Tripathi Lokesh P, Sowdhamini R
National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India.
BMC Genomics. 2006 Aug 9;7:200. doi: 10.1186/1471-2164-7-200.
Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species.
Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively). Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers. DegP proteases, prolyl oligopeptidases, Clp proteases and rhomboids share a significantly higher percentage orthology between the two genomes indicating substantial evolutionary divergence was set prior to speciation. Single domain architectures and paralogues for several putative subtilisins, serine carboxypeptidases and rhomboids suggest they may have been recruited for additional roles in secondary metabolism with spatial and temporal regulation. The analysis reveals some domain architectures unique to either or both of the plant species and some inactive proteases, like in rhomboids and Clp proteases, which could be involved in chaperone function.
The systematic analysis of the serine protease-like proteins in the two plant species has provided some insight into the possible functional associations of previously uncharacterised serine protease-like proteins. Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species.
丝氨酸蛋白酶是在所有生命王国中发现的最大的蛋白水解酶类群之一，与多种重要的生理途径相关。拟南芥和水稻（Oryza sativa）基因组序列的可得性使得对这两种植物中丝氨酸蛋白酶样蛋白的全部种类进行鉴定和比较成为可能。
尽管拟南芥和水稻的基因组大小存在差异，但我们在这两种植物中鉴定出了数量非常相似的丝氨酸蛋白酶样蛋白（分别为206个和222个）。上述序列中近40%被鉴定为潜在的直系同源物。在植物基因组中可以鉴定出Deg、Clp、Lon、菱形蛋白酶的非典型成员，并且在高度丰富的枯草杆菌蛋白酶和丝氨酸羧肽酶家族中观察到了物种特异性成员，这表明存在多次横向基因转移。DegP蛋白酶、脯氨酰寡肽酶、Clp蛋白酶和菱形蛋白酶在两个基因组之间共享的直系同源百分比显著更高，表明在物种形成之前就已经发生了实质性的进化分歧。几种假定的枯草杆菌蛋白酶、丝氨酸羧肽酶和菱形蛋白酶的单结构域架构和旁系同源物表明，它们可能已被招募用于次生代谢中的其他作用，并具有空间和时间调控。分析揭示了一些这两种植物中一种或两种特有的结构域架构，以及一些无活性的蛋白酶，如菱形蛋白酶和Clp蛋白酶中的无活性蛋白酶，它们可能参与伴侣功能。
对这两种植物中丝氨酸蛋白酶样蛋白的系统分析为先前未表征的丝氨酸蛋白酶样蛋白的可能功能关联提供了一些见解。对这些方面的进一步研究可能有助于我们理解具有商业重要性的作物物种中的类似过程。
