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.

The Integrative Conjugative Element (ICE) of Mycoplasma agalactiae : Key Elements Involved in Horizontal Dissemination and Influence of Coresident ICEs

“…The minimal ICEA chassis was consistent with the conservation of cds5 , cds17 , cds19 , and cds22 across documented ICEs of ruminant mycoplasma species ( 8 ) and with the occurrence of cds1 , cds14 , and cds16 at very similar locations in a majority of MICEs ( 2 , 4 – 6 , 23 ). Interestingly, the conjugative properties of M. agalactiae were also abrogated by mTn insertion in NCRs, raising questions regarding the presence of regulatory elements and/or key motifs, such as an oriT , in these regions.…”

The Integrative Conjugative Element (ICE) ofMycoplasma agalactiae: key elements involved in horizontal dissemination and influence of co-resident ICEs

“…The minimal ICEA chassis was consistent with the conservation of cds5, cds17, cds19 and cds22 across documented ICEs of ruminant mycoplasma species (8), and the occurrence of cds1, cds14 and cds16 at very similar location in a majority of MICEs (2, 4–6, 23). Interestingly, the conjugative properties of M. agalactiae were also abrogated by mTn insertion in NCRs raising questions regarding the presence of regulatory elements and/or key motifs, such as an oriT , in these regions.…”

Determination of metabolic activity in planktonic and biofilm cells of Mycoplasma fermentans and Mycoplasma pneumoniae by nuclear magnetic resonance

“…Mycoplasmas are characterised by limited biosynthetic capabilities, largely due to their minimal genome 32 , 33 . Loss of genes involved in biosynthesis of lipids, amino acids, vitamins and cofactors during their evolution 34 , 35 has resulted in a reliance on external nutrients from host cells in vivo or rich media in vitro 8 , 34 .…”

“…2 and 6 ). This finding would suggest that proline iminopeptidase (Pip) may release proline from peptide and the aspartate-ammonia ligase (AsnA) catalyses the interconversion of aspartate and asparagine 33 , and thus may be crucial for mycoplasma survival.…”