百人博士最新文章获酶分子进化研究新成果

生物通报道：来自中科院武汉植物园，中山大学生命科学学院等处的研究人员发现裸子植物3个科（罗汉松科、三尖杉科和红豆杉科）植物的Rubisco酶大亚基在漫长的地质历史时期内伴随着大气CO2浓度的改变发生了复杂的适应性进化。这不仅对理解Rubisco酶与环境因子的相互作用具有重要意义，而且有助于认识与Rubisco酶相关的功能网络。这一研究成果公布在国际重要学术刊物Biology Direct上。

文章的通讯作者是中国科学院“****”王艇研究员，和中山大学生命科学学院苏应娟教授，王艇研究员早年毕业于中山大学生命科学学院，2005年入选中国科学院“****”、中国科学院武汉植物园研究员。

为深入了解Rubisco酶的分子进化，研究人员以裸子植物3个科（罗汉松科、三尖杉科和红豆杉科）的rbcL基因为对象，利用“宽松分子钟”模型重建了物种系统发育关系，在时间尺度下开展了适应性进化和共进化分析；发现伴随着历史上大气层中CO2浓度的变化，RbcL亚基的部分位点受到了持续正选择，其中一些位点位于Rubisco酶大、小亚基的接触面上，而另一些位点则位于该酶及其活化酶接触面附近，这些结果说明Rubisco酶为了应对大气层CO2浓度的改变而发生了持续性的适应调整，期间还伴有Rubisco活化酶发生的共进化。

更重要的的是，RbcL亚基内存在着氨基酸位点共进化网络，其中6个核心位点曾经遭受过正选择，说明Rubisco大亚基可通过不同氨基酸位点的共进化改变其功能和结构，进而发生适应性进化。

这些结果不仅对理解Rubisco酶与环境因子的相互作用具有重要意义，而且有助于认识与Rubisco酶相关的功能网络。

另外王艇研究组近期还解析了蕨类叶绿体基因组的进化动态，证实其远比以往设想的更为复杂。研究结果于近期发表在国际重要学术刊物BMC Plant Biology上。

（生物通：万纹）

原文摘要：

Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

Background
The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure.

Results
We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2.

Conclusions
The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities.

作者简介：

王艇
中国科学院武汉植物园种群遗传学学科组首席研究员、博士生导师

简要履历：
2005年　中国科学院“****”、中国科学院武汉植物园研究员
2002年—2004年　英国Glasgow大学生物医学和生命科学研究所(IBLS)植物科学组Research Scientist
2001年—2002年　中山大学生命科学学院生物化学系
1998年—2001年　瑞典Lund大学植物生物学系博士后
1994年—1998年　中山大学生命科学学院生物化学系
1985年—1994年　中山大学生命科学学院学士、推荐提前攻博、博士

研究领域：
植物种群遗传结构和系统发育地理
进化叶绿体基因组学
植物重要功能基因的分子进化与利用

社会任职：
中国植物学会植物分类与系统进化专业委员会委员；中国花卉协会蕨类植物分会第四届理事会理事；《生物多样性》编委；《武汉植物学研究》编委；《Frontiers of Biology in China》客座编辑(Guest Editor)