title: Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes.
abstract: Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.
authors.affiliation: Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China. Electronic address: xyzhi@ynu.edu.cn.
authors.forename: Xiao-Yang
authors.initials: XY
authors.lastname: Zhi
authors.affiliation: Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.
authors.forename: Ji-Cheng
authors.initials: JC
authors.lastname: Yao
authors.affiliation: Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China; The First Hospital of Qujing City, Qujing Affiliated Hospital of Kunming Medical College, Qujing 655000, PR China.
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Li
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China; Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Ürűmqi 830011, PR China. Electronic address: wjli@ynu.edu.cn.
authors.forename: Wen-Jun
authors.initials: WJ
authors.lastname: Li
mesh_terms: D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase / Q000235:genetics; D019880:Aldehyde-Ketone Transferases / Q000235:genetics; D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D005075:Biological Evolution; D019295:Computational Biology; D022761:Gene Transfer, Horizontal; D008390:Markov Chains; D053858:Metabolic Networks and Pathways / Q000235:genetics; D005810:Multigene Family; D019761:Phosphorus-Oxygen Lyases / Q000235:genetics; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000235:genetics; D010802:Phylogeny; D020543:Proteome / Q000032:analysis; D017422:Sequence Analysis, DNA; D012765:Shikimic Acid / Q000378:metabolism*
chemical_list: D020543:Proteome; D012765:Shikimic Acid; D019880:Aldehyde-Ketone Transferases; D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase; D017853:Phosphotransferases (Alcohol Group Acceptor); C022642:shikimate kinase; C019895:chorismate synthase; D019761:Phosphorus-Oxygen Lyases
keywords: Domain architectures; Horizontal gene transfer; Pathway evolution; Phylogenetic analysis; Shikimate pathway