Chi Shan, Wu Shuangxiu, Yu Jun, Wang Xumin, Tang Xuexi, Liu Tao
Ocean University of China, Qingdao, Shandong Province, People's Republic of China.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China; Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
PLoS One. 2014 Oct 14;9(10):e110154. doi: 10.1371/journal.pone.0110154. eCollection 2014.
Both Calvin-Benson-Bassham (C3) and Hatch-Slack (C4) cycles are most important autotrophic CO2 fixation pathways on today's Earth. C3 cycle is believed to be originated from cyanobacterial endosymbiosis. However, studies on evolution of different biochemical variants of C4 photosynthesis are limited to tracheophytes and origins of C4-cycle genes are not clear till now. Our comprehensive analyses on bioinformatics and phylogenetics of novel transcriptomic sequencing data of 21 rhodophytes and 19 Phaeophyceae marine species and public genomic data of more algae, tracheophytes, cyanobacteria, proteobacteria and archaea revealed the origin and evolution of C4 cycle-related genes. Almost all of C4-related genes were annotated in extensive algal lineages with proteobacterial or archaeal origins, except for phosphoenolpyruvate carboxykinase (PCK) and aspartate aminotransferase (AST) with both cyanobacterial and archaeal/proteobacterial origin. Notably, cyanobacteria may not possess complete C4 pathway because of the flawed annotation of pyruvate orthophosphate dikinase (PPDK) genes in public data. Most C4 cycle-related genes endured duplication and gave rise to functional differentiation and adaptation in different algal lineages. C4-related genes of NAD-ME (NAD-malic enzyme) and PCK subtypes exist in most algae and may be primitive ones, while NADP-ME (NADP-malic enzyme) subtype genes might evolve from NAD-ME subtype by gene duplication in chlorophytes and tracheophytes.
卡尔文-本森-巴斯姆（C3）循环和哈奇-斯莱克（C4）循环都是当今地球上最重要的自养二氧化碳固定途径。C3循环被认为起源于蓝藻内共生。然而，关于C4光合作用不同生化变体的进化研究仅限于维管植物，且C4循环基因的起源至今仍不清楚。我们对21种红藻和19种褐藻海洋物种的新转录组测序数据以及更多藻类、维管植物、蓝细菌、变形菌和古菌的公共基因组数据进行了生物信息学和系统发育学综合分析，揭示了C4循环相关基因的起源和进化。几乎所有与C4相关的基因都在具有变形菌或古菌起源的广泛藻类谱系中被注释，除了磷酸烯醇式丙酮酸羧激酶（PCK）和天冬氨酸转氨酶（AST），它们具有蓝细菌和古菌/变形菌的双重起源。值得注意的是，由于公共数据中丙酮酸磷酸双激酶（PPDK）基因的注释有误，蓝细菌可能不具备完整的C4途径。大多数与C4循环相关的基因经历了复制，并在不同的藻类谱系中产生了功能分化和适应性。NAD-ME（NAD-苹果酸酶）和PCK亚型的C4相关基因存在于大多数藻类中，可能是原始基因，而NADP-ME（NADP-苹果酸酶）亚型基因可能是通过绿藻和维管植物中的基因复制从NAD-ME亚型进化而来。
