July 19, 2019  |  

Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.

In the bacterial world, methylation is most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, it is known that methylation plays functionally important roles, including timing of DNA replication, chromosome partitioning, DNA repair, and regulation of gene expression. However, full DNA methylome analyses are scarce due to a lack of a simple methodology for rapid and sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule Real-Time (SMRT) sequencing to determine the methylomes of two related human pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with single-base resolution. Our analysis identified two new methylation motifs not previously described in bacteria: a widespread 6 mA methylation motif common to both bacteria (5′-CTAT-3′), as well as a more complex Type I m6A sequence motif in M. pneumoniae (5′-GAN(7)TAY-3’/3′-CTN(7)ATR-5′). We identify the methyltransferase responsible for the common motif and suggest the one involved in M. pneumoniae only. Analysis of the distribution of methylation sites across the genome of M. pneumoniae suggests a potential role for methylation in regulating the cell cycle, as well as in regulation of gene expression. To our knowledge, this is one of the first direct methylome profiling studies with single-base resolution from a bacterial organism.


July 19, 2019  |  

Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.


July 7, 2019  |  

Analysis of the complete Mycoplasma hominis LBD-4 genome sequence reveals strain-variable prophage insertion and distinctive repeat-containing surface protein arrangements.

The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma arthritidis MAV-1. Comparative analysis with the genome of M. hominis PG21(T) reveals distinctive arrangements of repeat-containing surface proteins. Copyright © 2015 Calcutt and Foecking.


July 7, 2019  |  

Complete genome sequence of Mycoplasma flocculare strain Ms42T (ATCC 27399T).

Mycoplasma flocculare is a commensal or low-virulence pathogen of swine. The complete 778,866-bp genome sequence of M. flocculare strain Ms42(T) has been determined, enabling further comparison to genomes of the closely related pathogen Mycoplasma hyopneumoniae. The absence of the p97 and glpD genes may contribute to the attenuated virulence of M. flocculare. Copyright © 2015 Calcutt et al.


July 7, 2019  |  

Complete genome sequence of Mycoplasma yeatsii strain GM274B (ATCC 43094).

Mycoplasma yeatsii is a goat mycoplasma species that, although an obligate parasite, accommodates this lifestyle as an inapparent commensalist. High-frequency transformation has also been reported for this species. The complete 895,051-bp genome sequence of strain GM274B has been determined, enabling an analysis of the features of this potential cloning host. Copyright © 2015 Calcutt et al.


July 7, 2019  |  

Complete genome sequence of Mycoplasma synoviae strain WVU 1853T.

A hybrid sequence assembly of the complete Mycoplasma synoviae type strain WVU 1853T genome was compared to that of strain MS53. The findings support prior conclusions about M. synoviae, based on the genome of that otherwise uncharacterized field strain, and provide the first evidence of epigenetic modifications in M. synoviae.


July 7, 2019  |  

Complete genome sequence of Mycoplasma pneumoniae type 2 reference strain FH using single-molecule real-time sequencing technology.

Mycoplasma pneumoniae type 2 strain FH was previously sequenced with Illumina (FH-Illumina) and 454 (FH-454) technologies according to Xiao et al. (2015) and Krishnakumar et al. (2010). Comparative analyses revealed differences in genomic content between these sequences, including a 6-kb region absent from the FH-454 submission. Here, we present a complete genome sequence of FH sequenced with the Pacific Biosciences RSII platform. Copyright © 2017 Desai et al.


July 7, 2019  |  

Complete genome sequence of Mycoplasma bovis strain 08M.

Mycoplasma bovis is a major bacterial pathogen that can cause respiratory disease, mastitis, and arthritis in cattle. We report here the complete and annotated genome sequence of M. bovis strain 08M, isolated from a calf lung with pneumonia in China. Copyright © 2017 Chen et al.


July 7, 2019  |  

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate.

Mycoplasma hyopneumoniae is cultured on large-scale to produce antigen for inactivated whole-cell vaccines against respiratory disease in pigs. However, the fastidious nutrient requirements of this minimal bacterium and the low growth rate make it challenging to reach sufficient biomass yield for antigen production. In this study, we sequenced the genome of M. hyopneumoniae strain 11 and constructed a high quality constraint-based genome-scale metabolic model of 284 chemical reactions and 298 metabolites. We validated the model with time-series data of duplicate fermentation cultures to aim for an integrated model describing the dynamic profiles measured in fermentations. The model predicted that 84% of cellular energy in a standard M. hyopneumoniae cultivation was used for non-growth associated maintenance and only 16% of cellular energy was used for growth and growth associated maintenance. Following a cycle of model-driven experimentation in dedicated fermentation experiments, we were able to increase the fraction of cellular energy used for growth through pyruvate addition to the medium. This increase in turn led to an increase in growth rate and a 2.3 times increase in the total biomass concentration reached after 3-4 days of fermentation, enhancing the productivity of the overall process. The model presented provides a solid basis to understand and further improve M. hyopneumoniae fermentation processes. Biotechnol. Bioeng. 2017;114: 2339-2347. © 2017 Wiley Periodicals, Inc.© 2017 Wiley Periodicals, Inc.


July 7, 2019  |  

Complete genome sequence of Mycoplasma hyopneumoniae strain KM014, a clinical isolate from South Korea.

Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia, resulting in considerable economic losses in the swine industry. A few genome sequences of M. hyopneumoniae have been reported to date, implying that additional genome data are needed for further genetic studies. Here, we present the annotated genome sequence of M. hyopneumoniae strain KM014. Copyright © 2017 Han et al.


July 7, 2019  |  

Whole-genome sequence of Mycoplasma bovis strain Ningxia-1.

A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc. Copyright © 2018 Sun et al.


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