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DNA Research Advance Access originally published online on December 12, 2006
DNA Research 2006 13(5):205-228; doi:10.1093/dnares/dsl013
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© The Author 2006. 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

Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family

Akifumi Sugiyama1, Nobukazu Shitan1, Shusei Sato2, Yasukazu Nakamura2, Satoshi Tabata2 and Kazufumi Yazaki1,*

1 Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere Kyoto University, Gokasho, Uji 611–0011, Japan
2 Kazusa DNA Research Institute, 2–6–7 Kazusa-Kamatari, Kisarazu, Chiba, 292–0812, Japan

ATP-binding cassette (ABC) proteins constitute a large family in plants with more than 120 members each in Arabidopsis and rice, and have various functions including the transport of auxin and alkaloid, as well as the regulation of stomata movement. In this report, we carried out genome-wide analysis of ABC protein genes in a model legume plant, Lotus japonicus. For analysis of the Lotus genome sequence, we devised a new method ‘domain-based clustering analysis’, where domain structures like the nucleotide-binding domain (NBD) and transmembrane domain (TMD), instead of full-length amino acid sequences, are used to compare phylogenetically each other. This method enabled us to characterize fragments of ABC proteins, which frequently appear in a draft sequence of the Lotus genome. We identified 91 putative ABC proteins in L. japonicus, i.e. 43 ‘full-size’, 40 ‘half-size’ and 18 ‘soluble’ putative ABC proteins. The characteristic feature of the composition is that Lotus has extraordinarily many paralogs similar to AtMRP14 and AtPDR12, which are at least six and five members, respectively. Expression analysis of the latter genes performed with real-time quantitative reverse transcription–PCR revealed their putative involvement in the nodulation process.

Key words: ABC protein; domain-based clustering analysis; genome-wide analysis; Lotus japonicus; SMC subfamily

*To whom correspondence should be addressed. Tel. +81-774-38-3617, Fax +81-774-38-3623, E-mail: yazaki{at}rish.kyoto-u.ac.jp

Communicated by Mikio Nishimura


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