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DNA Research Advance Access published online on October 6, 2007
DNA Research, doi:10.1093/dnares/dsm016
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© The Author 2007. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

A Genome-wide Survey and Systematic RNAi-based Characterization of Helicase-like Genes in Caenorhabditis elegans

Toshihiko Eki1,2,*, Takeshi Ishihara3, {dagger}, Isao Katsura3 and Fumio Hanaoka2,4,5

1 Division of Life Science and Biotechnology, Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
2 Cellular Physiology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
3 Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
4 Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
5 SORST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan

Received 20 November 2006 ; accepted 27 August 2007.

Helicase-like proteins play a crucial role in nucleic acid- and chromatin-mediated reactions. In this study, we identified 134 helicase-like proteins in the nematode Caenorhabditis elegans and classified the proteins into 10 known subfamilies and a group of orphan genes on the basis of sequence similarity. We characterized loss-of-function phenotypes in RNA interference (RNAi)-treated animals for helicase family members, using the RNAi feeding method, and found several previously unreported phenotypes. Fifty-one (39.5%) of 129 genes tested showed development- or growth-defect phenotypes, and many of these genes were putative nematode homologs of essential genes in a unicellular eukaryote, budding yeast, suggesting conservation of these essential proteins in both species. Comparative analyses between these species identified evolutionarily diverged nematode proteins as well as conserved family members. Chromosome mapping of the nematode genes revealed 10 pairs of putative duplicated genes and clusters of C. elegans-specific SNF2-like genes and Helitrons. Analyses of transcriptional profile data revealed a predominantly oogenesis- and germline-enriched expression of many helicase-like genes. Finally, we identified the D2005.5(drh-3) gene in an RNAi-based screen for genes involved in resistance to X-ray irradiation. Analysis of DRH-3 will clarify the potentially novel mechanism by which it protects against X-ray-induced damage in C. elegans.

Key words: C. elegans; comparative genomics; drh-3; helicase family; RNAi-based screen

* To whom correspondence should be addressed. Tel. +81 532-44-6907. Fax. +81 532-44-6929. E-mail: eki{at}eco.tut.ac.jp

Edited by Yuji Kohara

{dagger} Current address: Molecular Genetics Laboratory, Department of Biology, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan.


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