title: Engineering microorganisms based on molecular evolutionary analysis: a succinate production case study.
abstract: Evolution has resulted in thousands of species possessing similar metabolic enzymes with identical functions that are, however, regulated by different mechanisms. It is thus difficult to select optimal gene to engineer novel or manipulated metabolic pathways. Here, we tested the ability of molecular evolutionary analysis to identify appropriate genes from various species. We calculated the fraction of synonymous substitution and the effective number of codons (ENC) for nine genes stemming from glycolysis. Our research indicated that an enzyme gene with a stronger selective constraint in synonymous sites would mainly regulate corresponding reaction flux through altering the concentration of the protein, whereas those with a more relaxed selective constraint would primarily affect corresponding reaction flux by changing kinetic properties of the enzyme. Further, molecular evolutionary analysis was investigated for three types of genes involved in succinate precursor supply by catalysis of pyruvate. In this model, overexpression of Corynebacterium glutamicum pyc should result in greater conversion of pyruvate. Succinate yields in two Escherichia coli strains that overexpressed each of the three types of genes supported the molecular evolutionary analysis. This approach may thus provide an alternative strategy for selecting genes from different species for metabolic engineering and synthetic biology.
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Xianghui
authors.initials: X
authors.lastname: Ma
authors.affiliation: School of Environmental and Municipal Engineering, Tianjin Chengjian University Tianjin, China ; Tianjin Key Laboratory of Aquatic Science and Technology Tianjin, China.
authors.forename: Xinbo
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Baiyun
authors.initials: B
authors.lastname: Wang
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Zhiwen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin, China.
authors.forename: Xueming
authors.initials: X
authors.lastname: Zhao
keywords: metabolic engineering; molecular evolution; succinate; synonymous substitution; synthetic biology