title: Complexity of the Mycoplasma fermentans M64 genome and metabolic essentiality and diversity among mycoplasmas.
abstract: Recently, the genomes of two Mycoplasma fermentans strains, namely M64 and JER, have been completely sequenced. Gross comparison indicated that the genome of M64 is significantly bigger than the other strain and the difference is mainly contributed by the repetitive sequences including seven families of simple and complex transposable elements ranging from 973 to 23,778 bps. Analysis of these repeats resulted in the identification of a new distinct family of Integrative Conjugal Elements of M. fermentans, designated as ICEF-III. Using the concept of "reaction connectivity", the metabolic capabilities in M. fermentans manifested by the complete and partial connected biomodules were revealed. A comparison of the reported M. pulmonis, M. arthritidis, M. genitalium, B. subtilis, and E. coli essential genes and the genes predicted from the M64 genome indicated that more than 73% of the Mycoplasmas essential genes are preserved in M. fermentans. Further examination of the highly and partly connected reactions by a novel combinatorial phylogenetic tree, metabolic network, and essential gene analysis indicated that some of the pathways (e.g. purine and pyrimidine metabolisms) with partial connected reactions may be important for the conversions of intermediate metabolites. Taken together, in light of systems and network analyses, the diversity among the Mycoplasma species was manifested on the variations of their limited metabolic abilities during evolution.
authors.affiliation: Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China.
authors.forename: Hung-Wei
authors.initials: HW
authors.lastname: Shu
authors.forename: Tze-Tze
authors.initials: TT
authors.lastname: Liu
authors.forename: Huang-I
authors.initials: HI
authors.lastname: Chan
authors.forename: Yen-Ming
authors.initials: YM
authors.lastname: Liu
authors.forename: Keh-Ming
authors.initials: KM
authors.lastname: Wu
authors.forename: Hung-Yu
authors.initials: HY
authors.lastname: Shu
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Tsai
authors.forename: Kwang-Jen
authors.initials: KJ
authors.lastname: Hsiao
authors.forename: Wensi S
authors.initials: WS
authors.lastname: Hu
authors.forename: Wailap Victor
authors.initials: WV
authors.lastname: Ng
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D017124:Conserved Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D016858:Mycoplasma fermentans / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial