Gene name - Eb1
Cytological map position-42C8-42C8
Function - cytoskeletal component, signaling
Symbol - Eb1
FlyBase ID: FBgn0027066
Genetic map position - 2R: 2,636,697..2,643,544 [+]
Classification - N-terminal calponin homology domain fold, microtubule binding domain, C-terminal domain for dimerization and for interaction with EB1-binding proteins
Cellular location - cytoplasmic
|Recent literature||Moriwaki, T. and Goshima, G. (2016). Five factors can reconstitute all three phases of microtubule polymerization dynamics. J Cell Biol 215: 357-368. PubMed ID: 27799364
Cytoplasmic microtubules (MTs) undergo growth, shrinkage, and pausing. However, how MT polymerization cycles are produced and spatiotemporally regulated at a molecular level is unclear, as the entire cycle has not been recapitulated in vitro with defined components. In this study, dynamic MT plus end behavior involving all three phases was reconstituted by mixing tubulin with five Drosophila melanogaster proteins (EB1, XMAP215Msps, Sentin, kinesin-13Klp10A, and CLASPMast/Orbit). When singly mixed with tubulin, CLASPMast/Orbit strongly inhibited MT catastrophe and reduced the growth rate. However, in the presence of the other four factors, CLASPMast/Orbit acted as an inducer of pausing. The mitotic kinase Plk1Polo modulated the activity of CLASPMast/Orbit and kinesin-13Klp10A and increased the dynamic instability of MTs, reminiscent of mitotic cells. These results suggest that five conserved proteins constitute the core factors for creating dynamic MTs in cells and that Plk1-dependent phosphorylation is a crucial event for switching from the interphase to mitotic mode.
End binding 1 (EB1) is an evolutionarily conserved protein that localizes to and controls the plus ends of growing microtubules (Vaughan, 2005). EB1 targets other MT-associated proteins to the plus end and thereby regulates interactions of MTs with the cell cortex, mitotic kinetochores, and different cellular organelles. EB1 also localizes to centrosomes and is required for centrosomal MT anchoring and organization of the MT network. Using a novel preparation of the Drosophila S2 cell line that promotes cell attachment and spreading, dynamics of single microtubules were visualized in real time, and it was found that depletion of EB1 by RNA-mediated inhibition (RNAi) in interphase cells causes a dramatic increase in nondynamic microtubules (neither growing nor shrinking), but does not alter overall microtubule organization. In contrast, several defects in microtubule organization are observed in RNAi-treated mitotic cells, including a drastic reduction in astral microtubules, malformed mitotic spindles, defocused spindle poles, and mispositioning of spindles away from the cell center. Similar phenotypes were observed in mitotic spindles of Drosophila embryos that were microinjected with anti-EB1 antibodies. In addition, live cell imaging of mitosis in Drosophila embryos reveals defective spindle elongation and chromosomal segregation during anaphase after antibody injection. These results reveal crucial roles for EB1 in mitosis, which is postulated to involve its ability to promote the growth and interactions of microtubules within the central spindle and at the cell cortex (Rogers, 2002).
The microtubule cytoskeleton functions as an essential scaffold that helps to organize the cytoplasm of eukaryotic cells in interphase. Microtubules, which emanate in a radial pattern from the centrosome during interphase in most eukaryotic cells, provide tracks for microtubule motors carrying membrane, RNA, and protein complexes toward and away from the cell center. Microtubules also play an important role in establishing cell polarity, as they align in the direction of cell migration and toward the interface between immune and antigen-presenting cells. During mitosis, microtubules reorganize to create a mitotic spindle that, in conjunction with motor proteins, segregates chromosomes during cell division. Mitotic spindle orientation, which is a process important in development, tissue morphogenesis, and stem cell differentiation, also involves interactions between astral microtubules, motors, and other proteins at the cell cortex (Rogers, 2002).
Microtubules are intrinsically dynamic, which allows the microtubule cytoskeleton to rapidly rearrange in response to internal or external cues. Within a population of microtubules at steady-state, individual microtubules undergo transitions between phases of prolonged polymerization and depolymerization. This behavior, known as 'dynamic instability,' is enabled by the hydrolysis of GTP after monomeric tubulin becomes incorporated into the microtubule. Dynamic instability is modulated by various microtubule-associated proteins (MAPs) and motor proteins, some of which act to promote microtubule assembly and stability, whereas others induce their depolymerization. Although many MAPs bind along the length of microtubules, two classes of MAPs localize selectively to the plus ends of growing microtubules: the Cap-Gly proteins (e.g., CLIP-170, p150glued subunit of dynactin) and the EB1 protein family (Schuyler, 2001). The mechanism by which these proteins interact selectively with microtubule plus ends and their biological roles are poorly understood. Current work, however, suggests that microtubule plus end-binding proteins mediate interactions between microtubule ends and the cell cortex, kinetochores, endosomes, and dynein motor complexes (Tirnauer, 2000; Schuyler, 2001; Rogers, 2002 and references therein).
EB1 was first discovered in a yeast two-hybrid screen for proteins that interact with the human adenomatous polyposis coli (APC) tumor suppressor protein (Su, 1995). Homologous proteins have been identified subsequently in many organisms including budding and fission yeast, Drosophila, and Caenorhabditis elegans (Tirnauer, 2000). The budding yeast EB1 homologue, BIM1, has received the most attention to date. In yeast, Bim1p is a nonessential gene product that performs at least three related functions: (1) it localizes to the plus ends of cytoplasmic microtubules, where it increases dynamic instability (Tirnauer, 1999); (2) Bim1p links microtubule ends to the cell cortex to facilitate orientation of the spindle toward the bud site by binding to a multiprotein complex containing Kar9 and myosin (Myo2p) (Korinek, 2000; Lee, 2000; Miller, 2000; Yin, 2000), and (3) through its participation in spindle orientation, Bim1p indirectly participates in a checkpoint that delays cytokinesis pending mitotic exit (Muhua, 1998). A mitotic function also has been assigned to the EB1 homologue Mal3 in (Beinhauer, 1997) Schizosaccharomyces pombe (Rogers, 2002).
In higher eukaryotes, the functions of EB1 proteins remain poorly understood. In epithelial cells of the early Drosophila embryo, EB1 is required to direct the axis of cell division (Lu, 2001), although the mechanism by which it performs this function was not resolved. In vertebrate cells, the only activity attributed to EB1 is its ability to bind the COOH terminus of the APC tumor suppressor protein (see Drosophila APC) and target it to the tips of growing microtubules (Mimori-Kiyosue, 2000a; Mimori-Kiyosue, 2000b). The functional significance of these interactions has not been ascertained, although truncations of the COOH-terminal EB1 binding domain of APC are frequently associated with sporadic and familial colorectal cancers (Rogers, 2002).
Given the high degree of evolutionary conservation, EB1 proteins very likely perform important functions in higher eukaryotes. However, given that budding yeast and higher eukaryotes exhibit considerable differences both in their interphase microtubule organization and in their mechanisms of mitosis, extrapolating results from yeast BIM1 to metazoan cells becomes precarious. This study investigated the role of EB1 in Drosophila cells in culture by decreasing EB1 protein levels using RNA-mediated inhibition (RNAi) technology and in Drosophila embryos by injecting antibodies against EB1. These complementary techniques and preparations have demonstrated that EB1 influences microtubule dynamics and plays a particularly critical role in the assembly, dynamics, and positioning of the mitotic spindle. Interference of EB1 function in these metazoan cells shows similar yet distinct phenotypes from those described in lower eukaryotes (Rogers, 2002).
Thus interfering with EB1 produces effects on spindle structure, the most common being an overall decrease in the length of the spindle, a lack of astral microtubules, a defocusing of the spindle poles, and dissociation of centrosomes from the spindle. Mitotic spindles in EB1-depleted cells lose the ability to self-center and are generally mispositioned within the cell. In living Drosophila embryos, where spindles proceed into anaphase without a checkpoint arrest, it was found that EB1 plays an important role late in mitosis during anaphase spindle elongation and chromosome segregation (Rogers, 2002).
During interphase, loss of EB1 does not alter microtubule length or distribution and produces no obvious effect on cell morphology. However, by imaging GFP-tubulin, it was found that loss of EB1 causes the majority (60%) of microtubules to enter a 'paused' state in which they are neither growing nor shrinking. Microtubules assembled from purified tubulin rarely exhibit such static behavior. Therefore, pausing most likely reflects the action of a cellular factor that suppresses microtubule dynamics, possibly by capping the microtubule end. EB1 appears to promote dynamic behavior, at least in part, by antagonizing the actions of this yet unknown factor, either by directly competing for tubulin sites or by inducing a conformation at the microtubule end that prevents capping. Interestingly, these findings are similar to those obtained for Bim1p in S. cerevisiae, which show that microtubules in bim1-null cells are less dynamic in G1 of the cell cycle, spending >60% of their lifetimes in a paused state (Tirnauer, 1999). Although these effects of EB1 on interphase microtubule dynamics are not crucial to the formation of the microtubule network in S2 cells, it is speculated that they may be important for dynamic rearrangements of the microtubule cytoskeletal network that occur during cell migration and other polarized cell shape changes (Rogers, 2002).
Although EB1 loss does not dramatically change the number of microtubules during interphase, it does decrease microtubule lengths and numbers in mitosis. In a study of microtubule dynamics at the G2/M transition in vertebrate cells, is has been observed that microtubule polymer levels dramatically decrease upon entry into prophase, but polymer levels increase as mitosis progresses and chromosomes become attached to microtubules. In EB1-depleted S2 cells, the extent of microtubule disassembly in prophase is more severe than in control cells, and may reflect an inability of the cell to reestablish microtubule polymer levels later in mitosis. This decrease in microtubule polymer was not observed with RNAi of another plus end-binding protein, CLIP-190. The basis for the mitotic-specific effect of EB1 on microtubule stability may be due either to a change in how EB1 interacts with microtubules or in the activities of other microtubule-associated proteins. The latter possibility is favored because it has been shown that assembly-promoting factors, such as XMAP215/TOG, are downregulated in mitosis, which allows depolymerization factors, such as the KIN-I kinesins or stathmin/OP18, to predominate. Thus, EB1 may play a particularly important role in mitosis in counteracting microtubule depolymerization factors. The most direct way to test these ideas would be to observe microtubule behavior in EB1-depleted mitotic cells in real time. However, due to the loss of astral microtubules and the bundling of microtubules in the interpolar regions, it was not possible to resolve the behavior of individual microtubules in GFP-tubulin-transfected, EB1-depleted cells (Rogers, 2002).
This finding for EB1 differs from that obtained for Bim1p in S. cerevisiae, since bim1Delta cells do not exhibit significant defects in microtubule behavior in preanaphase or anaphase, even though there are subtle changes in microtubule dynamics and spindle positioning (Tirnauer, 1999). The role of EB1 also differs from its orthologue Mal3 in fission yeast, as null mutants exhibit abnormally short cytoplasmic microtubules but no defects in their spindle morphology. These differences may not be due to different molecular mechanisms of EB1, but rather due to the distinct processes for creating the spindle and executing chromosome movements (Rogers, 2002).
The most frequent phenotype observed in EB1-depleted mitotic spindles is the failure to form astral microtubules, which may underlie many of the aberrant spindle phenotypes produced by EB1 RNAi- and antibody-injected embryos, although other unknown roles of EB1 (e.g., interactions with other proteins) may play a role as well. In the absence of EB1, the central spindle still contains kinetochore fibers, often they are partially or fully detached from the centrosomes, which gives rise to defocused or 'splayed apart' microtubules at the poles. In wild-type spindles, it is speculated that astral microtubules nucleated from the spindle poles intercalate with microtubule bundles in the central spindle to focus them to the poles via microtubule cross-linking proteins or through motor proteins such as Ncd or cytoplasmic dynein (Rogers, 2002).
Loss of astral microtubules is also likely to underlie the spindle positioning defects that were observe in EB1-depleted cells. Spindle positioning has been speculated to involve a balancing of forces generated either by growing astral microtubules pushing against the cell cortex or by cortically bound motor complexes containing dynein and Lis1 pulling on astral microtubules. Similarly, yeast Bim1p has been shown to be important in orienting the mitotic spindle into the bud neck by linking microtubules to the cortically bound Kar9p complex and the actin cytoskeleton (for review see Bloom, 2000). Mammalian EB1 also has been shown to interact with dynein intermediate chain and with subunits of the dynactin complex (Berrueta, 1999), and so it may mediate motor microtubule linkages at the plasma membrane of higher eukaryotes as well (Rogers, 2002).
These results also shed light upon the recent observations of Lu (2001) who demonstrated that EB1 is required for spindle orientation in epidermoblasts of the Drosophila embryo. In this cell type, cell divisions are normally oriented within the plane of the tissue in response to lateral polarity cues established by adherens junctions formed between neighboring cells. When EB1 was reduced by RNAi, epidermal cells instead divide randomly with respect to the plane of the tissue. It was generally assumed that this effect was due to impaired interactions of microtubules with adherens junction components that served as polarity cues. Although this may be true, the current results also reveal a drastic reduction in the number and length of astral microtubules that also may underlie the defect observed in these asymmetric cell divisions (Rogers, 2002).
Inhibition of EB1 in synctitial Drosophila embryos by injection of anti-EB1 antibodies also revealed important roles for this protein during the later stages of mitosis. In these cells, the most severe mitotic defects were observed closest to the injection site, and these included dramatically reduced rates of spindle elongation throughout mitosis and defective chromosome segregation. Spindles distal to the injection site exhibited less severe structural defects, but also exhibited lagging chromosomes during anaphase. These phenotypes were not directly observed in S2 cells depleted of EB1, and it is postulated that this is due to activation of the spindle checkpoint as the result of damage to the spindle (Rogers, 2002).
Why do mitotic spindles fail to elongate during anaphase? The forces that drive spindle elongation during anaphase B are derived, at least in part, from the activities of cortical cytoplasmic dynein pulling on astral microtubules and from bipolar kinesins that push spindle poles apart by sliding antiparallel interpolar microtubule bundles. Inhibition of EB1 suppresses the formation of both astral microtubules and interpolar microtubules and eliminates the formation of midbodies during late telophase. A role for EB1 in the formation or stabilization of these subpopulations of spindle microtubules is supported by immunolocalization data showing the protein enriched on astral microtubules and in interpolar bundles and midbodies in S2 cells and embryos. The inhibition of anaphase after EB1 depletion may be a consequence of the failure to produce spindles that form the specialized microtubule structures required for elongation in anaphase. Another possible mechanism is suggested by the observation that anaphase B is accompanied by microtubule polymerization in the central spindle that may contribute to the forces that drive spindle poles apart. Since EB1 appears necessary to promote microtubule growth during mitosis, it may be that in the absence of this protein, anaphase microtubule polymerization is inhibited and spindle elongation fails. These two potential mechanisms are not mutually exclusive (Rogers, 2002).
The question of why chromosome segregation fails when EB1 is inhibited is also an important one. The simplest explanation is that, in the absence of EB1, spindle elongation during anaphase is crippled to such an extent that chromosome-to-pole movement is insufficient to drive their segregation, leading to an increased number of 4N nuclei. Alternatively, it is possible that EB1 mediates interactions between kinetochores and microtubules and in the absence of this interaction, anaphase A is affected. This is an interesting possibility in light of recent work identifying APC as a kinetochore component, although no evidence exists for a direct interaction between Drosophila APC/APC2 and EB1 (Rogers, 2002).
In conclusion, these studies reveal that EB1 is not essential for creating the microtubule network in interphase but is essential for microtubule organization in mitosis. Such cell cycle specificity, which is not common among MAPs, raises the possibility that EB1 might constitute an attractive target for small molecule inhibition of cell division in cancer chemotherapy. At least three different genes for EB1 family proteins exist in the human genome; one of which is ubiquitously expressed, and the other two are tissue specific. Selective inhibition of these mammalian genes will be required to evaluate the utility of EB1 inhibition as means of interfering with cancer growth (Rogers, 2002).
In many differentiated cells, microtubules are organized into polarized noncentrosomal arrays, yet few mechanisms that control these arrays have been identified. For example, mechanisms that maintain microtubule polarity in the face of constant remodeling by dynamic instability are not known. Drosophila neurons contain uniform-polarity minus-end-out microtubules in dendrites, which are often highly branched. Because undirected microtubule growth through dendrite branch points jeopardizes uniform microtubule polarity, this study used this system to understand how cells can maintain dynamic arrays of polarized microtubules. Growing microtubules navigate dendrite branch points by turning the same way, toward the cell body, 98% of the time, and growing microtubules track along stable microtubules toward their plus ends. Using RNAi and genetic approaches, this study shows that kinesin-2, and the +TIPS EB1 and APC, are required for uniform dendrite microtubule polarity. Moreover, the protein-protein interactions and localization of Apc2-GFP and Apc-RFP to branch points suggests that these proteins work together at dendrite branches. The functional importance of this polarity mechanism is demonstrated by the failure of neurons with reduced kinesin-2 to regenerate an axon from a dendrite. It is concluded that microtubule growth is directed at dendrite branch points and that kinesin-2, APC, and EB1 are likely to play a role in this process. It is propose that Kinesin-2 is recruited to growing microtubules by +TIPS and that the motor protein steers growing microtubules at branch points. This represents a newly discovered mechanism for maintaining polarized arrays of microtubules (Mattie, 2010).
Most cells in multicellular organisms contain polarized noncentrosomal microtubule arrays. In interphase mammalian cultured cells, microtubules are nucleated at the centrosomal microtubule organizing center (MTOC), and plus ends grow towards the cell periphery. However, in many differentiated cells, minus ends are not focused at a centrosomal MTOC. In epithelial cells, a major population of microtubules has minus ends focused at the apical side and plus ends at the basal side. In muscle cells, minus ends spread out around the nuclear envelope, and neurons have perhaps the simplest and most strikingly polarized noncentrosomal microtubule arrays. The mechanisms that organize these noncentrosomal microtubule arrays are poorly understood (Mattie, 2010).
Neurons have two types of processes that extend from the cell body: axons and dendrites. Dendrites primarily receive signals from other neurons or the environment, and axons send signals to other neurons or output cells. One basic difference between axons and dendrites is the arrangement of microtubules. In axons microtubules are arranged into an overlapping array of uniform polarity plus-end-out microtubules. In dendrites of cultured mammalian neurons microtubules have mixed orientation near the cell body. In dendrites of Drosophila neurons 90%-95% of microtubules have minus ends distal to the cell body. As the dendritic array in Drosophila is very simple, and extremely different from a centrosomal array, This study used it as a model system to identify mechanisms that organize polarized noncentrosomal microtubules (Mattie, 2010).
It is not known how uniform dendrite microtubule polarity is established or maintained. Models for generating the plus-end-out axonal microtubule array focus on sliding of microtubules by motor proteins. In mammalian neurons, microtubules are thought to be nucleated in the cell body at the centrosome, then released from the centrosome and transported down the axon in the correct orientation by motors including dynein. Models to account for mixed orientation microtubules in dendrites of cultured neurons have also been proposed. In this case, the kinesin MKLP1 (Kif23) has been proposed to transport minus-end-out microtubules into dendrites along plus-end-out microtubules. The current study identified a new mechanism that is required for uniform microtubule polarity in dendrites (see Interactions between kinesin-2 and +TIPs, and localization of Apc2-GFP to dendrite branch points). As it uses conserved, generally expressed proteins, it could play a role in maintaining microtubule polarity in many other cell types (Mattie, 2010).
Using Drosophila dendrites as a model system, this study demonstrates that growing microtubule plus ends almost always turn towards the cell body at branch points, and that they track stable microtubules through branches. Kinesin-2, EB1 and APC are all required to maintain microtubule polarity and are linked in an interaction network. Based on these results, a model is proposed for directed growth of microtubules in dendrites. Apc2 most likely contains a branch localization signal because Apc2-GFP localizes well to dendrite branches even when overexpressed. Localization of Apc2 to dendrite branch points can recruit Apc to the branch. Apc can interact with the Kap3 subunit of kinesin-2, and so could increase concentration of the motor near the branch. EB1-GFP does not concentrate at branches, so it is proposed that a growing microtubule plus end coated with EB1 is transiently linked to kinesin-2 as it passes through the branch, through the interaction between Apc and the EB1 tail. SxIP motifs in Apc and Klp68D could also contribute to this interaction. As both Kap3 and the SxIP motif in Klp68D are in the kinesin-2 tail, the motor domain would be free to walk along a nearby stable microtubule towards the plus end and cell body (Mattie, 2010).
Even a very brief application of force pulling the growing microtubule towards the cell body should be sufficient to steer growth towards the cell body. Once the tip of the microtubule turns, growth would be constrained by the dendrite walls. The association of the growing plus end with stable microtubule would probably only need to be maintained over a distance of a micron. This model is consistent with the observations that kinesin-2 has shorter run lengths than kinesin-1, and that individual EB1 interactions with the microtubule plus end persist less than a second (Mattie, 2010).
Observations of plus end behavior in vivo also favor a model in which only transient interactions of the motor and microtubule plus end are involved, because plus ends turning sharply are frequently seen. Stable microtubules do not accommodate such sharp turns, so the sharp turns of plus ends are not likely to occur while the plus end is tracking along a stable microtubule. Instead they likely represent a switch from a freely growing plus end to one that is following a track (Mattie, 2010).
Directed growth of microtubules at dendrite branch points allows dendrites to maintain uniform minus-end-out polarity despite continued microtubule remodeling. This mechanism is also likely necessary to establish uniform microtubule polarity in branched dendrites, but probably cannot account for minus-end-out polarity on its own. It is hypothesized that directed microtubule growth is used in concert with an unidentified mechanism to control microtubule polarity in dendrites. Transport of oriented microtubule pieces has been proposed to contribute to axon microtubule polarity and a similar mechanism could play a role in dendrites. For example, a kinesin anchored to the cell cortex by its C-terminus could shuttle minus-end-out microtubule seeds into dendrites. Alternately, polarized microtubule nucleation sites could be localized within dendrites. Identifying directed growth as one mechanism that contributes to dendrite microtubule polarity should facilitate identification of the missing pieces of this puzzle (Mattie, 2010).
Because kinesin-2, APC, EB1 and polarized microtubules are found in many cell types, directed growth of microtubules along stable microtubule tracks could be very broadly used for maintaining microtubule polarity. This is a newly identified function for both the +TIP proteins and kinesin-2. APC has previously been localized to junctions between a microtubule tip and the side of another microtubule at the cortex of epithelial cells, and sliding of microtubule tips along the side of microtubules was also seen in this system, but there was no association with a particular direction of movement or overall microtubule polarity (Mattie, 2010).
As kinesin-2 has previously been shown to be enriched in tips of growing axons in cultured mammalian neurons, as has APC, it is possible that they could mediate tracking of growing microtubules along existing microtubule tracks in the growth cone. In fact, this type of microtubule tracking behavior has been observed in axonal growth cones under low actin conditions. Thus directed growth of microtubules could also be important during axon outgrowth. Indeed, the same principle of directed growth by a motor protein connected to a growing microtubule plus end could be used to align microtubules in many circumstances (Mattie, 2010).
Chromosome congression, the process of positioning chromosomes in the midspindle, promotes the stable transmission of the genome to daughter cells during cell division. Congression is typically facilitated by DNA-associated, microtubule (MT) plus end-directed motors called chromokinesins. The Drosophila melanogaster chromokinesin No distributive disjunction (NOD) contributes to congression, but the means by which it does so are unknown in large part because NOD has been classified as a nonmotile, orphan kinesin. It has been postulated that NOD promotes congression, not by conventional plus end-directed motility, but by harnessing polymerization forces by end-tracking on growing MT plus ends via a mechanism that is also uncertain. This study demonstrates that NOD possesses MT plus end-directed motility. Furthermore, NOD directly binds EB1 through unconventional EB1-interaction motifs that are similar to a newly characterized MT tip localization sequence. It is proposed that NOD produces congression forces by MT plus end-directed motility and tip-tracking on polymerizing MT plus ends via association with EB1 (Ye, 2018).
Equal distribution of duplicated DNA is required to maintain genomic stability through cell division. The microtubule (MT) cytoskeleton is reorganized to form a bipolar spindle as cells enter mitosis or meiosis. Chromosomes are positioned at the spindle equator during a process known as congression. Chromosome movements within the spindle are predominantly mediated by motor proteins that walk directionally on spindle MTs. An important class of congression motors is the chromokinesins, which include the kinesin families, kinesin-4, kinesin-10, and kinesin-12. Chromokinesins work cooperatively to promote chromosome alignment during cell division. Kinesin-10 and kinesin-4 are chromosome-associated, plus end-directed motors, although KIF4A suppresses plus end MT dynamics and may dampen polar ejection forces (PEFs) that push chromosome arms away from spindle poles, whereas kinesin-10's role is more intuitive and likely the predominant PEF-producing motor. The function of vertebrate kinesin-10 (Kid) was first described in Xenopus laevis egg extracts in which Xkid was required to establish and maintain chromosome arm congression. Although data from human cells have consistently shown that hKid contributes to congression, the alignment defects observed in tissue culture cells have not been as severe as in egg extracts. Vertebrate kinesin-10s have been shown to possess plus end-directed motility and to generate force when bound to chromatin (Ye, 2018).
The Drosophila melanogaster chromokinesin NOD shares sequence homology in its N-terminal motor with both kinesin-10 and kinesin-4 motor domains and in its C terminus with the kinesin-10 DNA-binding motif (helix-hairpin-helix), but it has been designated an orphan kinesin as a result of significant divergence in its structural elements and organization relative to conventional kinesins. NOD was initially identified and characterized genetically as the mutant no distributive disjunction (nod), which exhibited high frequencies of nondisjunction and chromosome loss in female meiosis. The nod gene encodes a kinesin-like protein (NOD) with an N-terminal motor domain. Achiasmate (nonexchange) chromosomes frequently failed to associate with spindles or were mispositioned near spindle poles in oocytes lacking functional NOD. The characterization of DNA binding activities in the C terminus of NOD, its N-terminal motor domain, and the misalignment phenotype of nod mutants led to the hypothesis that NOD is the PEF motor in fly oocytes, and later work in Drosophila tissue culture cells revealed a role for NOD in mitotic chromosome congression. Although NOD possesses a conserved N-terminal motor domain and MT-stimulated ATPase activity, efforts to reconstitute directional motility in vitro have failed leading to NOD being classified as a nonmotile kinesin. How could a nonmotile kinesin generate force? An alternative theory posits that, as a result of the unique mechanochemical properties of its motor domain, NOD moves chromosomes by associating with the plus ends of polymerizing MTs, although direct evidence for this mechanism is lacking. High resolution imaging of NOD-coated chromatin stretching events in living cells were suggestive of both plus end-directed motility and end-tracking coincident with EB1 comets (Ye, 2018).
NOD possesses an N-terminal motor domain and two distinct C-terminal DNA binding regions comprised of high mobility group (HMG) repeats and a helix-hairpin-helix motif that mediate chromatin-association of full length (FL) NOD-mCherry throughout the cell cycle in Drosophila S2 cells. Between the motor and DNA-binding domains, NOD is predicted to contain intrinsically disordered regions (~50%), as well as four α-helices, one of which has a low probability of forming a parallel two-stranded coiled coil (CC). To dissect NOD motor function in vivo, truncations of NOD tagged at their C termini with mCherry were expressed in GFP-α-tubulin expressing Drosophila S2 cells. The motor domain (1-324) did not bind MTs in mitosis or interphase and was diffuse in the cytosol. Thus, unlike many well-characterized motor proteins, the NOD324 motor domain exhibits weak or no MT binding activity in cells. Given the high physiological concentration of ATP, this observation is consistent with in vitro studies in which NOD motor domain exhibited significantly lower MT binding affinities in the presence of excess ATP than conventional kinesin motors (Ye, 2018).
Most kinesins with N-terminal motor domains possess a neck linker and a well-defined neck CC downstream of the motor; however, some kinesins, including NOD, have noncanonical neck regions that contribute to their functions in cells. The localization was examined of a NOD truncation (1-485) that encompasses the motor domain and the noncanonical neck extension region. Addition of the neck extension conferred MT-binding activity in cells as NOD485 uniformly coated MTs throughout the cell cycle. Inclusion of the nonconventional extension could promote MT binding through numerous nonexclusive mechanisms, including the introduction of a second MT binding site, which has been shown for hKID, posttranslational modifications, association with regulatory factors, or dimerization through the low probability CC. The MT localization of NOD485 was significantly reduced upon fixation conditions suggestive of the interaction, while stronger than NOD324, being relatively low affinity. Nonetheless, the localization of NOD485 led to the idea that the oligomeric state of NOD warranted further investigation. Several structural and functional aspects of NOD are reminiscent of the monomeric plus end-directed kinesin Unc104/KIF1A. Kinesin-10 family members have been shown to be monomeric in vitro. Furthermore, NOD and Unc104/KIF1A possess low-probability/weak CC regions adjacent to their N-terminal motors, whereas their C termini contain domains that cluster the motors on the surface of cargos: chromosomes and synaptic vesicles, respectively. Prior work on Unc104 demonstrated that constitutive dimerization of the Unc104 motor domain and its adjacent 'weak' CC converted the monomer into a processive, plus end-directed motor with physiological velocities. A comparable approach as that applied to Unc104, specifically fusion to the kinesin-1 'stalk' CC, was next used to examine how dimerization of the NOD motor domain affected its behavior (Ye, 2018).
The motor domain alone (1-324) was first dimerized. NOD324CC evenly coated interphase MTs and robustly associated with spindle MTs during mitosis, exhibiting a slight enrichment toward the plus ends of kinetochore fibers in the vicinity of aligned chromosomes with some evident MT bundling. NOD485CC exhibited a striking localization pattern in which it was highly enriched near MT plus ends in mitosis and interphase. Significant MT bundling was also observed throughout the cell cycle especially in cells with high NOD485CC levels, which was not observed in the NOD485-expressing cells. The localization patterns and behavior of the dimerized NOD truncations were not attributable to the kinesin-1 CC because CC-mCherry only weakly associated with a subset of MTs in some cells and exhibited no obvious or consistent localization pattern. Furthermore, the neck extension region, while necessary, was not sufficient for MT binding, as the localization patterns of NOD325-485 and NOD325-485CC were identical to mCherry and CC-mCherry, respectively (Ye, 2018).
The localization pattern of NOD485CC suggested dimerized NOD could possess plus end-directed motility in cells. This possibility was further examined by imaging cells using total internal reflection fluorescence (TIRF) microscopy to visualize NOD on the MTs closest to the cell cortex. Puncta of both NOD485 and NOD324CC were visible on MTs, but motility was not obvious. The behavior of NOD485CC was markedly different from the other truncations as NOD puncta were clearly observed moving processively on MTs toward the cell periphery. The distribution of fluorescence intensities of motile NOD485CC-mCherry puncta was indistinguishable from that of motile kinesin-1-mCherry dimers, demonstrating that NOD485CC was assembling into motile dimers. Measurements of motile NOD485CC dimers in cells yielded a mean velocity of 8.70 ± 3.61 micrometers/min. These data demonstrate that dimerization of the NOD motor domain alone (NOD324CC) promotes MT binding but not motility, most likely because it lacks a functional neck linker, which plays an important role in coordinating motor head functions, whereas dimerization of the motor domain and nonconventional neck extension region converts NOD into a directional motor (Ye, 2018).
To further characterize NOD motility in vitro, TIRF-based imaging was applied to cell extracts in which NOD485CC was the only fluorescently tagged component. Using this technique, NOD motility could be studied in near physiological conditions, but in a chamber in which the state of the MTs, which are attached to the cover-glass, as well as the buffering conditions can be controlled. In cell lysates prepared from NOD485CC-expressing cells, NOD walked unidirectionally on taxol stabilized MTs in an ATP-dependent manner. The mean velocity of 8.62 2.32 micrometers/min measured for motile NOD485CC dimers in cell lysates was indistinguishable from live-cell measurements (Ye, 2018).
NOD motility has never been reconstituted in vitro and, like others,this study could not purify active NOD485CC from bacteria. Furthermore, NOD485CC activity in cell lysates was labile and sensitive to buffer conditions. Thus, NOD485CC-mCherry was purified from Drosophila S2 cells using a C-terminal Strep tag that allows for affinity purification on a streptavidin-based matrix and gentle elution using biotin-containing buffers to better preserve protein activity. Silver staining of the purification revealed a unique band, when compared with a mock purification from wild-type cell extracts, at the predicted size of NOD485CC-mCherry (~110 kD), which was confirmed by Western blot using an mCherry antibody. Although it is probable that NOD-associated proteins were copurified in the preparation, the majority of background bands were likely biotinylated proteins or nonspecific because a nearly identical banding pattern was observed in mock purifications from wild-type cell extracts. In TIRF assays, the affinity purified NOD485CC-mCherry exhibited ATP-dependent, unidirectional motility, although the mean velocity of 5.79 ± 1.56 micrometers/min was slower than velocities measured in cells and lysates (Ye, 2018).
NOD485CC dimers often moved toward the cell periphery where the MT plus ends are typically oriented during interphase. To define the directionality of NOD485CC motility, purified GFP-labeled human kinesin-1 (Kif5B) motor, a plus end-directed motor, was added to lysates from NOD485CC-mCherry expressing cells. NOD485CC and kinesin-1 walked in the same direction, establishing that NOD is a plus end-directed motor. Collectively, the data in cells and in vitro demonstrate that dimerized NOD is a plus end-directed motor with velocities similar to those measured for Xkid and hKID, which in combination with the presence of a C-terminal helix-hairpin-helix DNA-binding motif warrants consideration of NOD as the Drosophila kinesin-10 orthologue (Ye, 2018).
Next, it was tested if chemically induced dimerization was sufficient to support NOD motility by building cell lines coexpressing dark (no fluorescent tag) NOD485-FRB and NOD485-FKBP-EGFP. Like NOD485, NOD485-FKBP-EGFP localized uniformly to MTs in the absence of rapamycin. Upon addition of 100 nM rapamycin, motile puncta of NOD485-FKBP-EGFP moved on MTs toward the cell periphery. Extracts were next prepared from NOD485-FKBP-EGFP, NOD485-FRB-expressing cells to visualize NOD on MTs by TIRF microscopy in vitro. Without rapamycin, nonmotile puncta of NOD485-FKBP-EGFP associated with MTs. Unidirectional motility of NOD485-FKBP-EGFP puncta was achieved within minutes of adding 100 nM rapamycin to the same cell extracts that did not exhibit motility in the absence of rapamycin. Cell lines coexpressing NOD485-FKBP-EGFP and NOD485-FRB-mCherry were next visualized. In the absence of rapamycin, the mCherry and EGFP-tagged NOD uniformly coated the MTs similar to NOD485, but NOD localization changed upon addition of 100 nM rapamycin as EGFP- and mCherry-tagged, chemically dimerized NOD485 accumulated toward MT plus ends at the cell periphery similar to NOD485CC. Altogether, the kinesin-1 CC and chemically induced dimerization data support the conclusion that multiple modes of NOD485 dimerization can support directional motility (Ye, 2018).
Although earlier work visualizing MT-associated stretching of NOD-coated chromatin was indicative of plus end-directed motility (Cane, 2013), it is technically challenging to assess the activity of nonartificially dimerized NOD in cells as a result of its constitutive chromatin localization. Fortuitously, NOD contains an endogenous nuclear export signal (NES) computationally predicted and borne out by the localization of various NOD truncations. Although NOD possesses an NES, it is not typically observed in the cytosol because it is tightly associated with chromatin throughout the cell cycle. It was reasoned that the affinity of NOD for chromatin could be reduced by deleting one of its two chromosome-associating domains (HMG14/17 repeats), a truncation called NODΔHMG. In ~10% of cells expressing NODΔHMG, possibly as a result of reduced affinity for the chromatin and the presence of an NES, cytosolic NOD puncta were visible. Therefore, it was possible to visualize nearly FL cytosolic NOD that was not artificially dimerized with CC or FKBP-FRB domains. Importantly, the cytosolic NODΔHMG exhibited plus end-directed motility toward the cell periphery along interphase MTs. Compared with the kinesin-1-mCherry standard, motile NODΔHMG puncta spanned a range of fluorescence intensities corresponding to ~5-200 NOD molecules with a mean of 52 motors per puncta, suggesting that NOD may function as clusters of dimers or more complex oligomers. Nevertheless, the velocity of NODΔHMG clusters was comparable to the velocities measured for NOD485CC dimers in cells and cell lysates in vitro (7.6 micrometers/min for NODΔHMG in cells vs. 8.6-8.7 micrometers/min for NOD485CC in cells and lysates) (Ye, 2018).
Prior work characterized NOD-coated chromatin stretch events that colocalized with EB1 comets, as well as occasional cytoplasmic NOD fragments that tracked polymerizing and depolymerizing MT plus ends (Cane, 2013), and NODΔHMG puncta also tracked growing plus ends. Spinning disc confocal imaging of cells coexpressing NOD485CC-EGFP and EB1-TagRFP-T revealed that a subset of NOD485CC puncta colocalized with EB1 tracks on MT plus ends. It is worth noting that NOD often remained associated with depolymerizing MTs through a mechanism that is presently unclear, but that could be similar to the bidirectional tracking activity of CENP-E because NOD, like hKID, may possess low-affinity MT binding regions outside of the motor domain. Plus end-directed NOD485CC dimers were evident behind tip-tracking NOD puncta in kymographs from NOD485CC-, EB1-expressing cells. Given the utility of cell lysates in visualizing NOD motility, extracts from NOD485CC-EGFP-expressing cells were added to dynamic rather than taxol-stabilized MTs in an effort to better visualize NOD end tracking by TIRF microscopy in vitro. The cell-based observations were fully validated in vitro using dynamic MTs as NOD485CC clearly walked toward the faster growing plus ends while a subpopulation of NOD485CC tip tracked on growing MT plus ends (Ye, 2018).
NOD's end-tracking activity combined with the observed colocalization of NOD with EB1 comets led to an investigation of whether NOD and EB1 directly interact in pulldown assays using purified components. GST-EB1-TagRFP-T pulled down with MBP-NOD485CC-EGFP, but not the MBP-EGFP control protein. To further characterize the NOD-EB1 interaction, attention turned to amino acids 325-485 because NOD485CC exhibited MT plus end-tracking activity, and NOD324CC did not. NOD contains multiple regions that are predicted to be disordered, centered around proline (P) and threonine (T) residues between residues 430-480. These motifs are similar to unconventional EB1-binding motifs recently identified in fungal species in the Saccharomyces cerevisiae Kar9 motor and Schizosaccharomyces pombe Dis1/Tog MAP. To identify EB1-interacting regions in NOD, overlapping peptide SPOT arrays encompassing what were deemed the 'PT' motifs were synthesized onto a cellulose membrane, and their interactions with purified EB1 were probed. The SPOT arrays comprised 15 amino acid peptides spanning NOD residues 430-480 with an offset of two residues and included a 'perfect' SxIP aptamer as a positive control peptide. The NOD peptides exhibiting the strongest association with purified Drosophila EB1-TagRFP-T centered on the PT motifs (Ye, 2018).
The amino acids surrounding SxIP motifs impact their affinities for EB1. To examine how PT-flanking amino acids contributed to EB1 binding, the peptides that exhibited the strongest association with EB1 on the array were subjected to alanine scanning. In each peptide, mutation of a surrounding arginine (R) residue approximately three to six amino acids upstream or downstream of the PT sequence eliminated EB1 binding. The results suggest that, like the SxIP motif, neighboring basic residues contribute to the affinity of NOD PT motifs for EB1. During the preparation of this manuscript, the unconventional Ka9-EB1 interaction was further characterized, leading to the designation of LxxPTPh as a novel tip-localization motif. Although the PT motifs in NOD resemble the LxxPTPh motif, the compositional differences may indicate that the Drosophila EB1 PT motif has diverged somewhat and/or that variability in the motif still supports EB1 interactions (Ye, 2018).
Microscale thermophoresis (MST) was used to measure the binding affinity of the NOD PT motif-1 for EB1. The N terminus of either the PT motif-1 or a bona fide 'perfect' SxIP peptide (positive control) was labeled with fluorescein (FITC) dye, and the movement of each fluorescently labeled peptide (fixed at 50 nM) in a temperature gradient was measured by MST while varying concentrations of unlabeled Drosophila GST-EB1. The binding affinity measured by MST for the SxIP motif was 807 nM, which is relatively close to the Kd (~570 nM) measured by isothermal titration calorimetry using the 'perfect' SxIP peptide and Drosophila EB1. The affinity of the PT motif-1 for Drosophila EB1 was measured to be 725 nM, slightly higher than the Kd of the positive control SxIP aptamer. Thus, the NOD PT motif-1 possesses an affinity for Drosophila EB1 that is comparable to other bona fide SxIP motifs and higher than affinities measured for EB1-CAP-Gly interactions (Ye, 2018).
How the Drosophila kinesin-10 NOD generates PEFs has long been a mystery. Prior work led to a hypothesis that NOD possesses two force producing activities: (1) MT plus end-directed motility, which had never been directly demonstrated and (2) end tracking on polymerizing MTs, the mechanism of which was speculative. This study demonstrates, for the first time, that NOD exhibits plus end-directed motility in cells and in vitro and that NOD directly interacts with the tip-tracking protein EB1 via a new type of conserved MT tip localization sequence. It is noteworthy that both MT polymerization and motor activity were originally proposed as sources of the PEF when the phenomenon was first described, more than 30 years later the current findings reveal NOD as a molecular nexus of both force-producing mechanisms (Ye, 2018).
To begin analysis of EB1 function in Drosophila, the fly genome was examined for genes that exhibited homology to human EB1 (MAPRE1) (Su, 2001). The Drosophila genome contains four predicted gene products that encode proteins with a high degree of sequence similarity (>40%) to human EB1: genes CG3265, CG18190, CG15306, and CG2955. One gene (CG3265, termed here Drosophila EB1) exhibits a higher degree of sequence identity throughout its length to both human EB1 (52%) and Saccharomyces cerevisiae Bim1p (33%), making it the most likely orthologue. This gene encodes a predicted protein of 294 residues (32.5 kD) with a similar domain organization to human EB1 and Bim1p. Residues 1-134, which have the highest degree of sequence conservation among EB1 family members, constitutes the domain of the protein implicated in microtubule binding (Juwana, 1999). Residues 129-212 are enriched in serines and prolines and hence may be unstructured, and residues 213-273 are predicted to form a coiled coil. In Bim1p, the COOH-terminal coiled-coil domain binds to Kar9 (Miller, 2000), and it may mediate protein-protein interactions in other species as well (Rogers, 2002).
date revised: 15 August 2007
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