Identification of conserved C2H2 zinc-finger gene families in the Bilateria.
Ontology highlight
ABSTRACT: Background
Identification of orthologous relationships between genes from widely divergent taxa allows partial reconstruction of the gene complement of ancestral genomes. C2H2 zinc-finger genes are one of the largest and most complex gene superfamilies in metazoan genomes, with hundreds of members in the human genome. Here we analyze C2H2 zinc-finger genes from three taxa - Drosophila, Caenorhabditis elegans and human - from which near-complete genome sequence data are available.Results
Our analyses conclusively identify 39 families of genes, of which 38 can be defined as orthology groups in that they are descended from single ancestral genes in the common ancestor of Drosophila, C. elegans and humans.Conclusions
On the basis of current metazoan phylogeny, these 39 groups represent the minimum complement of C2H2 zinc-finger genes present in the genome of the bilaterian common ancestor.
SUBMITTER: Knight RD
PROVIDER: S-EPMC32188 | biostudies-literature | 2001
REPOSITORIES: biostudies-literature
Publications
Identification of conserved C2H2 zinc-finger gene families in the Bilateria.
Genome biology 20010424 5
<h4>Background</h4>Identification of orthologous relationships between genes from widely divergent taxa allows partial reconstruction of the gene complement of ancestral genomes. C2H2 zinc-finger genes are one of the largest and most complex gene superfamilies in metazoan genomes, with hundreds of members in the human genome. Here we analyze C2H2 zinc-finger genes from three taxa - Drosophila, Caenorhabditis elegans and human - from which near-complete genome sequence data are available.<h4>Resu ...[more]
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Project description:BackgroundA recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians" (i.e. worms, flies, and humans). Here we extend that analysis to include a second arthropod genome from the crustacean, Daphnia pulex.ResultsMost of the 40 orthologous groups of C2H2 zinc-finger proteins are represented by just one or two proteins within each of the previously surveyed species. Likewise, Daphnia were found to possess a similar number of orthologs for all of these small orthology groups. In contrast, the number of Sp/KLF homologs tends to be greater and to vary between species. Like the corresponding mammalian Sp/KLF proteins, most of the Drosophila and Daphnia homologs can be placed into one of three sub-groups: Class I-III. Daphnia were found to have three Class I proteins that roughly correspond to their Drosophila counterparts, dSP1, btd, CG5669, and three Class II proteins that roughly correspond to Luna, CG12029, CG9895. However, Daphnia have four additional KLF-Class II proteins that are most similar to the vertebrate KLF1/2/4 proteins, a subset not found in Drosophila. Two of these four proteins are encoded by genes linked in tandem. Daphnia also have three KLF-Class III members, one more than Drosophila. One of these is a likely Bteb2 homolog, while the other two correspond to Cabot and KLF13, a vertebrate homolog of Cabot.ConclusionConsistent with their likely roles as fundamental determinants of bilaterian form and function, most of the 40 groups of C2H2 zinc-finger proteins are conserved in kind and number in Daphnia. However, the KLF family includes several additional genes that are most similar to genes present in vertebrates but missing in Drosophila.
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Project description:BackgroundThe C2H2 zinc-finger (ZNF) containing gene family is one of the largest and most complex gene families in metazoan genomes. These genes are known to exist in almost all eukaryotes, and they constitute a major subset of eukaryotic transcription factors. The genes of this family usually occur as clusters in genomes and are thought to have undergone a massive expansion in vertebrates by multiple tandem duplication events (BMC Evol Biol 8:176, 2008).ResultsIn this study, we combined two popular approaches for homolog detection, Reciprocal Best Hit (RBH) (Proc Natl Acad Sci USA 95:6239-6244, 1998) and Hidden-Markov model (HMM) profiles search (Bioinformatics 14:755-763, 1998), on a diverse set of complete genomes of 124 eukaryotic species ranging from excavates to humans to identify all detectable members of 37 C2H2 ZNF gene families. We succeeded in identifying 3,890 genes as distinct members of 37 C2H2 gene families. These 37 families are distributed among the eukaryotes as progressive additions of gene blocks with increasing complexity of the organisms. The first block featuring the protists had 7 families, the second block featuring plants had 2 families, the third block featuring the fungi had 2 families (one of which was also present in plants) and the final block consisted of metazoans with 25 families. Among the metazoans, the simpler unicellular metazoans had just 15 of the 25 families while most of the bilaterians had all 25 families making up a total of 37 families. Multiple potential examples of lineage-specific gene duplications and gene losses were also observed.ConclusionsOur hybrid approach combines features of the both RBH and HMM methods for homolog detection. This largely automated technique is much faster than manual methods and is able to detect homologs accurately and efficiently among a diverse set of organisms. Our analysis of the 37 evolutionarily conserved C2H2 ZNF gene families revealed a stepwise appearance of ZNF families, agreeing well with the phylogenetic relationship of the organisms compared and their presumed stepwise increase in complexity (Science 300:1694, 2003).
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