Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants.
Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants.
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植物12-氧代植物二烯酸还原酶基因家族的系统发育分析、结构进化和功能分化
DOI：
10.1186/1471-2148-9-90
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发表时间：
2009-05-05
影响因子：
3.4
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Li W;Liu B;Yu L;Feng D;Wang H;Wang J
12-氧代-植物二烯酸还原酶（OPR）是催化α，β-不饱和醛或酮中双键还原的酶，并且是将亚麻酸转化为茉莉酸的十八烷酸途径的一部分。在植物中，OPR属于古老的黄酶家族，形成多基因家族。虽然在拟南芥和其他物种中已经发现了该家族，但植物中多个OPR的进化和功能尚不清楚。通过比较基因组分析，研究了植物OPR旁系同源物的系统发育关系、结构进化和功能分化。在代表6个主要绿色植物谱系的11个物种中，总共鉴定了74个OPR基因：绿色藻类、苔藓、石松、裸子植物、单子叶植物和双子叶植物。系统发育分析表明，植物中存在7个保守的亚科。所有来自绿色藻类的OPR基因都聚在一个亚科中，而来自陆地植物的OPR基因则聚在另外6个亚科中，这表明导致OPR家族扩大的事件发生在陆地植物中。进一步的分析表明，谱系特异性扩展，特别是串联重复，有助于目前的OPR亚科在陆地植物从水生植物分化后。有趣的是，外显子/内含子结构分析表明，OPR旁系同源物的基因结构在内含子数量和长度上表现出多样性，而内含子位置和相位在不同谱系物种中高度保守。这些观察结果与系统发育树一起揭示了OPR旁系同源物在结构进化过程中发生了连续的单个内含子丢失以及内含子内的插入缺失。功能分歧分析表明，改变功能的限制发生在特定的氨基酸位置后，多样化的旁系同源物。最值得注意的是，除了II/IV、II/V和V/VI对之外，在所有对中也发现了显著的功能分歧。通过后验概率建立的位点特异性图谱分析发现，正选择位点和/或功能分化的关键氨基酸残基主要分布在α螺旋和底物结合环（substrate binding loop，SBL）中，表明这些区域对该蛋白家族的功能具有重要意义。这项研究突出了OPR基因家族在所有植物谱系中的分子进化，并表明可能与旁系同源物的不同功能特性相关的关键氨基酸残基。这些发现的进一步实验验证可能提供有价值的信息OPRs的生化和生理功能。
The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-bonds in α, β-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multigene families. Although discoveries about this family in Arabidopsis and other species have been reported in some studies, the evolution and function of multiple OPRs in plants are not clearly understood. A comparative genomic analysis was performed to investigate the phylogenetic relationship, structural evolution and functional divergence among OPR paralogues in plants. In total, 74 OPR genes were identified from 11 species representing the 6 major green plant lineages: green algae, mosses, lycophytes, gymnosperms, monocots and dicots. Phylogenetic analysis showed that seven well-conserved subfamilies exist in plants. All OPR genes from green algae were clustered into a single subfamily, while those from land plants fell into six other subfamilies, suggesting that the events leading to the expansion of the OPR family occurred in land plants. Further analysis revealed that lineage-specific expansion, especially by tandem duplication, contributed to the current OPR subfamilies in land plants after divergence from aquatic plants. Interestingly, exon/intron structure analysis showed that the gene structures of OPR paralogues exhibits diversity in intron number and length, while the intron positions and phase were highly conserved across different lineage species. These observations together with the phylogenetic tree revealed that successive single intron loss, as well as indels within introns, occurred during the process of structural evolution of OPR paralogues. Functional divergence analysis revealed that altered functional constraints have occurred at specific amino acid positions after diversification of the paralogues. Most notably, significant functional divergence was also found in all pairs, except for the II/IV, II/V and V/VI pairs. Strikingly, analysis of the site-specific profiles established by posterior probability revealed that the positive-selection sites and/or critical amino acid residues for functional divergence are mainly distributed in α-helices and substrate binding loop (SBL), indicating the functional importance of these regions for this protein family. This study highlights the molecular evolution of the OPR gene family in all plant lineages and indicates critical amino acid residues likely relevant for the distinct functional properties of the paralogues. Further experimental verification of these findings may provide valuable information on the OPRs' biochemical and physiological functions.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
10.7
作者：
Gu, X
通讯作者：
Gu, X
影响因子：
4.3
作者：
Biesgen, C;Weiler, EW
通讯作者：
Weiler, EW
影响因子：
3.5
作者：
Kniskern, Joel M.;Traw, M. Brian;Bergelson, Joy
通讯作者：
Bergelson, Joy