Hox gene evolution in nematodes: novelty conserved

Transcriptional upregulation of the C. elegans Hox gene lin-39 during vulval cell fate specification

Extracellular signaling pathways and transcriptional regulatory networks function during development to specify metazoan cell fates. During Caenorhabditis elegans vulval development, the specification of three vulval precursor cells (VPCs) requires the activity of Wnt, Notch, and Ras signaling pathways, and function of the Hox gene lin-39. LIN-39 protein levels are regulated in the VPCs by both Wnt and Ras signaling. In particular, activation of Ras signaling leads to an increase in LIN-39 protein in P6.p at the time of VPC fate specification. We wish to understand the regulation of lin-39 by these pathways. We first show that LIN-39 is a target for MAP kinase in vitro, suggesting that the Ras-dependent LIN-39 upregulation could be mediated post-translationally. To test this idea, we created transcriptional and translational lin-39::GFP fusions that include the entire lin-39 genomic region, allowing observation of lin-39 expression in live animals. The reporters express GFP in most, if not all, sites of expression previously observed by LIN-39 antibody staining. We used these constructs to show that at the time of vulval induction both lin-39::GFP reporters are upregulated in P6.p, indicating that the accumulation of high levels of LIN-39 protein detected previously corresponds to transcriptional upregulation of lin-39 expression. This transcriptional upregulation of lin-39 is dependent on Ras signaling. We tested the requirement for several transcription factors acting downstream of Ras signaling in the VPCs, and found that P6.p upregulation requires the transcription factors LIN-1 and LIN-25, but appears to be independent of LIN-31, SEM-4, EOR-1 and EOR-2.Finally, we found that when the Wnt pathway is over activated, expression from the transcriptional lin-39::GFP increases, suggesting that the Wnt pathway also regulates lin-39 at the transcriptional level.

Terminal addition, the Cambrian radiation and the Phanerozoic evolution of bilaterian form

We examine terminal addition, the process of addition of serial elements in a posterior subterminal growth zone during animal development, across modern taxa and fossil material. We argue that terminal addition was the basal condition in Bilateria, and that modification of terminal addition was an important component of the rapid Cambrian evolution of novel bilaterian morphology. We categorize the often-convergent modifications of terminal addition from the presumed ancestral condition. Our focus on terminal addition and its modification highlights trends in the history of animal evolution evident in the fossil record. These trends appear to be the product of departure from the initial terminal addition state, as is evident in evolutionary patterns within-fossil groups such as trilobites, but is also more generally related to shifts in types of morphologic change through the early Phanerozoic. Our argument is contingent on dates of metazoan divergence that are roughly convergent with the first appearance of metazoan fossils in the latest Proterozoic and Cambrian, as well as on an inference of homology of terminal addition across bilaterian Metazoa.

Comparative genomics of nematodes

Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals.

Evidence for a Dispersed Hox Gene Cluster in the Platyhelminth Parasite Schistosoma mansoni

In most bilaterian organisms so far studied, Hox genes are organized in genomic clusters and determine development along the anteroposterior axis. It has been suggested that this clustering, together with spatial and temporal colinearity of gene expression, represents the ancestral condition. However, in organisms with derived modes of embryogenesis and lineage-dependent mechanisms for the determination of cell fate, temporal colinearity of expression can be lost and Hox cluster organization disrupted, as is the case for the ecdysozoans Drosophila melanogaster and Caenorhabditis elegans and the urochordates Ciona intestinalis and Oikopleura dioica. We sought to determine whether a lophotrochozoan, the platyhelminth parasite Schistosoma mansoni, possesses a conserved or disrupted Hox cluster. Using a polymerase chain reaction (PCR)-based strategy, we have cloned and characterized three novel S. mansoni genes encoding orthologues of Drosophila labial (SmHox1), deformed (SmHox4), and abdominal A (SmHox8), as well as the full-length coding sequence of the previously described Smox1, which we identify as an orthologue of fushi tarazu. Quantitative reverse transcriptase-PCR showed that the four genes were expressed at all life-cycle stages but that levels of expression were differentially regulated. Phylogenetic analysis and the conservation of "parapeptide" sequences C-terminal to the homeodomains of SmHox8 and Smox1 support the grouping of platyhelminths within the lophotrochozoan clade. However, Bacterial Artificial Chromosome (BAC) library screening followed by genome walking failed to reconstitute a cluster. The BAC clones containing Hox genes were sequenced, and in no case were other Hox genes found on the same clone. Moreover, the SmHox4 and SmHox8 genes contained single very large introns (>40 kbp) further indicating that the schistosome Hox cluster is highly extended. Localization of the Hox genes to chromosomes using fluorescence in situ hybridization showed that SmHox4 and SmHox8 are on the long arm of chromosome 4, whereas SmHox1 and Smox1 are on chromosome 3. In silico screening of the available genome sequences corroborated results of Southern blotting and BAC library screening that indicate that there are no paralogues of SmHox1, SmHox4, or SmHox8. The schistosome Hox cluster is therefore not duplicated, but is both dispersed and disintegrated in the genome.

Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex

Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been rearranged differently in several Drosophila species, producing a striking diversity of Hox gene organizations. We investigated the genomic and functional consequences of the two HOM-C splits present in Drosophila buzzatii. Firstly, we sequenced two regions of the D. buzzatii genome, one containing the genes labial and abdominal A, and another one including proboscipedia, and compared their organization with that of D. melanogaster and D. pseudoobscura in order to map precisely the two splits. Then, a plethora of conserved noncoding sequences, which are putative enhancers, were identified around the three Hox genes closer to the splits. The position and order of these enhancers are conserved, with minor exceptions, between the three Drosophila species. Finally, we analyzed the expression patterns of the same three genes in embryos and imaginal discs of four Drosophila species with different Hox-gene organizations. The results show that their expression patterns are conserved despite the HOM-C splits. We conclude that, in Drosophila, Hox-gene clustering is not an absolute requirement for proper function. Rather, the organization of Hox genes is modular, and their clustering seems the result of phylogenetic inertia more than functional necessity.

Caenorhabditis elegans Geminin Homologue Participates in Cell Cycle Regulation and Germ Line Development

Cdt1 is an essential component for the assembly of a pre-replicative complex. Cdt1 activity is inhibited by geminin, which also participates in neural development and embryonic differentiation in many eukaryotes. Although Cdt1 homologues have been identified in organisms ranging from yeast to human, geminin homologues had not been described for Caenorhabditis elegans and fungi. Here, we identify the C. elegans geminin, GMN-1. Biochemical analysis reveals that GMN-1 associates with C. elegans CDT-1, the Hox protein NOB-1, and the Six protein CEH-32. GMN-1 inhibits not only the interaction between mouse Cdt1 and Mcm6 but also licensing activity in Xenopus egg extracts. RNA interference-mediated reduction of GMN-1 is associated with enlarged germ nuclei with aberrant nucleolar morphology, severely impaired gametogenesis, and chromosome bridging in intestinal cells. We conclude that the Cdt1-geminin system is conserved throughout metazoans and that geminin has evolved in these taxa to regulate proliferation and differentiation by directly interacting with Cdt1 and homeobox proteins.

Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates

MOTIVATION

To identify genetic conservation relative to precise aspects of developmental diversity, an essential question in computational biology, we developed a new comparative method that allows conserved modules for the best balance between protein sequence similarity and gene co-expression to be constructed, in invertebrates.

RESULTS

Our method, referred to as the best-balance constraint procedure (BBCP), yielded 719 functionally conserved modules (FCMs) comprising 2-23 gene pairs. These modules were consistent with the developmental roles of orthologues as inferred from Gene Ontology, RNAi knockouts, InterPro and process-specific microarray data. New relationships were defined between genetic conservation and developmental diversity. Novel gene associations were indeed found in 94% of the FCMs, 150 modules being completely new. A significant proportion of the FCMs (18%, 132 modules) described cell type-specific mechanisms, comprising neuronal, muscle and germ cell signaling, new associations being found in 125 modules. Also found were gene associations for cell fate specification activities previously not highlighted by computational means, e.g. in FCMs containing homeogenes. These data indicate that highly discriminative description of genetic conservation can be deduced using BBCP, and reveal new correlations between cellular and developmental diversity and gene essentiality in invertebrates.

CONTACT

christian.neri@broca.inserm.fr

SUPPLEMENTARY INFORMATION

For supplementary information, please refer to Bioinformatics online.