title: Positive selection on D-lactate dehydrogenases of Lactobacillus delbrueckii subspecies bulgaricus.
abstract: Lactobacillus delbrueckii has been widely used for yogurt fermentation. It has genes encoding both D- and L-type lactate dehydrogenases (LDHs) that catalyse the production of L(+) or D(-) stereoisomer of lactic acid. D-lactic acid is the primary lactate product by L. delbrueckii, yet it cannot be metabolised by human intestine. Since it has been domesticated for long time, an interesting question arises regarding to whether the selection pressure has affected the evolution of both L-LDH and D-LDH genes in the genome. To answer this question, in this study the authors first investigated the evolution of these two genes by constructing phylogenetic trees. They found that D-LDH-based phylogenetic tree could better represent the phylogenetic relationship in the acidophilus complex than L-LDH-based tree. They next investigated the evolutions of LDH genes of L. delbrueckii at amino acid level, and found that D-LDH gene in L. delbrueckii is positively selected, possibly a consequence of long-term domestication. They further identified four amino acids that are under positive selection. One of them, V261, is located at the centre of three catalytic active sites, indicating likely functional effects on the enzyme activity. The selection from the domestication process thus provides direction for future engineering of D-LDH.
authors.affiliation: Department of Life Sciences, Huainan Normal University, Huainan 232001, People's Republic of China.
authors.forename: Jifeng
authors.initials: J
authors.lastname: Zhang
authors.affiliation: School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China.
authors.forename: Guangyu
authors.initials: G
authors.lastname: Gong
authors.affiliation: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200082, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200082, People's Republic of China. weidong.tian@fudan.edu.cn.
authors.forename: Weidong
authors.initials: W
authors.lastname: Tian
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D003198:Computer Simulation; D019143:Evolution, Molecular; D045022:Lactate Dehydrogenases / Q000235:genetics*; D048668:Lactobacillus delbrueckii / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D013045:Species Specificity
chemical_list: D045022:Lactate Dehydrogenases; C071195:D-lactate dehydrogenase