title: Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family.
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.
authors.affiliation: Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere Kyoto University, Gokasho, Uji 611-0011, Japan.
authors.forename: Akifumi
authors.initials: A
authors.lastname: Sugiyama
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Shitan
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.forename: Kazufumi
authors.initials: K
authors.lastname: Yazaki
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D000070116:Lotus / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D017434:Protein Structure, Tertiary
chemical_list: D018528:ATP-Binding Cassette Transporters; D029681:Arabidopsis Proteins; D017931:DNA Primers; D018744:DNA, Plant; D010940:Plant Proteins