TY - JOUR
T1 - Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus
T2 - Comparison with Arabidopsis ABC protein family
AU - Sugiyama, Akifumi
AU - Shitan, Nobukazu
AU - Sato, Shusei
AU - Nakamura, Yasukazu
AU - Tabata, Satoshi
AU - Yazaki, Kazufumi
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
KW - ABC protein
KW - Domain-based clustering analysis
KW - Genome-wide analysis
KW - Lotus japonicus
KW - SMC subfamily
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U2 - 10.1093/dnares/dsl013
DO - 10.1093/dnares/dsl013
M3 - Article
C2 - 17164256
AN - SCOPUS:33845898463
VL - 13
SP - 205
EP - 228
JO - DNA Research
JF - DNA Research
SN - 1340-2838
IS - 5
ER -