A survey of well conserved families of C2H2 zinc-finger genes in Daphnia

Arun Seetharam,Yang Bai,Gary W Stuart

doi:10.1186/1471-2164-11-276

Abstract

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.

Highlights

A recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians"
* Correspondence: gstuart@indstate.edu 1 Department of Biology, Indiana State University, Terre Haute, IN 47809, USA Full list of author information is available at the end of the article the Daphnia pulex genome[1], we focused our attention on a subset of roughly 40 orthologous groups of C2H2 Zinc-finger proteins (ZFP) identified in a recent comparative genomic analysis to be well conserved in "bilaterians"[2]
Updating a previous analysis of C2H2 ZFP present in the common ancestor of bilaterians based on a survey of Homo sapiens, Drosophila melanogaster and Caenorhabditis elegans, we identified 58 well conserved C2H2 ZFP genes in Daphnia that belong to 40 distinct families

Summary

Introduction

A 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). Zinc-finger proteins (ZFP) represent the largest family of DNA-binding transcription factors in eukaryotes. Many proteins are predicted to contain single zinc-finger domains, two zinc fingers in close proximity appear to be required for high-affinity DNA binding. Many of these proteins contain either multiple tandem pairs of zinc-fingers or tandem arrays of three or more zinc-fingers As transcription factors, they participate generally in the fundamental mechanism of gene expression. They participate generally in the fundamental mechanism of gene expression They usually play more specific roles in a wide variety of regulated biological processes, including signal transduction, cell growth, differentiation, and development. As part of our collaborative role in annotating the draft genome assembly v1.1 of

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