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

Akifumi Sugiyama, Nobukazu Shitan, Shusei Sato, Yasukazu Nakamura, Satoshi Tabata, Kazufumi Yazaki

Research output: Contribution to journalArticlepeer-review

52 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)205-228
Number of pages24
JournalDNA Research
Volume13
Issue number5
DOIs
Publication statusPublished - 2006

Keywords

  • ABC protein
  • Domain-based clustering analysis
  • Genome-wide analysis
  • Lotus japonicus
  • SMC subfamily

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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