Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family.
Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family.
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DOI：
10.1093/dnares/dsl013
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发表时间：
2006-12
期刊：
影响因子：
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通讯作者：
A. Sugiyama;N. Shitan;Shusei Sato;Yasukazu Nakamura;S. Tabata;K. Yazaki
中科院分区：
文献类型：
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作者：
A. Sugiyama;N. Shitan;Shusei Sato;Yasukazu Nakamura;S. Tabata;K. Yazaki
ATP结合盒（ATP binding cassette，ABC）蛋白是植物中的一个大家族，在拟南芥和水稻中各有120多个成员，具有多种功能，包括运输生长素和生物碱，调节气孔运动等。在这份报告中，我们进行了ABC蛋白基因的模式豆科植物，百脉根全基因组分析。为了分析莲花基因组序列，我们设计了一种新的方法“基于结构域的聚类分析”，其中结构域结构，如核苷酸结合结构域（NBD）和跨膜结构域（TMD），而不是全长氨基酸序列，用于相互比较遗传学。这种方法使我们能够表征ABC蛋白的片段，这些片段经常出现在Lotus基因组的草图序列中。我们在L.即43个“全尺寸”、40个“半尺寸”和18个“可溶性”推定的ABC蛋白。该组合物的特征是Lotus具有非常多的与AtMRP 14和AtPDR 12相似的旁系同源物，它们分别至少有六个和五个成员。后者的基因进行实时定量逆转录-PCR的表达分析揭示了他们的推定参与的过程。
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.