摘要：近日，在武汉植物园种群遗传学学科组组长、中国科学院“百人计划”王艇研究员指导下，武汉植物园森林博士等人与国外专家Mario A Fares研究员、中山大学生命科学学院苏应娟教授课题组合作，在裸子植物Rubisco酶（加氧酶）的分子进化研究方面取得重要进展。研究发现裸子植物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。
为深入了解Rubisco酶的分子进化，他们以裸子植物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。
该研究结果已于近日发表在国际重要学术刊物《生物学快讯》（Biology Direct） 上。
生物探索推荐英文论文摘要：
Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns
Abstract
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.
Reviewers
This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.
