Genomics in C. elegans: so many genes, such a little worm

The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and analyses, including a curated set of 19,735 protein-coding genes--with >90% directly supported by experimental evidence--and >1300 noncoding RNA genes. High-throughput efforts are under way to complete the gene sets, along with studies to characterize gene expression, function, and regulation on a genome-wide scale. The success of the worm project has had a profound effect on genome sequencing and on genomics more broadly. We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health.

A genome-wide map of conserved microRNA targets in C. elegans

BACKGROUND

Metazoan miRNAs regulate protein-coding genes by binding the 3' UTR of cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for understanding their function.

RESULTS

By using a new version of PicTar and sequence alignments of three nematodes, we predict that miRNAs regulate at least 10% of C. elegans genes through conserved interactions. We have developed a new experimental pipeline to assay 3' UTR-mediated posttranscriptional gene regulation via an endogenous reporter expression system amenable to high-throughput cloning, demonstrating the utility of this system using one of the most intensely studied miRNAs, let-7. Our expression analyses uncover several new potential let-7 targets and suggest a new let-7 activity in head muscle and neurons. To explore genome-wide trends in miRNA function, we analyzed functional categories of predicted target genes, finding that one-third of C. elegans miRNAs target gene sets are enriched for specific functional annotations. We have also integrated miRNA target predictions with other functional genomic data from C. elegans.

CONCLUSIONS

At least 10% of C. elegans genes are predicted miRNA targets, and a number of nematode miRNAs seem to regulate biological processes by targeting functionally related genes. We have also developed and successfully utilized an in vivo system for testing miRNA target predictions in likely endogenous expression domains. The thousands of genome-wide miRNA target predictions for nematodes, humans, and flies are available from the PicTar website and are linked to an accessible graphical network-browsing tool allowing exploration of miRNA target predictions in the context of various functional genomic data resources.

Comparative analysis of the expressed genome of the infective juvenile entomopathogenic nematode, Heterorhabditis bacteriophora

We report the first cDNA-sequencing project of the entomopathogenic nematode, Heterorhabditis bacteriophora. A total of 1246 expressed sequence tags (ESTs) were generated by random sequencing of clones from a cDNA library of the infective juvenile stage. The ESTs were annotated resulting in 1072 useful ESTs that were categorized into functional categories according to Kyoto Encyclopedia of Genes and Genomes. Approximately 459 of 1072 ESTs (43%) had significant similarities to annotated sequences in GenBank. Of these, 417 had significant similarities to the free-living nematode Caenorhanditis elegans proteins. Most ESTs (18%) belonged to the genetic information processing category followed by metabolism (15% ESTs) and environmental information processing (15%) pathways. Several interesting ESTs were found that may have roles in the infectivity and survival of infective juveniles. These included proteases, dauer pathway genes (akt-1, pdk-1 & daf-7) and aging and stress resistance genes such as superoxide dismutase (sod-4), heat shock genes (hsp-4 & hsp-6), and eat genes, and signaling proteins like G-protein coupled receptors, regulators of G-protein signaling (rgs), and serine/threonine kinases. Other interesting ESTs include systemic RNAi defective protein (sid-1), ribonuclease III family members (rnh-2 &rnc) and transposase gene (Tc3A). About 67% of the ESTs did not find matches in any of the searched databases suggesting potentially novel genes in this enomopathogenic nematode. Note: Sequences described in this paper have been deposited in Genbank under the accessions DN 152655-DN 152999, and DN 153000-DN 153726.

The dingo non-long terminal repeat retrotransposons from the genome of the hookworm, Ancylostoma caninum

Members of the retrotransposable element (RTE) clade of non-long terminal repeat (LTR) retrotransposon are widely distributed among eukaryote taxa, with representatives known from Caenorhabditis elegans, mammals, mosquitoes, schistosomes, and other taxa. An RTE retrotransposon has not, however, been characterized in detail from a parasitic nematode. Here, we characterize two discrete copies of an RTE-like non-LTR retrotransposon from the genome of the dog hookworm, Ancylostoma caninum. The elements were named dingo-1 and dingo-2. The full-length dingo-1 and dingo-2 elements were 3421 and 3171bp in length, respectively. They exhibited 54% nucleotide sequence identity to one another across their entire length and 40%/58% amino-acid sequence identity/similarity across their open reading frames. dingo-1 and dingo-2 exhibited hallmark structures and sequences of non-LTR retrotransposons of the RTE family including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT), in that order. Phylogenetic analyses targeting the RT and the EN domains both confirmed that dingo-1 and dingo-2 were members of the RTE clade and that they were closely related to RTE-1 from C. elegans, to BDDF from Bos taurus and to SR2 from Schistosoma mansoni. Dot blot hybridization indicated that as many as 100-1000 copies of dingo-1 reside within the genome of A. caninum, while detection by RT-PCR of transcripts encoding dingo-like elements suggested that dingo-1 and -2 may be retrotranspositionally active within the genome of A. caninum. The dingo elements are the first retrotransposons to be characterized from a hookworm genome.

Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes

Root-knot nematodes (RKN) of the genus Meloidogyne are biotrophic plant parasites of major agricultural importance, which exhibit very variable modes of reproduction, from classical amphimixis to mitotic parthenogenesis. This review focuses on those RKN species that reproduce exclusively by mitotic parthenogenesis (apomixis), in contrast to those that have meiotic/amphimitic events in their life cycle. Although populations of clonal organisms are often represented as being ecologically isolated and evolutionary inert, a considerable volume of literature provides evidence that asexual RKN are neither: they are widely distributed, extremely polyphagous, and amenable to selection and adaptive variation. The ancestors of the genus are unknown, but it is assumed that the parthenogenetic RKN have evolved from amphimictic species through hybridization and subsequent aneuploidization and polyploidization events. Molecular studies have indeed confirmed that the phylogenetic divergence between meiotic and mitotic RKN lineages occurred early, and have revealed an unexpected level of clonal diversity among populations within apomictic species. Laboratory experiments have shown that asexual RKN can rapidly adapt to new environmental constraints (eg host resistance), although with some fitness costs. Lastly, the molecular and chromosomal mechanisms that could contribute to genome plasticity leading to persistent genetic variation and adaptive evolution in apomictic RKN are discussed. It is concluded that RKN provide an excellent model system in which to study the dynamic nature and adaptive potential of clonal genomes.

What is Asian Taenia?

Asian Taenia is a human tapeworm which was first recognized in Taiwan aborigines and subsequently from Asian countries: Korea, Indonesia, Vietnam, and China. It was originally described as T. asiatica Eom and Rim, 1993 based on the morphology in its adult and larval stage. A taxonomic disagreement on whether it is species or subspecies level is mainly due to the morphological similarity of this tapeworm with T. saginata, but a sympatric distribution of these two tapeworms is also known in China. The life cycle is quite distinct from T. saginata in using the pig as intermediate host and parasitizing visceral organs such as liver, lung and omentum. A long unresolved question in Asian countries concerns the inconsistency between worm ratio and the food preferences was clarified with this viscerotropic tapeworm. Molecular biological differentiation is possible with DNA techniques and a complete genome of mtDNA was sequenced recently which may provide a resource for comparative mitochondrial genomics and systematic studies of parasitic cestodes. This is a young parasite discovered most recently with many research questions yet to be clarified.

DNA motifs and sequence periodicities

Genomic DNA sequences contain a wealth of information about the bendability and curvature of the DNA molecule. For example, the well-known 10-11 bp periodicities within genomes can be attributed to supercoiled structures or wrapping around nucleosomes. Such periodic signals have previously been examined mainly based on mono- or dinucleotide correlations. In this study, we generalize this approach and analyze correlation functions of longer motifs such as tetramers or poly(A) sequences. Periodically placed motifs may indicate regular protein binding or curvature signals. We detected various periodic signals e.g. strong 10-11 bp oscillations of periodically placed poly(A), poly(T) or poly(W) stretches. These observations lead to a new view on the intensively studied 10-11 bp periodicities.

The genome project of Taenia solium

We have constituted a consortium of key laboratories at the National Autonomous University of Mexico to carry out a genomic project for Taenia solium. This project will provide powerful resources for the study of taeniasis/cysticercosis, and, in conjunction with the Echinococcus granulosus and Echinococcus multilocularis genome project of expressed sequence tags (ESTs), will mark the advent of genomics for cestode parasites. Our project is planned in two consecutive stages. The first stage is being carried out to determine some basic parameters of the T. solium genome. Afterwards, we will evaluate the best strategy for the second stage, a full blown genome project. We have estimated the T. solium genome size by two different approaches: cytofluorometry on isolated cyton nuclei, as well as a probabilistic calculation based on approximately 2000 sequenced genomic clones, approximately 3000 ESTs, resulting in size estimates of 270 and 251 Mb, respectively. In terms of sequencing, our goal for the first stage is to characterize several thousand EST's (from adult worm and cysticerci cDNA libraries) and genomic clones. Results obtained so far from about 16,000 sequenced ESTs from the adult stage, show that only about 40% of the T. solium coding sequences have a previously sequenced homologue. Many of the best hits are found with mammalian genes, especially with humans. However, 1.5% of the hits lack homologues in humans, making these genes immediate candidates for investigation on pharmaco-therapy, diagnostics and vaccination. Most T. solium ESTs are related to gene regulation, and signal transduction. Other important functions are housekeeping, metabolism, cell division, cytoskeleton, proteases, vacuolar transport, hormone response, and extracellular matrix activities. Preliminary results also suggest that the genome of T. solium is not highly repetitive.

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira-Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida-Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.

Gene duplication and the properties of biological networks

Patterns of network connection of members of multigene families were examined for two biological networks: a genetic network from the yeast Saccharomyces cerevisiae and a protein-protein interaction network from Caenorhabditis elegans. In both networks, genes belonging to gene families represented by a single member in the genome ("singletons") were disproportionately represented among the nodes having large numbers of connections. Of 68 single-member yeast families with 25 or more network connections, 28 (44.4%) were located in duplicated genomic segments believed to have originated from an ancient polyploidization event; thus, each of these 28 loci was thus presumably duplicated along with the genomic segment to which it belongs, but one of the two duplicates has subsequently been deleted. Nodes connected to major "hubs" with a large number of connections, tended to be relatively sparsely interconnected among themselves. Furthermore, duplicated genes, even those arising from recent duplication, rarely shared many network connections, suggesting that network connections are remarkably labile over evolutionary time. These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature.

The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes

The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present.

The molecular biology of schistosomes

Twenty years ago, an article by Carter and Colley was published in an early issue of this journal. The report outlined pioneering studies by several laboratories into schistosome molecular biology and molecular genetics. To commemorate that prescient report and, in like fashion, to provide a brief (and non-comprehensive) synopsis of progress in this field up to the present time, I will outline some key aspects of the molecular biology of schistosomes that have been reported in the intervening years.

Identification of Novel Non-autonomous CemaT Transposable Elements and Evidence of their Mobility within the C. elegans Genome

We describe here two new transposable elements, CemaT4 and CemaT5, that were identified within the sequenced genome of Caenorhabditis elegans using homology based searches. Five variants of CemaT4 were found, all non-autonomous and sharing 26 bp inverted terminal repeats (ITRs) and segments (152-367 bp) of sequence with similarity to the CemaT1 transposon of C. elegans. Sixteen copies of a short, 30 bp repetitive sequence, comprised entirely of an inverted repeat of the first 15 bp of CemaT4's ITR, were also found, each flanked by TA dinucleotide duplications, which are hallmarks of target site duplications of mariner-Tc transposon transpositions. The CemaT5 transposable element had no similarity to maT elements, except for sharing identical ITR sequences with CemaT3. We provide evidence that CemaT5 and CemaT3 are capable of excising from the C. elegans genome, despite neither transposon being capable of encoding a functional transposase enzyme. Presumably, these two transposons are cross-mobilised by an autonomous transposon that recognises their shared ITRs. The excisions of these and other non-autonomous elements may provide opportunities for abortive gap repair to create internal deletions and/or insert novel sequence within these transposons. The influence of non-autonomous element mobility and structural diversity on genome variation is discussed.

Features of coding and noncoding sequences based on 3-tuple distributions

The origin of non-coding sequences, especially introns,is an outstanding issue that has been receiving continuous debate for the last two decades. In the current work we use a mathematical model to characterize DNA sequences and find that the 3-tuple distributions in different reading frames of a given coding sequence differ sharply from each other, while they are almost identical to each other in introns or other non-coding sequences. SREs (Symmetric relative entropies) decrease progressively from coding sequences of primitive prokaryotes to those of advanced eukaryotes and from non-coding sequences of low eukaryotes to those of high eukaryotes with a correlation coefficient of 0.86. In silico evolution experiments show that SREs typical of higher eukaryotic introns can be achieved from prokaryotic coding sequences as the mutation ratio reaches 2/100. The fact that (a total of 25 introns) from all three different genomes S. pombe, C. elegans and H. sapiens searched are found to share high sequence identity with coding regions indicates that at least some introns may have come directly from CDS (coding sequences). We suggest that SREs may be a useful feature for evolutionary study.

Imprinting capacity of gamete lineages in Caenorhabditis elegans

We have observed a gamete-of-origin imprinting effect in C. elegans using a set of GFP reporter transgenes. From a single progenitor line carrying an extrachromosomal unc-54::gfp transgene array, we generated three independent autosomal integrations of the unc-54::gfp transgene. The progenitor line, two of its three integrated derivatives, and a nonrelated unc-119:gfp transgene exhibit an imprinting effect: single-generation transmission of these transgenes through the male germline results in approximately 1.5- to 2.0-fold greater expression than transmission through the female germline. There is a detectable resetting of the imprint after passage through the opposite germline for a single generation, indicating that the imprinted status of the transgenes is reversible. In cases where the transgene is maintained in either the oocyte lineage or sperm lineage for multiple, consecutive generations, a full reset requires passage through the opposite germline for several generations. Taken together, our results indicate that C. elegans has the ability to imprint chromosomes and that differences in the cell and/or molecular biology of oogenesis and spermatogenesis are manifest in an imprint that can persist in both somatic and germline gene expression for multiple generations.

X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis

Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.

An historical and genomic view of schistosome conjugal biology with emphasis on sex-specific gene expression

The genetic programmes associated with the sexual biology of dioecious schistosomes remain a critically important but significantly understudied area of parasitology. Throughout the last four decades, progress has been slow in describing the gross antigenic and proteomic differences linked to sexually mature schistosomes and in characterizing some of the sex-associated transcripts and regulatory mechanisms induced during developmental maturation. These investigations have been severely hindered by the lack of complete EST/genomic information, as well as corresponding post- and functional-genomic tools for studying these pathogenic parasites. As near complete transcriptomes forSchistosoma japonicumandS. mansonihave recently been reported, and both DNA microarrays and post-transcriptional gene silencing have been applied to schistosomes, the tools and techniques for the high-throughput identification and characterization of transcripts involved in conjugal biology are now readily available. Here, an historical review is presented that summarizes some of the most significant findings associated with schistosome sex and sexual maturation during the last several decades. Following this discussion is a current overview of some modern day genomic approaches used to study schistosomes, which illustrates how major advances in the field of conjugal biology will be achieved.

Biochemical clustering of monomeric GTPases of the Ras superfamily

To date phylogeny has been used to compare entire families of proteins based on their nucleotide or amino acid sequence. Here we developed a novel analytical platform allowing a systematic comparison of protein families based on their biochemical properties. This approach was validated on the Rho subfamily of GTPases. We used two high throughput methods, referred to as AlphaScreen and FlashPlate, to measure nucleotide binding capacity, exchange, and hydrolysis activities of small monomeric GTPases. These two technologies have the characteristics to be very sensitive and to allow homogenous and high throughput assays. To analyze and integrate the data obtained, we developed an algorithm that allows the classification of GTPases according to their enzymatic activities. Integration and hierarchical clustering of these results revealed unexpected features of the small Rho GTPases when compared with primary sequence-based trees. Hence we propose a novel phylobiochemical classification of the Ras superfamily of GTPases.