Int J Biol Sci 2015; 11(1):11-21. doi:10.7150/ijbs.10320 This issue
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
3. College of Life Science and Agriculture, Cornell University, Ithaca 14850, NY, USA
4. School of Medicine, Lishui College, Lishui 323000, China
5. Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
6. The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
7. The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
# These authors contributed equally to this work.
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.
Keywords: comparative genomics, homocysteine methyltransferase gene, horizontal gene transfer, molecular variation