As good as they get: cells in nematode vulva development and evolution

Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift

Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda

BACKGROUND

The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored.

RESULTS

We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination.

CONCLUSIONS

Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model.

The nature of nurture and the future of evodevo: toward a theory of developmental evolution

This essay has three parts. First, I posit that much research in contemporary evodevo remains steeped in a traditional framework that views traits and trait differences as being caused by genes and genetic variation, and the environment as providing an external context in which development and evolution unfold. Second, I discuss three attributes of organismal development and evolution, broadly applicable to all organisms and traits that call into question the usefulness of gene- and genome-centric views of development and evolution. I then focus on the third and main aim of this essay and ask: what conceptual and empirical opportunities exist that would permit evodevo research to transcend the traditional boundaries inherited from its parent disciplines and to move toward the development of a more comprehensive and realistic theory of developmental evolution? Here, I focus on three conceptual frameworks, the theory of facilitated variation, the theory of evolution by genetic accommodation, and the theory of niche construction. I conclude that combined they provide a rich, interlocking framework within which to revise existing and develop novel empirical approaches toward a better understanding of the nature of developmental evolution. Examples of such approaches are highlighted, and the consequences of expanding existing frameworks are discussed.

Barrier to autointegration factor blocks premature cell fusion and maintains adult muscle integrity in C. elegans

Barrier to autointegration factor (BAF) binds double-stranded DNA, selected histones, transcription regulators, lamins, and LAP2-emerin-MAN1 (LEM) domain proteins. During early Caenorhabditis elegans embryogenesis, BAF-1 is required to organize chromatin, capture segregated chromosomes within the nascent nuclear envelope, and assemble lamin and LEM domain proteins in reforming nuclei. In this study, we used C. elegans with a homozygous deletion of the baf-1 gene, which survives embryogenesis and larval stages, to report that BAF-1 regulates maturation and survival of the germline, cell migration, vulva formation, and the timing of seam cell fusion. In the seam cells, BAF-1 represses the expression of the EFF-1 fusogen protein, but fusion still occurs in C. elegans lacking both baf-1 and eff-1. This suggests the existence of an eff-1-independent mechanism for cell fusion. BAF-1 is also required to maintain the integrity of specific body wall muscles in adult animals, directly implicating BAF in the mechanism of human muscular dystrophies (laminopathies) caused by mutations in the BAF-binding proteins emerin and lamin A.

The versatile worm: genetic and genomic resources for Caenorhabditis elegans research

Since its establishment as a model organism, Caenorhabditis elegans has been an invaluable tool for biological research. An immense spectrum of questions can be addressed using this small nematode, making it one of the most versatile and exciting model organisms. Although the many tools and resources developed by the C. elegans community greatly facilitate new discoveries, they can also overwhelm newcomers to the field. This Review aims to familiarize new worm researchers with the main resources, and help them to select the tools that are best suited for their needs. We also hope that it will be helpful in identifying new research opportunities and will promote the development of additional resources.

The SynMuv genes of Caenorhabditis elegans in vulval development and beyond

For a nonessential diminutive organ comprised of only 22 nuclei, the Caenorhabditis elegans vulva has done very well for itself. The status of the vulva as an overachiever is in part due to its inherent structural simplicity as well as to the intricate regulation of its induction and development. Studies over the past twenty years have shown the vulva to be a microcosm for organogenesis and a model for the integration of complex signaling pathways. Furthermore, many of these signaling molecules are themselves associated with cancer in mammals. This review focuses on what is perhaps the most intriguing and complex story to emerge from these studies thus far, the role of the Synthetic Multivulval (SynMuv) genes in controlling vulval cell-fate adoption. Recent advances have led to a greater mechanistic understanding of how these genes function during vulval development and have also identified roles for these genes in diverse developmental processes.

Evolution and Development: Anchors away!

Developmental mechanisms can evolve even when the trait they produce does not, and the nematode vulva has become a model organ for detecting such "developmental system drift". A new study reveals what may be the very earliest stages of this process by experimentally modifying key vulval signaling pathways in different species of Caenorhabditis, and carefully quantifying the results.

Endomesoderm specification in Caenorhabditis elegans and other nematodes

The endomesoderm gene regulatory network (GRN) of C. elegans is a rich resource for studying the properties of cell-fate-specification pathways. This GRN contains both cell-autonomous and cell non-autonomous mechanisms, includes network motifs found in other GRNs, and ties maternal factors to terminal differentiation genes through a regulatory cascade. In most cases, upstream regulators and their direct downstream targets are known. With the availability of resources to study close and distant relatives of C. elegans, the molecular evolution of this network can now be examined. Within Caenorhabditis, components of the endomesoderm GRN are well conserved. A cursory examination of the preliminary genome sequences of two parasitic nematodes, Haemonchus contortus and Brugia malayi, suggests that evolution in this GRN is occurring most rapidly for the zygotic genes that specify blastomere identity.

Developmental constraints vs. variational properties: How pattern formation can help to understand evolution and development

This article suggests that apparent disagreements between the concept of developmental constraints and neo-Darwinian views on morphological evolution can disappear by using a different conceptualization of the interplay between development and selection. A theoretical framework based on current evolutionary and developmental biology and the concepts of variational properties, developmental patterns and developmental mechanisms is presented. In contrast with existing paradigms, the approach in this article is specifically developed to compare developmental mechanisms by the morphological variation they produce and the way in which their functioning can change due to genetic variation. A developmental mechanism is a gene network, which is able to produce patterns in space though the regulation of some cell behaviour (like signalling, mitosis, apoptosis, adhesion, etc.). The variational properties of a developmental mechanism are all the pattern transformations produced under different initial and environmental conditions or IS-mutations. IS-mutations are DNA changes that affect how two genes in a network interact, while T-mutations are mutations that affect the topology of the network itself. This article explains how this new framework allows predictions not only about how pattern formation affects variation, and thus phenotypic evolution, but also about how development evolves by replacement between pattern formation mechanisms. This article presents testable inferences about the evolution of the structure of development and the phenotype under different selective pressures. That is what kind of pattern formation mechanisms, in which relative temporal order, and which kind of phenotypic changes, are expected to be found in development.

sem-4/spalt and egl-17/FGF have a conserved role in sex myoblast specification and migration in P. pacificus and C. elegans

Evolutionary comparisons between Caenorhabditis elegans and the satellite organism Pristionchus pacificus revealed major differences in the regulation of nematode vulva development. For example, Wnt signaling is part of a negative signaling system that prevents vulva formation in P. pacificus, whereas it plays a positive role in C. elegans. We wondered if the genetic control of the second major part of the nematode egg-laying system, the sex muscles, has diverged similarly between P. pacificus and C. elegans. The sex muscles derive from the mesoblast M, which has an identical lineage in both species. Here, we describe a large-scale mutagenesis screen for mutations that disrupt the M lineage and the sex myoblast (SM) sublineage. We isolated and characterized mutations that result in a failure of proper SM fate specification and SM migration and showed that the corresponding genes encode Ppa-sem-4 and Ppa-egl-17, respectively. Ppa-sem-4 mutants have additional defects in the specification of the vulva precursor cells P(5, 7).p and experimental studies in the Ppa-egl-17 mutant background indicate a complex set of gonad-dependent and gonad-independent mechanisms required for SM migration. Mutations in Cel-sem-4 and Cel-egl-17 cause similar defects. Thus, the molecular mechanisms of SM cell specification and migration are conserved between P. pacificus and C. elegans.

Conservation and diversification of Wnt signaling function during the evolution of nematode vulva development

Cell-fate specification and cell-cell signaling have been well studied during vulva development in Caenorhabditis elegans and provide a paradigm in evolutionary developmental biology. Pristionchus pacificus has been developed as a 'satellite' organism with an integrated physical and genetic map that allows detailed comparisons to C. elegans. A common aspect of vulva formation in both species is the polarization of the P7.p lineage, which is responsible for vulval symmetry. In C. elegans, Wnt signaling is crucial for P7.p cell-fate patterning; nothing is known about vulval symmetry in P. pacificus. We isolated mutations that disrupt polarization of the P7.p lineage in P. pacificus and found that the corresponding gene encodes a Frizzled-like molecule. In addition, mutations in Ppa-lin-17 (encoding Frizzled) and morpholino knock-down of Ppa-lin-44 (encoding Wnt), Ppa-egl-20 (encoding Wnt), Ppa-mig-5 (encoding Dsh), Ppa-apr-1 (encoding APC) and Ppa-bar-1 (encoding beta-catenin) results in gonad-independent vulva differentiation, indicating that these genes have a role in a negative signaling process. In contrast, in C. elegans, Wnt signaling has a positive role in vulva induction, and mutations in bar-1 result in a hypoinduced phenotype. Therefore, whereas the molecular mechanisms that generate vulval symmetry are conserved, the genetic control of vulva induction diversified during evolution.

Gonadogenesis in Pristionchus pacificus and organ evolution: development, adult morphology and cell–cell interactions in the hermaphrodite gonad

The nematode gonad is an exemplary system for the study of organogenesis and fundamental problems in developmental and cellular biology. Nematode gonads vary dramatically across species (Chitwood, B.G., Chitwood, M.B., 1950. Introduction to Nematology." University Park Press, Baltimore; Felix, M.A., Sternberg, P.W., 1996. Symmetry breakage in the development of one-armed gonads in nematodes. Development 122, 2129-2142). As such, comparative developmental biology of gonadogenesis offers the potential to investigate changes in developmental and cellular processes that result in novel organ morphologies and thus may give insights into how these changes can affect animal bauplane. Pristionchus pacificus is a free-living nematode that diverged from the model nematode Caenorhabditis elegans around 200-300 million years ago. The morphology and development of P. pacificus is highly homologous to that of C. elegans. However, many differences in morphology and the underlying molecular signaling networks are easy to identify, making P. pacificus ideal for a comparative approach. Here, we report a detailed description of the P. pacificus hermaphrodite gonad using electron and fluorescent microscopy that will provide a basis for both phenotypic studies of genetic mutations and in vivo molecular studies of cloned genes involved in P. pacificus gonad development. We report that the morphology of the P. pacificus gonad is distinct from that of C. elegans. Among these differences are germ line patterning differences, heterochronic differences, novel gonadal arm-migrations, novel cellular composition of some somatic tissues (e.g., the number of cells that comprise the sheath and different spermathecal regions are different), the absence of a somatic tissue (e.g., the spermathecal valve cells), a novel architecture for the sheath, and changes in the cellular and sub-cellular morphology of the individual sheath cells. Additionally, we report a set of cell ablations in P. pacificus that indicate extensive cell communication between the somatic gonadal tissues and the germ line. Individual ablation experiments in P. pacificus show significant differences in the effects of individual somatic tissues on germ line patterning in comparison to C. elegans.

Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae

Whole genome sequencing of several metazoan model organisms provides a platform for studying genome evolution. How representative are the genomes of these model organisms for their respective phyla? Within nematodes, for example, the free-living soil nematode Caenorhabditis elegans is a highly derived species with unusual genomic characters, such as a reduced Hox cluster (Curr. Biol., 13, 37-40) and the absence of a Hedgehog signaling system. Here, we describe the recent loss of a DNA methyltransferase-2 gene (dnmt-2) in C.elegans. A dnmt-2-like gene is present in the satellite model organism Pristionchus pacificus, another free-living nematode that diverged from C.elegans 200-300 million years ago. In contrast, C.elegans, Caenorhabditis briggsae and P.pacificus all contain an mbd-2-like gene, which encodes another essential component of the methylation system of higher animals and fungi. Cel-mbd-2 is expressed throughout development and RNA interference (RNAi) experiments result in variable phenotypes. In contrast, Cbr-mbd-2 RNAi results in paralyzed larval or adult worms suggesting recent changes of gene function within the genus Caenorhabditis. We speculate that both genes were part of an ancestral DNA methylation system in nematodes and that gene loss and sequence divergence have abolished DNA methylation in C.elegans.

Evolutionary diversification of specification mechanisms within the O/P equivalence group of the leech genus Helobdella

Developmental fates and cell lineage patterns are highly conserved in the teloblast lineages that give rise to the segmental ectoderm of clitellate annelids. But previous studies have shown that the pathways involved in specification of the ventrolateral O lineage and the dorsolateral P lineage differ to some degree in distantly related clitellate species such as the leeches Helobdella and Theromyzon, and the sludgeworm Tubifex. To examine this developmental variation at a lower taxonomic level, we have explored the specification pathways of the O and P lineages in the leech genus Helobdella. In leech, the O and P lineages arise from a developmental equivalence group of O/P teloblasts. In this study, we demonstrate that the cell-cell interactions involved in cell fate specification of the O/P equivalence group differ among three laboratory colonies of closely related species. In two populations, the Q lineage is necessary to specify the P fate in the dorsalmost O/P lineage, but in the third population the P fate can be specified by a redundant pathway involving the M lineage. We also observe interspecific variation in the role played by cell interactions within the O/P equivalence group, and in the apparent significance of extrinsic signals from the micromere cell lineages. Our data suggest that cell fate specification in the O/P equivalence group is a complex process that involves multiple cell-cell interactions, and that the developmental architecture of the O/P equivalence group has undergone evolutionary diversification in closely related species, despite maintaining a conserved morphology.

Conservation of the global sex determination gene tra-1 in distantly related nematodes

Sex determination has long intrigued evolutionists, geneticists, and developmental biologists in a similar way. Substantial evidence indicates that sex determination evolves rapidly and, therefore, can be used to study how molecular patterning processes evolve. In Caenorhabditis elegans, sex determination relies on a signaling pathway that involves a cascade of negatively acting factors, finally triggering the GLI-family zinc-finger transcription factor TRA-1. We have started to investigate sex determination in the nematode satellite species Pristionchus pacificus that is separated from C. elegans for 200-300 million years. In P. pacificus, animals with two X chromosomes develop as hermaphrodites, whereas XO animals develop as males. We used an unbiased forward genetic approach and isolated several mutants with a hermaphrodite to male transformation of the XX karyotype. We identified one complementation group as representing the P. pacificus ortholog of tra-1, providing the first evidence for the conservation of a global sex determination gene over a time period of at least 200 million years. A Ppa-tra-1 morpholino phenocopies Ppa-tra-1 mutants and establishes the morpholino technology as a reverse genetic approach in P. pacificus.

The two steps of vulval induction in Oscheius tipulae CEW1 recruit common regulators including a MEK kinase

The cell interactions that specify the spatial pattern of vulval precursor cell (VPC) fates differ between the nematodes Oscheius tipulae CEW1 and Caenorhabditis elegans. In the former, the centered pattern of fates is obtained by two successive inductions from the gonadal anchor cell, whereas in the latter, a single inductive step by the anchor cell (EGF-Ras-MAP kinase pathway) can act as a morphogen and is reinforced by lateral signaling between the vulval precursors (Notch pathway). We performed a genetic screen for vulva mutants in O. tipulae CEW1. Here we present the mutants that specifically affect the vulval induction mechanisms. Phenotypic and epistatic analyses of these mutants show that both vulval induction steps share common components, one of which appears to be MEK kinase(s). Moreover, the inductive pathway (including MEK kinase) influences the competence of the vulval precursor cells and more strikingly their division pattern as well, irrespective of their vulval fate. Finally, a comparison of vulval mutant phenotypes obtained in C. elegans and O. tipulae CEW1 highlights the evolution of vulval induction mechanisms between the two species.

An integrated physical and genetic map of the nematode Pristionchus pacificus

The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.

Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans

Nematodes are an attractive group of organisms for studying the evolution of developmental processes. Pristionchus pacificus was established as a satellite organism for comparing vulva development and other processes to Caenorhabditis elegans. The generation of a genetic linkage map of P.pacificus has provided a first insight into the structure and organization of the genome of this species. Pristionchus pacificus and C.elegans are separated from one another by >100 000 000 years such that the structure of the genomes of these two nematodes might differ substantially. To evaluate the amount of synteny between the two genomes, we have obtained 126 kb of continuous genomic sequence of P.pacificus, flanking the developmental patterning gene pal-1. Of the 20 predicted open reading frames in this interval, 11 have C.elegans orthologs. Ten of these 11 orthologs are located on C.elegans chromosome III, indicating the existence of synteny. However, most of these genes are distributed over a 12 Mb interval of the C.elegans genome and only three pairs of genes show microsynteny. Thus, intrachromosomal rearrange ments occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes.

Evolution of development in closely related species of flies and worms

One of the main challenges in evolutionary biology is to identify the molecular changes that underlie phenotypic differences that are of evolutionary significance. Comparative studies of early development have shown that changes in the spatio-temporal use of regulatory genes, as well as changes in the specificity of regulatory proteins, are correlated with important differences in morphology between phylogenetically distant species. However, it is not known how such changes take place in natural populations, and whether they result from a single, or many small, additive events. Extending this approach to the study of development of closely related species promises to enrich this debate.

A Bacterial Artificial Chromosome-Based Genetic Linkage Map of the Nematode Pristionchus pacificus

To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems. Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species. In the nematode Pristionchus pacificus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans. However, substantial changes in gene function between P. pacificus and C. elegans limit the use of candidate gene approaches in studying P. pacificus mutations. To facilitate map-based cloning of mutations in P. pacificus, we constructed a BAC-based genetic linkage map. A BAC library of 13,440 clones was generated and completely end sequenced. By comparing BAC end and EST sequences between the “wild-type” strain P. pacificus var. California and the polymorphic strain P. pacificus var. Washington, 133 single-stranded conformational polymorphisms were identified. These markers were tested on a meiotic mapping panel of 46 randomly picked F2 animals after a cross of the two strains, providing the first genetic linkage map of P. pacificus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene.