgut endoderm independently of Mad. In fact labial does not get induced in Mad mutants even when dpp is expressed ubiquitously, indicating that MAD acts downstream of dpp. When MAD is artifically expressed in mesoderm, it fails to rescue labial induction in embryos otherwise deficient in MAD, but artificial expression of MAD in endoderm does rescue labial induction (Newfeld, 1996). Thus MAD appears to be a component in DPP signaling acting downstream of dpp in cells that are the recipients of DPP signaling.
Daughters against dpp (Dad), whose transcription is induced by Dpp shares, weak homology with Drosophila Mad, a protein required for transduction of Dpp signals. Dad is expressed in a wide stripe that straddles the A/P compartment boundary of the imaginal discs, in contrast to Dpp, whose expression is confined to the anterior side. This pattern of expression suggests that Dad expression is positively regulated by the secreted Dpp molecule, and in fact ectopic Dpp expression results in abnormally large discs and in ectopic expression of Dad. In contrast to Mad or the activated Dpp receptor, whose overexpression hyperactivates the Dpp signaling pathway, overexpression of Dad blocks Dpp activity. Dpp target gene optomotor blind is absent in Dad-overexpressing cells. Expression of Dad together with either Mad or the activated receptor rescues phenotypic defects induced by either protein alone. Dad can also antagonize the activity of a vertebrate homolog of Dpp, bone morphogenetic protein, as evidenced by induction of dorsal or neural fate following overexpression in Xenopus embryos. It is concluded that the pattern-organizing mechanism governed by Dpp involves a negative-feedback circuit in which Dpp induces expression of its own antagonist, Dad. This feedback loop appears to be conserved in vertebrate development (Tsuneizumi, 1997).
Drosophila Medea encodes a homolog of Smad4. Smad4 is relatively divergent from other vertebrate Smads and does not appear to be regulated by signal-dependent phosphorylation. However, overexpression of vertebrate Smad4 stimulates TGF-beta and activin responses. Smad4 associates with Smad1 (the mammalian homolog of Mad) in response to BMP2/4 or with Smad2 in response to TGF-beta, and dominant negative Smad4 blocks both BMP and activin responses. These observations have generated a model in which Smad4 is essential for signal transduction by all TGF-beta family members through its interaction with phosphorylated receptor-regulated Smads. Medea functions downstream of Dpp; complete removal of the Medea gene product causes the same embryonic phenotype as dpp null mutations. Mad undergoes signal-dependent translocation to the nucleus in the absence of Medea; in contrast, Medea is localized in the cytoplasm and requires Mad in order to accumulate in the nucleus. Specific mutations identified in strong alleles of Medea disrupt either Medea interaction with Mad or nuclear translocation of the Mad/Medea complex. Thus, interaction with Mad and nuclear import are critical for Medea function. However, unlike Mad, Medea is not required for expression of all Dpp-dependent genes and in its absence intracellular Dpp signaling rapidly attenuates with distance from the Dpp source. It is propose that the presence of Medea in heteromeric nuclear complexes with Mad modifies or enhances Dpp signaling (Wisotzkey, 1998).
Hox proteins control the differentiation of serially iterated structures in arthropods and chordates by differentially regulating many target genes. It is yet unclear to what extent Hox target gene selection is dependent upon other regulatory factors and how these interactions might affect target gene activation or repression. Two Smad proteins, effectors of the Drosophila Dpp/TGF-ß pathway, that are genetically required for the activation of the spalt (sal) gene in the wing, collaborate with the Hox protein Ultrabithorax (Ubx) to directly repress sal in the haltere. The repression of sal is integrated by a cis-regulatory element (CRE) through a remarkably conserved set of Smad binding sites flanked by Ubx binding sites. If the Ubx binding sites are relocated at a distance from the Smad binding sites, the proteins no longer collaborate to repress gene expression. These results support an emerging view of Hox proteins acting in collaboration with a much more diverse set of transcription factors than has generally been appreciated (Walsh, 2007).
The activation of sal in the wing and its repression in the haltere are regulated by a 1.1 kb CRE, sal1.1 (Galant, 2002). Previous studies have shown that sal1.1 is directly repressed by Ubx in the haltere (Galant, 2002). In order to test whether Mad/Med binds to and directly represses the activity of the sal1.1 CRE in the haltere, candidate Mad/Med binding sites were sought in the sal1.1 CRE. One candidate Mad/Med binding site, M1 (5'-AGACGGGCAC-3'), was identified that lies between Ubx binding sites 5 and 6 in sal1.1, using binding site prediction and electrophoretic mobility shift assays (EMSAs). The sequence of M1 deviates somewhat from published Mad/Med silencer consensus binding sites (5'-AGAC-5 bp-GNCGYC-3') (Gao, 2005; Pyrowolakis, 2004), and Mad and Med bound with >10-fold and >25-fold lower affinities, respectively, to the M1 site than to the bam (Gao, 2005) and brk (Pyrowolakis, 2004) silencer elements (Walsh, 2007).
In order to test whether Mad/Med bound specifically to the M1 site, a series of point mutations were introduced within the M1 site, and their effect on protein binding was examined in vitro. Of four point mutations to the M1 site, the single mutation at position 808 reduced the binding of a Med fusion protein (GST-MedMH1) to M1 as compared with the wild-type sequence. The remaining three point mutations did not affect the affinity of GST-MedMH1 for the probe. These results suggest that Med might contact the sequence 5'-AGAC-3' in sal1.1. By contrast, the four individual point mutations each decreased, but did not abolish, binding of a Mad fusion protein (GST-MadN) in vitro, with the point mutation at bp 814 having the strongest effect. The weaker effect of the individual point mutations in M1 on Mad binding affinity in vitro is likely to be due to the affinity of MadN for both 5'-AGAC-3' Smad sites and GC-rich sequence. Combining these four mutations (sal798-824 kM1) had the greatest effect on GST-MadN binding to the probe. This analysis of individual point mutations indicates a putative orientation for a Mad/Med compound-binding site in the sal1.1 CRE (Walsh, 2007).
Most importantly, in transgenic flies, each point mutation of M1 introduced into an otherwise wild-type sal1.1 reporter construct caused derepression of the reporter gene lacZ in the haltere imaginal disc. The strength of derepression correlates with the decreased affinity of Mad for its binding site with the pm814 mutation, the strongest point mutation in vitro, showing the strongest level of derepression in vivo. Full derepression was observed when all four point mutations were combined into a sal1.1 reporter construct. No effect of mutations in M1 were observed on sal1.1-driven reporter gene expression in the wing as compared with the wild-type sal1.1 element or with endogenous sal expression, indicating that this site is not required for gene activation in the wing or haltere disc. Together, the biochemical, reporter gene and genetic evidence indicate that Mad/Med/Shn are directly required for sal repression in the haltere imaginal disc (Walsh, 2007).
This study demonstrates that Mad/Med and Ubx bind to adjacent sites in the sal1.1 CRE and that each protein is required for the direct repression of sal expression in the haltere. Furthermore, the sequence and spacing of Ubx and Smad binding sites are highly conserved and their proximity is required for target gene repression in the haltere. Because no evidence was found that these proteins interact directly, it is suggested this is an example of 'collaboration' or target gene co-regulation without direct cooperative interaction. These results have general implications for understanding how Hox proteins regulate diverse sets of target genes in animal development (Walsh, 2007).
The direct role for Smads in the repression of sal in the haltere is surprising in the light of previous genetic and molecular studies that had indicated that the Dpp pathway and Mad/Med were involved in sal activation in the wing. No direct evidence was found that this is the case and the fact that sal is activated in Mad and Med clones in the haltere indicates that sal is activated independently of Mad/Med in the flight appendages. The requirement for Mad/Med/Shn in shaping the pattern of sal expression in the wing appears to be indirect -- the protein complex represses the expression of brk, a repressor of sal, in cells in the central region of the developing wing and thereby permits sal expression (Walsh, 2007).
The Mad-Med-Shn complex is also active within cells in the central region of the haltere as a consequence of Dpp signaling. However, whereas sal is expressed and the sal1.1CRE is active in the wing, sal and the sal1.1 CRE are repressed in the haltere. These observations raise the question of how the Mad-Med-Shn complex selectively represses sal in the haltere but not in the wing disc? The results suggest that there are two key determinants in the selective repression of sal in the haltere. The first is collaboration with Ubx, which is expressed in the haltere and not in the wing disc. The second key determinant might be the affinity of Mad/Med binding to the sal CRE (Walsh, 2007).
The different responses of the brk and sal genes to Mad/Med/Shn suggests how the different affinities of proteins for binding sites might determine how available transcriptional regulatory inputs are integrated by CREs. Mad/Med binding to the brk CRE is of high affinity (Pyrowolakis, 2004) and apparently sufficient to impart repression, whereas that to the sal CRE is of much lower affinity and insufficient to impart repression in the wing. In the haltere, although Mad-Med-Shn or Ubx binding are alone insufficient, they act together either via simultaneous or sequential occupancy of their binding sites to repress sal (Walsh, 2007).
The requirement for two or more regulators to act together to control gene expression, i.e. combinatorial regulation, is fundamental to the generation of the great diversity of gene expression patterns by a finite set of transcription factors. Several previous studies have revealed the dual requirement for Hox and Smad functions for the activation of a target gene. Studies have suggested a general combinatorial mechanism for gene activation in which apparently separate transcriptional inputs act synergistically in gene activation and, in at least one case, the Hox response element and Dpp response element are separable. In this study, however, a requirement was observed for strict evolutionary conservation of the close topology of Hox and Smad binding sites in the sal CRE. It is suggested that collaboration is a distinct mode of combinatorial regulation in which two or more regulatory proteins must bind to nearby sites, but not necessarily to each other (Walsh, 2007).
The integration of Hox and Smad inputs could work through a number of possible mechanisms in the absence of direct physical interaction. One appealing possibility that might explain the requirement for the close proximity of binding sites is that Ubx and Mad-Med-Shn might interact with, and could therefore cooperatively recruit, the same co-repressor(s) for the repression of sal. Alternatively, if Mad-Med-Shn and Ubx bind sequentially to sal1.1, they might recruit different co-repressors and thereby orchestrate the assembly of a co-repressor complex. A third possibility is that because the Ubx and Mad/Med sites are embedded within a larger block of conserved regulatory DNA sequence in the sal1.1 CRE, the binding of other interacting transcription factors might also be involved in the repression of sal by Ubx and Mad-Med-Shn (Walsh, 2007).
These and recent results raise the question of whether collaboration is a general feature of target gene selection by Hox proteins. It is suggested that collaboration might be a widespread requirement for Hox function in vivo. This proposal is prompted by three observations: (1) Hox proteins alone have low DNA-binding specificity; (2) some, and perhaps all, Hox proteins might act as both repressors and activators; (3) Hox proteins regulate a great diversity of target genes that are also regulated by other transcription factors. In order to be such versatile regulators, it would be too great a constraint to require that Hox proteins always interact cooperatively with the diverse repertoire of transcription factors with which they act. Indeed, it may be argued that too much weight has been ascribed to the cooperative binding of Hox proteins and co-factors to DNA (Walsh, 2007).
Previously, much attention has focused on Exd and Hth, which interact with Hox proteins and bind cooperatively to DNA, thereby increasing Hox DNA-binding selectivity. However, it was only recently shown that the binding of these complexes alone was not sufficient to regulate target gene expression. Rather, Hox-Exd-Hth collaborate with and require the segmentation proteins Slp and En to repress the target gene Dll. This study has shown that the Exd- and Hth-independent target gene repression of sal requires collaboration between Ubx and Mad-Med-Shn. Although still a tiny sample of target genes, cases of transcription factors of various structural types acting as collaborators with Hox proteins are now available. The picture of Hox proteins relying on dedicated interacting co-factors such as Exd and Hth is expanding to a larger pool of collaborating transcription factors that modulate target gene selection (Walsh, 2007).
Indeed, collaboration might be the key to another unresolved mystery of the Hox proteins - the regulation of Hox protein activity. Some Hox proteins appear to act in both gene activation and repression; this is certainly the case for Ubx. This versatility would appear to be crucial to their role as sculptors of major features of body patterns, but how does the same transcription factor act positively in some contexts but negatively in others? There is evidence to suggest that the identity of the collaborating proteins and/or CRE sequences determines the 'sign' of Hox action (Walsh, 2007).
For instance, there is no evidence that the mere binding of Hox-Exd-Hth to a site determines the sign of Hox activity. These co-factors are involved in both Hox target gene activation (e.g., dpp in the midgut) and target repression (e.g.,Dll in the embryonic abdomen). But, in the latter case, En and Slp, two proteins that each harbor motifs for interaction with the co-repressor Groucho, are required collaborators for Dll repression. The roles of En and Slp in this instance might not be so much a matter of facilitating Hox target selection, but rather in regulating the sign of the output of the collaboration (Walsh, 2007).
Similar to the Hox proteins, the Smads can either activate or repress target genes. Furthermore, it has been demonstrated that the topology of Smad binding sites on DNA appears to be critical for determining whether a target gene is activated or repressed. In Drosophila, the topology of Mad and Med binding sites is critical for the recruitment of the co-repressor Shn. The recruitment of Shn was shown here to be necessary for sal repression. These two examples suggest that the positive or negative regulatory activity of a Hox protein depends on the context of surrounding binding sites and how they influence the activity of collaborating factors (Walsh, 2007).
The dependence of Hox proteins upon co-factors and collaborators indicates that, at the molecular level, Hox proteins are not 'master' regulatory proteins that dictate how target genes behave. Rather, they exert their great influence by virtue of their simple binding specificity, broad domains of expression and versatile, collaborative properties (Walsh, 2007).
Deciphering the specific contribution of individual motifs within cis-regulatory modules (CRMs) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation. But despite vast improvements in the ability to identify where transcription factors (TFs) bind throughout the genome, the ability to relate information on motif occupancy to function from sequence alone is limited. This study engineered 63 synthetic CRMs to systematically assess the relationship between variation in the content and spacing of motifs within CRMs to CRM activity during development using Drosophila transgenic embryos. In over half the cases, very simple elements containing only one or two types of TF binding motifs were capable of driving specific spatio-temporal patterns during development. Different motif organizations provide different degrees of robustness to enhancer activity, ranging from binary on-off responses to more subtle effects including embryo-to-embryo and within-embryo variation. By quantifying the effects of subtle changes in motif organization, it was possible to model biophysical rules that explain CRM behavior and may contribute to the spatial positioning of CRM activity in vivo. For the same enhancer, the effects of small differences in motif positions varied in developmentally related tissues, suggesting that gene expression may be more susceptible to sequence variation in one tissue compared to another. This result has important implications for human eQTL studies in which many associated mutations are found in cis-regulatory regions, though the mechanism for how they affect tissue-specific gene expression is often not understood (Erceg, 2014).
While quantifying the activity of a simple 'two-TF motif' CRM (pMad-Tin), the results show that enhancer activity can exhibit very different sensitivity to motif organization in one tissue compared to another. Several mechanisms could account for this interesting effect, including different concentrations of the TF (i.e. pMad or Tin) in the different tissues, the availability of tissue-specific co-factors, or tissue-specific priming of the enhancer, which may increase the ease by which the enhancer is activated (Erceg, 2014).
An elegant dissection of the endogenous sparkling enhancer has demonstrated that completely rearranging the relative order and spacing of TF binding sites could switch its cell type-specific activity from cone cells to photoreceptors in the eye. In comparison, the changes in motif organisation introduced in the current study were much more subtle such that the relative order of motifs was completely preserved. Yet only changing the spacing or orientation of motifs altered the robustness of enhancer activity in a tissue-specific manner. This result indicates that small insertions or deletions in CRMs, that do not affect the TF motifs themselves, could still have significant effects on gene expression in one tissue while having no effect in another. A study examining the activity of neuroectoderm enhancers between Drosophila species supports this model, where reduced spacing between Dorsal and Twist sites results in broader neuroectodermal stripes of CRM activity, while increased motif spacing resulted in progressively narrower stripes. Studies of both endogenous enhancers and the synthetic CRMs described in this study provide compelling evidence that the exact positioning of motifs within CRMs is crucial for the robustness of their activity in one tissue, while it may be largely dispensable in another. Different cell types can therefore interpret the same motif content of a given enhancer in different manners (Erceg, 2014).
The Drosophila heart is composed of two cell types, cardioblasts and pericardial cells, each of which requires the integration of many regulatory proteins for proper specification and diversification. A characterized pericardial enhancer, eve MHE, for example, contains pMad and Tin binding sites in addition to sites for dTCF, Twi, Ets proteins, and Zfh1. Given this complexity, it was surprising that a simple element built from pMad and Tin sites alone was sufficient to drive expression in the heart, albeit at a later developmental stage. This analyses indicate that this activity is due to cooperativity binding between Tin and pMad, facilitated by a very specific motif arrangement. Using crystal structure data from close homologues of pMad, the two TFs interaction on DNA were modelled, using a similar range of motif spacing. This 3D structural model indicates that it is possible for the DNA binding domains of these two proteins to both bind to DNA at a 2 bp spacing and to physically interact at a 2 bp and 4 bp spacing, but not at 6 bp spacing. Although done by homologue mapping, this structural data is consistent with the functional analyses of CRM activity, and further supports direct DNA binding cooperativity between these two TFs (Erceg, 2014).
It is interesting to note, that although pMad and Tin sites are sufficient to drive expression in the heart from stage 13 to 14 (when placed in a limited motif arrangement), nature appears to use other enhancer configurations to regulate this critical function. There are two important aspects to this finding. First, heart activity arising from CRMs containing pMad and Tin sites alone is not robust. The enhancers are on 'the edge' of activation, where subtle changes in motif positioning or enhancer location switch activity between embryos and within embryos. Second, endogenous enhancers that are bound only by pMad and Tin - with no known input from other factors - direct expression in the dorsal mesoderm and not in the heart, at stage 10. In the synthetic situation, pMad and Tin sites also drive robust expression in the dorsal mesoderm, in addition to variable weak expression in the heart. Therefore, although pMad and Tin sites alone are sufficient to drive heart activity in limited motif contexts, this mechanism is most likely not robust enough to be generally used to drive heart expression in vivo. This is consistent with recent studies showing that heart enhancer activity is elicited by the collective action of many TFs, which can occupy enhancers with considerable flexibility in terms of their motif content and configuration. The pMad-Tin synthetic elements uncovered a very simple, although not very robust, alternative mechanism to regulate heart activity, and represent a nice example of how combinatorial regulation can lead to emergent expression profiles more than the simple sum of its parts (Erceg, 2014).
The expression of key developmental genes is generally buffered against variation in genetic backgrounds and environmental conditions. This may occur at many levels including RNA polymerase II pausing and the presence of partially redundant enhancers. However, robust expression may also be buffered by the motif content within an enhancer to ensure a stable regulatory function. CRMs, for example, often include additional binding sites to those that are minimal and necessary. In the context of the pMad-Tin synthetic CRMs, the motif organization can also act to ensure robust activity. The results demonstrate that even in situations where the composition of motifs and their relative arrangement are maintained, subtle changes in the spacing between the motifs could have dramatic effects on enhancer output. Interestingly, this effect seems to be very tissue-specific, with some tissues maintaining robust activity whilst others lost all enhancer activity (Erceg, 2014).
Taken together, the data presented in this study demonstrate that subtle alterations in motif organization can affect the ability of different tissues to 'read' an enhancer, which in turn may allow each tissue to fine-tune enhancer activity based on fluctuations in its molecular components (Erceg, 2014).
Bases in 5' UTR -346
Bases in 3' UTR - 937
MAD and its homolog in vertebrates (Smad1) are essential for signaling in DPP and BMP-2/4 pathways and can elicit biological responses characteristic of BMP-2/4 (Newfeld, 1996). SMAD proteins share a high degree of homology in their amino-terminal MH1 (Mad homology) and carboxy-terminal MH2 domains. The MH2 domain is considered the effector domain, whose activity is opposed by its physical interaction with the MH1 domain. SMAD4 is a central signaling molecule of several TGFbeta-related pathways. In contrast to the pathway-restricted SMADs, SMAD4 rapidly associates with both SMAD1 in response to BMPR-1 signaling and SMAD2 in response to TbetaR-I and ActR-IB signaling. Unlike SMAD4, SMAD1 and SMAD2 contain consensus phosphorylation sites for receptor type I Ser/Thr kinases within their MH2 domains. The model emerging from recent biochemical and crystallographic studies implies that phosphorylation of the receptor-regulated SMADs relieves them of the MH1 inhibitory effect, allowing their interaction with SMAD4 and subsequent translocation to the nucleus (Sirard, 1998 and references).
Signal transduction specificity in the transforming growth factor-beta (TGF-beta) system is determined by ligand activation of a receptor complex, which then recruits and phosphorylates a subset of SMAD proteins, including Smads 1 and 2. In vertebrates, Smad1, and presumably its close homologs Smad5 and Smad8, are phosphorylated by BMP receptors and mediate BMP responses. Smad2 and its close homolog Smad3 are phosphorylated by TGF-beta receptors and mediate TGF-beta and activin responses. In Drosophila, Mad (a close homolog of Smad1) mediates the effects of the BMP-like factor, Dpp. After phosphorylation by receptors, Smads 1 and 2 associate with Smad4 and move into the nucleus where they regulate transcription. A discrete surface structure has been identified in Smads 1 and 2 that mediates and specifies their receptor interactions. This structure is the L3 loop, a 17 amino acid region that protrudes from the core of the conserved SMAD C-terminal domain. The L3 loop sequence is invariant among TGF-beta and bone morphogenetic protein (BMP)-activated SMADS, but differs at two positions between these two groups. Swapping these two amino acids in Smads 1 and 2 induces a gain or loss, respectively, in their ability to associate with the TGF-beta receptor complex and causes a switch in the phosphorylation of Smads 1 and 2 by the BMP and TGF-beta receptors, respectively. A full switch in phosphorylation and activation of Smads 1 and 2 is obtained by swapping these two amino acids while, in addition, swapping four amino acids near the C-terminal receptor phosphorylation sites. These studies identify the L3 loop as a determinant of specific SMAD-receptor interactions, and indicate that the L3 loop, together with the C-terminal tail, specifies SMAD activation (Lo, 1998).
date revised: 21 APR 97
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