蔓花生PEPC基因家族的生物信息学分析

Bioinformatics Analysis of PEPC Gene Family in Arachis duranensis

摘要:

为了解花生中磷酸烯醇式丙酮酸羧化酶（phosphoenolpyruvate carboxylase，PEPC）的功能，对二倍体祖先种野生蔓花生（Arachis duranensis）基因组数据库进行分析，发现存在9个AdPEPC基因家族成员，这些基因的序列长度为3 584~12 956 bp，开放阅读框（ORF）长度为702~3 168 bp，分布在3、5、7、8、9、10号染色体上。蔓花生AdPEPC家族蛋白的氨基酸序列中均含有HCO₃^-结合位点和PEP结合位点等保守结构域，根据序列特征可分为植物型、细菌型和序列较短的PEPC等3类，同类蛋白序列的同源性较高，基因结构中的内含子与外显子的数目也较相似。基因表达分析表明，多数成员在花或茎中的表达量较高，AdPEPC1；2和AdPEPC4；2在茎中的表达量最高，其他家族成员尤其是AdPEPC2、AdPEPC1；5和AdPEPC1；3在花中的表达量明显高于其他组织，AdPEPC1；5基因在叶中不表达。AdPEPC3在根、茎、叶和花中均不表达，推测该基因为假基因。这为深入研究AdPEPC家族基因的功能奠定了基础。

Abstract:

To understand the function of phosphoenolpyruvate carboxylase (PEPC) in peanut, PEPC sequences of the diploid progenitor Arachis duranensis genome database were analyzed. Nine gene family members were found, and their sequence lengths ranged from 3 584 to 12 956 bp with 702-3 168 bp open reading frame (ORF), distributed in the 3, 5, 7, 8, 9, and 10th chromosomes. In the amino acid sequences of AdPEPC proteins, there were conserved domains, such as HCO₃^- binding sites and PEP binding sites, et al. According to the sequence characteristics, AdPEPC proteins could be divided into 3 groups as plant type, bacterium type and short sequence type. Protein homologies of the same type were high, and the number of intron and exon in gene structures was similar. Gene expression analysis showed that the expressions of most members were high in flowers or stems. AdPEPC1;2 and AdPEPC4;2 had the highest expression in stem. Other family members, especially AdPEPC2, AdPEPC1;5 and AdPEPC1;3, expressions were significantly higher in flower than other tissues. AdPEPC1;5 expression was not detected in leaf. No expression of AdPEPC3 was detected in root, stem, leaf and flower, and it was presumed to be pseudogenes based on its gene structure. These would lay a foundation for further study on the functions of AdPEPC family genes.