title: Molecular variation and horizontal gene transfer of the homocysteine methyltransferase gene mmuM and its distribution in clinical pathogens.
abstract: The homocysteine methyltransferase encoded by mmuM is widely distributed among microbial organisms. It is the key enzyme that catalyzes the last step in methionine biosynthesis and plays an important role in the metabolism process. It also enables the microbial organisms to tolerate high concentrations of selenium in the environment. In this research, 533 mmuM gene sequences covering 70 genera of the bacteria were selected from GenBank database. The distribution frequency of mmuM is different in the investigated genera of bacteria. The mapping results of 160 mmuM reference sequences showed that the mmuM genes were found in 7 species of pathogen genomes sequenced in this work. The polymerase chain reaction products of one mmuM genotype (NC_013951 as the reference) were sequenced and the sequencing results confirmed the mapping results. Furthermore, 144 representative sequences were chosen for phylogenetic analysis and some mmuM genes from totally different genera (such as the genes between Escherichia and Klebsiella and between Enterobacter and Kosakonia) shared closer phylogenetic relationship than those from the same genus. Comparative genomic analysis of the mmuM encoding regions on plasmids and bacterial chromosomes showed that pKF3-140 and pIP1206 plasmids shared a 21 kb homology region and a 4.9 kb fragment in this region was in fact originated from the Escherichia coli chromosome. These results further suggested that mmuM gene did go through the gene horizontal transfer among different species or genera of bacteria. High-throughput sequencing combined with comparative genomics analysis would explore distribution and dissemination of the mmuM gene among bacteria and its evolution at a molecular level.
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Jianchao
authors.initials: J
authors.lastname: Ying
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 2. National Institute of Biological Sciences, Beijing 102206, China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Wang
authors.affiliation: 3. College of Life Science and Agriculture, Cornell University, Ithaca 14850, NY, USA.
authors.forename: Bokan
authors.initials: B
authors.lastname: Bao
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Jinfang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhang
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Aifang
authors.initials: A
authors.lastname: Li
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 4. School of Medicine, Lishui College, Lishui 323000, China.
authors.forename: Junwan
authors.initials: J
authors.lastname: Lu
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Peizhen
authors.initials: P
authors.lastname: Li
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ying
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 5. Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Teng
authors.initials: T
authors.lastname: Xu
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Huiguang
authors.initials: H
authors.lastname: Yi
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Jinsong
authors.initials: J
authors.lastname: Li
authors.affiliation: 6. The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhou
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 6. The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China.
authors.forename: Tieli
authors.initials: T
authors.lastname: Zhou
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Zuyuan
authors.initials: Z
authors.lastname: Xu
authors.affiliation: 7. The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China.
authors.forename: Liyan
authors.initials: L
authors.lastname: Ni
authors.affiliation: 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China.
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Bao
mesh_terms: D001419:Bacteria / Q000201:enzymology*; D001483:Base Sequence; D002874:Chromosome Mapping; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D050904:Homocysteine S-Methyltransferase / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D050904:Homocysteine S-Methyltransferase
keywords: comparative genomics; homocysteine methyltransferase gene; horizontal gene transfer; molecular variation