Convergent evolution of RuBisCO genes in aquatic plants

CAO Yang; HE Xionglei; WANG Jianguo

doi:10.13471/j.cnki.acta.snus.ZR20240195

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Convergent evolution of RuBisCO genes in aquatic plants

Column of academic collection（Contributing editor: HU Jianxun） | 更新时间：2024-11-25

- Convergent evolution of RuBisCO genes in aquatic plants
- Acta Scientiarum Naturalium Universitatis Sunyatseni Vol. 63, Issue 6, Pages: 161-170(2024)
- 作者机构：
  
  中山大学生命科学学院，广东广州 510275
- 作者简介：
- 基金信息：
- DOI：10.13471/j.cnki.acta.snus.ZR20240195
  CLC： Q33
- Published：25 November 2024，
  
  Published Online：26 September 2024，
  
  Received：07 June 2024，
  
  Accepted：09 August 2024
- 稿件说明：
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曹阳,贺雄雷,王建国.水生植物RuBisCO基因的趋同演化[J].中山大学学报(自然科学版)(中英文),2024,63(06):161-170.

CAO Yang,HE Xionglei,WANG Jianguo.Convergent evolution of RuBisCO genes in aquatic plants[J].Acta Scientiarum Naturalium Universitatis Sunyatseni,2024,63(06):161-170.
曹阳,贺雄雷,王建国.水生植物RuBisCO基因的趋同演化[J].中山大学学报(自然科学版)(中英文),2024,63(06):161-170. DOI： 10.13471/j.cnki.acta.snus.ZR20240195.

CAO Yang,HE Xionglei,WANG Jianguo.Convergent evolution of RuBisCO genes in aquatic plants[J].Acta Scientiarum Naturalium Universitatis Sunyatseni,2024,63(06):161-170. DOI： 10.13471/j.cnki.acta.snus.ZR20240195.

摘要

植物碳固定，作为碳循环中的核心环节，对全球粮食产量与气候变迁具有深远影响。在此过程中，核酮糖-1，5-二磷酸羧化酶（RuBisCO）的作用举足轻重。其催化速率与特异性间存在微妙的平衡：特异性降低，催化速率上升，但副反应中的有毒副产物亦随之增多，从而影响整体效率。然而，水生植物却拥有独特的CO

富集机制，有效减少了副反应的影响，为酶创造了优越的工作环境。本文以高等水生植物入水事件为切入点，深入研究了其核酮糖-1，5-二磷酸羧化酶大亚基蛋白的趋同进化。旨在寻找与入水事件紧密相关的趋同进化位点，并探究CO

富集机制下该酶理化性质的变化，为酶的优化提供新思路。收集了泽泻目、唇形目、虎耳草目、水韭目、山茱萸目和金鱼藻目等6个目共48个物种的酶蛋白质序列信息，并确定了6次关键的入水事件。采用PCOC分析方法，整合了这6次入水事件的数据，深入剖析了水生植物的进化趋势。分析结果显示，水生植物中可能存在一个关键的趋同进化位点，位于蛋白质序列的第328号位置，紧邻酶的活性中心。推测该位点的替换可能增强了反应底物进入活性中心区域的灵活性，使CO

更易进入，从而提升了酶的催化速率。这一发现为后续的酶改进突变实验指明了方向，提供了坚实的理论依据。研究成果不仅有助于优化该酶的催化效率和适应性，也为深入研究植物碳固定机制提供了新的视角。

Abstract

The fixation of carbon in plants is a crucial step in the carbon cycle， significantly impacting global food production and climate change. Within this process， the ribulose-1，5-bisphosphate carboxylase enzyme plays a pivotal role. There exists a delicate balance between the enzyme's catalytic rate and its specificity： as the specificity decreases， the catalytic rate rises， but this is accompanied by an increase in toxic by-products from side reactions， ultimately affecting overall efficiency. However， aquatic plants possess a unique mechanism for carbon dioxide enrichment， effectively minimizing the impact of side reactions and creating a more favorable environment for the enzyme. Using the submergence events of higher aquatic plants as a starting point， we comprehensively studied the convergent evolution of the large subunit protein of ribulose-1，5-bisphosphate carboxylase （RuBisCO） in these plants. Our aim was to identify convergent evolutionary sites related to submergence events and explore changes in the enzyme's physicochemical properties following the emergence of the carbon dioxide enrichment mechanism， providing new insights for optimizing the enzyme. We collected protein sequence information for ribulose-1，5-bisphosphate carboxylase from 48 species belonging to six orders： Alismatales， Lamiales， Saxifragales， Hydrocharitales， Cornales， and Ceratophyllales， and identified six submergence events. Employing the PCOC analysis method， we integrated data from these six submergence events to investigate common evolutionary trends in aquatic plants. Our analysis revealed the potential existence of a convergent evolutionary site in aquatic plants， located at position 328 in the protein sequence， adjacent to the enzyme's active center. We hypothesize that substitutions at this site may enhance the flexibility of controlling the entry of reaction substrates into the active center， thereby facilitating the entry of carbon dioxide and increasing the enzyme's catalytic rate. The discovery of this convergent evolutionary site provides a research direction and theoretical basis for subsequent enzyme improvement and mutation experiments. Our findings will contribute to further optimizing the catalytic efficiency and adaptability of this enzyme.

关键词

核酮糖-1，5-二磷酸羧化酶高等水生植物入水事件CO2富集机制趋同进化

Keywords

ribulose-1，5-bisphosphate carboxylasesubmergence events of higher aquatic plantscarbon dioxide enrichment mechanismconvergent evolution

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