Distinct roles for Galpha and Gbetagamma in regulating spindle position and orientation in Caenorhabditis elegans embryos.

Correct placement and orientation of the mitotic spindle is essential for segregation of localized components and positioning of daughter cells. Although these processes are important in many cells, few factors that regulate spindle placement are known. Previous work has shown that GPB-1, the Gbeta subunit of a heterotrimeric G protein, is required for orientation of early cell division axes in C. elegans embryos. Here we show that GOA-1 (a Galphao) and the related GPA-16 are the functionally redundant Galpha subunits and that GPC-2 is the relevant Ggamma subunit that is required for spindle orientation in the early embryo. We show that Galpha and Gbetagamma are involved in controlling distinct microtubule-dependent processes. Gbetagamma is important in regulating migration of the centrosome around the nucleus and hence in orientating the mitotic spindle. Galpha is required for asymmetric spindle positioning in the one-celled embryo.

Turn to the worm!

Caenorhabditis elegans will be the first multicellular animal to have its entire genome sequenced. This is not just good news for those currently working in the field, but also for those trying to understand the biology of more complex animals, including humans. C elegans is a relatively simple animal that is amenable to studies of genetics and developmental processes that are common to all animals, making this an attractive model in which to study basic processes that are altered in human disease. Powerful forward and reverse genetics mean that virtually any gene of interest can be studied at the functional level.

Axis determination in C. elegans: initiating and transducing polarity.

The anterior-posterior axis in Caenorhabditis elegans is determined by the sperm and leads to the asymmetric localisation of PAR (partitioning-defective) proteins, which are critical for polarity. New findings demonstrate that sperm asters play a critical role and suggest models for how PAR asymmetry is established. In addition, studies of blastomere fate determination and heterotrimeric G proteins have started to uncover how initial polarity may be translated into the asymmetric distribution of maternal proteins and the control of spindle position.

NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans.

Chromatin-modifying complexes are important for transcriptional control, but their roles in the regulation of development are poorly understood. Here, we show that components of the nucleosome remodelling and histone deacetylase (NURD) complex [1] [2] [3] [4] [5] antagonise vulval development, which is induced by the Ras signal transduction pathway. In three of the six equivalent vulval precursor cells, the Ras pathway is active, leading to the production of vulval fates [6]; in the remaining three, the Ras pathway is inhibited and vulval fates repressed. Inhibition of Ras signaling occurs in part through the action of the synthetic multivulval (synMuv) genes, which comprise two functionally redundant pathways (synMuvA and synMuvB) [7]. We found that five Caenorhabditis elegans members of the NURD chromatin remodelling complex inhibit vulval development through both the synMuvA and synMuvB pathways (hda-1, rba-1, lin-53, chd-3 and chd-4); a further two members, the MTA1-related genes egr-1 and egl-27, act only in the synMuvA pathway. We propose that the synMuvA and synMuvB pathways function redundantly to recruit or activate a core NURD complex, which then represses vulval developmental target genes by local histone deacetylation. These results emphasise the importance of chromatin regulation in developmental decisions. Furthermore, inhibition of Ras signaling suggests a possible link between NURD function and cancer.

CDC-42 controls early cell polarity and spindle orientation in C. elegans.

BACKGROUND: Generation of asymmetry in the one-cell embryo of C. elegans establishes the anterior--posterior axis (A-P), and is necessary for the proper identity of early blastomeres. Conserved PAR proteins are asymmetrically distributed and are required for the generation of this early asymmetry. The small G protein Cdc42 is a key regulator of polarity in other systems, and recently it has been shown to interact with the mammalian homolog of PAR-6. The function of Cdc42 in C. elegans had not yet been investigated, however. RESULTS: Here, we show that C. elegans cdc-42 plays an essential role in the polarity of the one-cell embryo and the proper localization of PAR proteins. Inhibition of cdc-42 using RNA interference results in embryos with a phenotype that is nearly identical to par-3, par-6, and pkc-3 mutants, and asymmetric localization of these and other PAR proteins is lost. We further show that C. elegans CDC-42 physically interacts with PAR-6 in a yeast two-hybrid system, consistent with data on the interaction of human homologs. CONCLUSIONS: Our results show that CDC-42 acts in concert with the PAR proteins to control the polarity of the C. elegans embryo, and provide evidence that the interaction of CDC-42 and the PAR-3/PAR-6/PKC-3 complex has been evolutionarily conserved as a functional unit.

NuRD and SIN3 histone deacetylase complexes in development.

Transcription repression mediated through histone deacetylase (HDAC) complexes is widespread, and mechanisms by which HDAC complexes act have been revealed by extensive studies in vitro and in cell culture. However, until recently, little has been known about the developmental roles of histone deacetylation. Mutants now exist for a number of members of the two major HDAC complexes (NuRD and SIN3) and some associated proteins. The emerging picture is that these complexes have specific functions in development, rather than being required for most cellular processes.

Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans.

We used genome-wide RNA interference (RNAi) to identify genes that affect apoptosis in the C. elegans germ line. RNAi-mediated knockdown of 21 genes caused a moderate to strong increase in germ cell death. Genetic epistasis studies with these RNAi candidates showed that a large subset (16/21) requires p53 to activate germ cell apoptosis. Apoptosis following knockdown of the genes in the p53-dependent class also depended on a functional DNA damage response pathway, suggesting that these genes might function in DNA repair or to maintain genome integrity. As apoptotic pathways are conserved, orthologues of the worm germline apoptosis genes presented here could be involved in the maintenance of genomic stability, p53 activation, and fertility in mammals.

Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7.

Patterning of the posterior end in animals is not well understood. Homologs of Drosophila even-skipped (eve) have a similar posterior expression pattern in many animals, and in vertebrates they are linked physically to the "posterior" ends of homeotic clusters (HOM-C), suggesting a conserved role in posterior development. However, the function of this posterior expression is not known. Here I show that the Caenorhabditis elegans gene vab-7 encodes an eve homolog that is required for posterior development and expressed in a pattern strikingly similar to that of vertebrate eve genes. Using a four-dimensional recording system, I found that posterior body muscles and the posterior epidermis are patterned abnormally in vab-7 mutants, but commitment to muscle and epidermal fates is normal. Furthermore, vab-7 activity is required for the complete expression of the most posterior HOM-C gene egl-5 in muscle cells, supporting the idea that eve homologs may act with the HOM-C to determine posterior cell fates. The conservation of sequence and expression pattern between vab-7 and eve homologs in other animals argues that most eve genes have posterior mesodermal and ectodermal patterning functions.

Embryonic tissue differentiation in Caenorhabditis elegans requires dif-1, a gene homologous to mitochondrial solute carriers.

The dif-1 gene was identified in a general screen for maternal-effect embryonic lethal (Mel) mutants. dif-1 mutant embryos complete gastrulation and embryonic cell division normally, but then arrest development with only a small amount of tissue differentiation. Either maternal or zygotic dif-1 activity is sufficient for wild-type development. The temperature-sensitive period of a cold-sensitive dif-1 mutant shows that dif-1 activity is essential only for 3 h, corresponding to the major period of embryonic tissue differentiation, and is not required post-embryonically. The results point to a role for dif-1 in the maintenance of tissue differentiation in the developing embryo, but not for its initiation. Cloning and sequencing of the dif-1 gene revealed that its product is homologous to proteins in the mitochondrial carrier family. Although dif-1 activity is required only during embryogenesis, dif-1 RNA is expressed at all stages of development. In situ hybridization to embryos showed that dif-1 RNA is initially present in all cells of the embryo; this most likely corresponds to maternal dif-1 RNA. Later, the presumable zygotic dif-1 RNA is found only in the gut and hypodermis of the embryo. This tissue-specific expression raises the possibility that the dif-1 protein acts non-cell autonomously and that some communication or molecular transport dependent on DIF-1 takes place during embryonic tissue differentiation. dif-1 is the first mitochondrial carrier homologue known to be needed specifically for a developmental process.

Maternal control of a zygotic patterning gene in Caenorhabditis elegans.

The transition from maternal to zygotic gene control is a key process in embryogenesis. Although many maternal effect genes have been studied in the C. elegans embryo, how their activities lead to the positional expression of zygotic patterning genes has not yet been established. Evidence is presented showing that expression of the zygotic patterning gene vab-7 does not depend on cell position or cell contacts, but rather on the production of a C blastomere. Furthermore, pal-1, a caudal homologue with maternal product necessary for the proper development of the C blastomere, is both necessary and sufficient for vab-7 expression. This provides a link between maternal gene activity and zygotic patterning gene expression in C. elegans. The results suggest that zygotic patterning genes might be generally controlled at the level of blastomere fate and not by position.

Control of the sperm-oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3' untranslated region.

In the Caenorhabditis elegans hermaphrodite germ line, sperm and then oocytes are made from a common pool of germ-cell precursors. The decision to differentiate as a sperm or an oocyte is regulated by the sex-determining gene, fem-3. Expression of fem-3 in the hermaphrodite germ line directs spermatogenesis and must be negatively regulated to allow the switch to oogenesis. In adult hermaphrodites (which are producing oocytes), most fem-3 RNA is found in the germ line, consistent with both the requirement for fem-3 in hermaphrodite spermatogenesis and the maternal effects of fem-3 on embryonic sex determination. Whereas loss-of-function mutants in fem-3 produce only oocytes, hermaphrodites carrying any of nine fem-3 gain-of-function (gf) mutations make none; instead sperm are produced continuously and in vast excess over wild-type amounts. Genetic analyses suggest that fem-3(gf) mutations have escaped a negative control required for the switch to oogenesis. Here we report that all nine fem-3(gf) mutants carry sequence alterations in the fem-3 3' untranslated region (3' UTR). There is no increase in the steady-state level of fem-3(gf) RNA over wild-type, but there is an increase in the polyadenylation of fem-3(gf) RNA that is coincident with the unregulated fem-3 activity. Results of a titration experiment support the hypothesis that a regulatory factor may bind the fem-3 3' UTR. We speculate that fem-3 RNA is regulated through its 3' UTR by binding a factor that inhibits translation, and discuss the idea that this control may be part of a more general regulation of maternal RNAs.

The Caenorhabditis elegans genes egl-27 and egr-1 are similar to MTA1, a member of a chromatin regulatory complex, and are redundantly required for embryonic patterning.

We show here that two functionally redundant Caenorhabditis elegans genes, egl-27 and egr-1, have a fundamental role in embryonic patterning. When both are inactivated, cells in essentially all regions of the embryo fail to be properly organised. Tissue determination and differentiation are unaffected and many zygotic patterning genes are expressed normally, including HOX genes. However, hlh-8, a target of the HOX gene mab-5, is not expressed. egl-27 and egr-1 are members of a gene family that includes MTA1, a human gene with elevated expression in metastatic carcinomas. MTA1 is a component of a protein complex with histone deacetylase and nucleosome remodelling activities. We propose that EGL-27 and EGR-1 function as part of a chromatin regulatory complex required for the function of regional patterning genes.

Repression by the 3' UTR of fem-3, a sex-determining gene, relies on a ubiquitous mog-dependent control in Caenorhabditis elegans.

The fem-3 sex-determining gene is repressed post-transcriptionally via a regulatory element in its 3' untranslated region (UTR) to achieve the switch from spermatogenesis to oogenesis in the Caenorhabditis elegans hermaphrodite germ line. In this paper, we investigate the fem-3 3' UTR control in somatic tissues using transgenic reporter assays, and we also identify six genes essential for this control. First, we find that a reporter transgene bearing a wild-type fem-3 3' UTR is repressed in somatic tissues, whereas one bearing a mutant fem-3 3' UTR is derepressed. Moreover, control by mutant 3' UTRs is temperature sensitive as predicted from the temperature sensitivity of the fem-3 gain-of-function (gf) mutations. Secondly, we find a fem-3 3' UTR RNA-binding activity in somatic tissues, in addition to the previously reported germ-line-specific binding by FBF. Thirdly, we find that each of six genes, mog-1-mog-6, is required for repression by the fem-3 3' UTR. Therefore, the mog genes not only affect the sperm/oocyte switch in the germ line, but also function in somatic tissues. We suggest that the mog genes may encode components of a ubiquitous machinery that is used for fem-3 3' UTR-mediated repression and the sperm/oocyte switch.

The Caenorhabditis elegans sex determining gene fem-3 is regulated post-transcriptionally.

The fem-3 gene of Caenorhabditis elegans is required for male development. Both maternal and zygotic fem-3 activities are required for spermatogenesis in the XX hermaphrodite germline and for male development in somatic and germline tissues XO (male) animals. Here we show that fem-3 RNA is contributed to embryos as a maternal product and that this RNA is degraded early in embryonic development. The poly(A) tail of embryonic fem-3 RNA is substantially longer than that of adult hermaphrodites which indicates that poly(A) tail lengthening probably occurs at or soon after fertilization. During subsequent development, fem-3 poly(A) tails shorten. The amount of fem-3 RNA in XX and XO embryos is equivalent, suggesting sex-specific regulation of maternal fem-3 activity occurs post-transcriptionally. The sequence of fem-3 predicts an open reading frame that could encode a soluble protein; putative fem-3 null mutants truncate this open reading frame. We discuss the implications of these results for the regulation and function of fem-3.

Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy.

Early embryonic development involves complex events such as the regulation of cell division and the establishment of embryonic polarity. To identify genes involved in these events, we collected four-dimensional time-lapse video recordings of the first three cell divisions and analysed terminal phenotypes after RNA interference of 147 embryonic lethal genes previously identified in a systematic screen of Caenorhabditis elegans chromosome I. Over half gave defects in early processes such as meiosis, the assembly or position of the first mitotic spindle, cytokinesis, and proper nuclear positioning. For some phenotypic classes, the majority of genes are involved in a shared biochemical process. In addition, we identified loss-of-function phenotypes for genes of unknown function, but for which homologues exist in other organisms, shedding light on the function of these uncharacterized genes. When applied to the whole genome, this approach should identify the vast majority of genes required for early cell processes, paving the way for a greatly improved understanding of these processes and their regulation at the molecular level.

Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans.

BACKGROUND: In Caenorhabditis elegans, injection of double-stranded RNA (dsRNA) results in the specific inactivation of genes containing homologous sequences, a technique termed RNA-mediated interference (RNAi). It has previously been shown that RNAi can also be achieved by feeding worms Escherichia coli expressing dsRNA corresponding to a specific gene; this mode of dsRNA introduction is conventionally considered to be less efficient than direct injection, however, and has therefore seen limited use, even though it is considerably less labor-intensive. RESULTS: Here we present an optimized feeding method that results in phenotypes at least as strong as those produced by direct injection of dsRNA for embryonic lethal genes, and stronger for genes with post-embryonic phenotypes. In addition, the interference effect generated by feeding can be titrated to uncover a series of hypomorphic phenotypes informative about the functions of a given gene. Using this method, we screened 86 random genes on consecutive cosmids and identified functions for 13 new genes. These included two genes producing an uncoordinated phenotype (a previously uncharacterized POU homeodomain gene, ceh-6, and a gene encoding a MADS-box protein) and one gene encoding a novel protein that results in a high-incidence-of-males phenotype. CONCLUSIONS: RNAi by feeding can provide significant information about the functions of an individual gene beyond that provided by injection. Moreover, it can be used for special applications for which injection or the use of mutants is sometimes impracticable (for example, titration, biochemistry and large-scale screening). Thus, RNAi by feeding should make possible new experimental approaches for the use of genomic sequence information.

G proteins are required for spatial orientation of early cell cleavages in C. elegans embryos.

Heterotrimeric G proteins are signal-transducing molecules activated by seven transmembrane domain receptors. In C. elegans, gpb-1 encodes the sole Gbeta subunit; therefore, its inactivation should affect all heterotrimeric G protein signaling. When maternal but no zygotic gpb-1 protein (GPB-1) is present, development proceeds until the first larval stage, but these larvae show little muscle activity and die soon after hatching. When, however, the maternal contribution of GPB-1 is also reduced, spindle orientations in early cell divisions are randomized. Cell positions in these embryos are consequently abnormal, and the embryos die with the normal number of cells and well-differentiated but abnormally distributed tissues. These results indicate that maternal G proteins are important for orientation of early cell division axes, possibly by coupling a membrane signal to centrosome position.

Functional genomic analysis of C. elegans chromosome I by systematic RNA interference.

Complete genomic sequence is known for two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and it will soon be known for humans. However, biological function has been assigned to only a small proportion of the predicted genes in any animal. Here we have used RNA-mediated interference (RNAi) to target nearly 90% of predicted genes on C. elegans chromosome I by feeding worms with bacteria that express double-stranded RNA. We have assigned function to 13.9% of the genes analysed, increasing the number of sequenced genes with known phenotypes on chromosome I from 70 to 378. Although most genes with sterile or embryonic lethal RNAi phenotypes are involved in basal cell metabolism, many genes giving post-embryonic phenotypes have conserved sequences but unknown function. In addition, conserved genes are significantly more likely to have an RNAi phenotype than are genes with no conservation. We have constructed a reusable library of bacterial clones that will permit unlimited RNAi screens in the future; this should help develop a more complete view of the relationships between the genome, gene function and the environment.

PTL-1, a microtubule-associated protein with tau-like repeats from the nematode Caenorhabditis elegans.

Tau, MAP2 and MAP4 are structural microtubule-associated proteins (MAPs) that promote the assembly and stability of microtubules. They share three or four imperfect tandem repeats of an amino acid motif, which is involved in the binding to microtubules. All sequences to data containing this motif are of mammalian origin. We report here the cloning and functional characterisation of a new member of this family of proteins from the nematode Caenorhabditis elegans. This protein exists as two isoforms of 413 and 453 amino acids with four or five tandem repeats that are 50% identical to the tau/MAP2/MAP4 repeats. Both isoforms bind to microtubules and promote microtubule assembly, with the five-repeat isoform being more effective at promoting assembly than the four-repeat isoform. When expressed in COS cells, the five-repeat isoform co-localises with microtubules and induces the formation of microtubule bundles, whereas its expression in Sf9 cells leads to the extension of long unipolar processes. In view of its length, amino acid sequence and functional characteristics, we have named this invertebrate structural MAP 'Protein with Tau-Like Repeats' (PTL-1). In C. elegans PTL-1 is expressed in two places known to require microtubule function. It is first seen in the embryonic epidermis, when circumferentially oriented microtubules help to distribute forces generated during elongation. Later, it is found in mechanosensory neurons which contain unusual 15 protofilament microtubules required for the response to touch. These findings indicate that MAPs of the tau/MAP2/MAP4 family are found throughout much of the animal kingdom, where they may play a role in specialised processes requiring microtubules.