Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses
Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses
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DOI：
10.1104/pp.103.035584
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发表时间：
2004-06-01
期刊：
影响因子：
7.4
通讯作者：
Reumann, S
中科院分区：
文献类型：
--
作者：
Reumann, S
为了指定高等植物的 C 端过氧化物酶体靶向信号类型 1 (PTS1) 和 N 端 PTS2，从公共数据库中检索了与 PTS1 和 PTS2 靶向植物蛋白同源的最大数量的植物 cDNA 和表达序列标签，并分析了其靶向结构域的一级结构的保守特性。根据其在同源物中的高总体频率及其在不同直系同源群体中的广泛出现，定义了九种主要的 PTS1 三肽（[SA][RK][LM]> 无 AKM> 加 SRI> 和 PRL>）和两种主要的 PTS2 九肽 (R[LI]x(5)HL)，如果存在于未知蛋白质中，它们被认为是过氧化物酶体定位的良好指标。较少但数量显着的同源物含有 11 种次要 PTS1 三肽或 9 种次要 PTS2 九肽，其中许多以前在植物过氧化物酶体蛋白中尚未鉴定过。与 PTS 肽相邻的区域也具有特定的保守特性，例如碱性和 Pro 残基的显着出现以及高正净电荷，这可能在过氧化物酶体靶向中发挥辅助作用。相比之下，在 550 个同系物中没有发现几种具有假设的过氧化物酶体靶向特性的肽，因此在过氧化物酶体靶向中仅发挥次要作用。基于这些主要和次要PTS的定义以及对其他保守特性的认识，可以提高预测过氧化物酶体蛋白的准确性，并且可以更成功地筛选植物基因组中的过氧化物酶体新蛋白。
To specify the C-terminal peroxisome targeting signal type 1 (PTS1) and the N-terminal PTS2 for higher plants, a maximum number of plant cDNAs and expressed sequence tags that are homologous to PTS1- and PTS2-targeted plant proteins was retrieved from the public databases and the primary structure of their targeting domains was analyzed for conserved properties. According to their high overall frequency in the homologs and their widespread occurence in different orthologous groups, nine major PTS1 tripeptides ([SA][RK][LM]> without AKM> plus SRI> and PRL>) and two major PTS2 nonapeptides (R[LI]x(5)HL) were defined that are considered good indicators for peroxisomal localization if present in unknown proteins. A lower but significant number of homologs contained I of 11 minor PTS1 tripeptides or of 9 minor PTS2 nonapeptides, many of which have not been identified before in plant peroxisomal proteins. The region adjacent to the PTS peptides was characterized by specific conserved properties as well, such as a pronounced incidence of basic and Pro residues and a high positive net charge, which probably play an auxiliary role in peroxisomal targeting. By contrast, several peptides with assumed peroxisomal targeting properties were not found in any of the 550 homologs and hence play-if at all-only a minor role in peroxisomal targeting. Based on the definition of these major and minor PTS and on the recognition of additional conserved properties, the accuracy of predicting peroxisomal proteins can be raised and plant genomes can be screened for novel proteins of peroxisomes more successfully.