The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria: amino acid, purine and pyrimidine metabolism in mollicutes

J., Dennis Pollack

doi:10.2741/pollack

Cited by 15 publications

(8 citation statements)

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“…Mycoplasmas contain a reduced genome; therefore, they lack many metabolic pathways, particularly biosynthetic pathways, such as those involved in cell-wall production, de novo purine biosynthesis and the biosynthesis of amino acids [73]. These organisms also lack a functional tricarboxylic acid (TCA) cycle because they are extremely fastidious in their nutritional requirements and dependent on nutrients supplied by their hosts.…”

Section: Resultsmentioning

confidence: 99%

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

et al. 2013

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BackgroundMycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.ResultsThe overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.ConclusionsThe comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host’s immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.

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Section: Resultsmentioning

confidence: 99%

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

et al. 2013

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“…Manual curation (supplementary materials) was performed using a decision scheme based on the presence or absence of functional protein domains and comparison to annotated genes in the M. hyopneumoniae reference genomes (strains: 232, J, 168, 168L, 7422, and 7448) and to the gene content of the M. pneumoniae metabolic model (Wodke et al, ). In line with previous studies (Pollack, ; Yus et al, ), we assumed broad substrate specificity for a number of enzymes in nucleotide metabolism. For instance, pyruvate kinase and the 5′‐nucleotidase were assumed to function with 8 nucleotide diphosphates as substrate.…”

Section: Methodsmentioning

confidence: 94%

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

Kamminga

Slagman

Bijlsma

et al. 2017

Biotech & Bioengineering

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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 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc.

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“…Note that samples were loaded onto the gel at different times, and thus, the plasmid migrated different distances in each lane. superfamily (MFS) primary active transporter, could be involved in nucleic acid precursor import (43). In addition, mollicutes are believed to have a relatively large number of multifunctional or substitute proteins, as exemplified by one protein that performs as both a lactate dehydrogenase and a malate dehydrogenase (44).…”

Section: Discussionmentioning

confidence: 99%

Disruption of the Membrane Nuclease Gene (MBOVPG45_0215) of Mycoplasma bovis Greatly Reduces Cellular Nuclease Activity

et al. 2015

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Although the complete genome sequences of three strains of Mycoplasma bovis are available, few studies have examined gene function in this important pathogen. Mycoplasmas lack the biosynthetic machinery for the de novo synthesis of nucleic acid precursors, so nucleases are likely to be essential for them to acquire nucleotide precursors. Three putative membrane nucleases have been annotated in the genome of M. bovis strain PG45, MBOVPG45_0089 and MBOVPG45_0310, both of which have the thermonuclease (TNASE_3) functional domain, and MBOVPG45_0215 (mnuA), which has an exonuclease/endonuclease/phosphatase domain. While previous studies have demonstrated the function of TNASE_3 domain nucleases in several mycoplasmas, quantitative comparisons of the contributions of different nucleases to cellular nuclease activity have been lacking. Mapping of a library of 319 transposon mutants of M. bovis PG45 by direct genome sequencing identified mutants with insertions in MBOVPG45_0310 (the ⌬0310 mutant) and MBOVPG45_0215 (the ⌬0215 mutant). In this study, the detection of the product of MBOVPG45_0215 in the Triton X-114 fraction of M. bovis cell lysates, its cell surface exposure, and its predicted signal peptide suggested that it is a surface-exposed lipoprotein nuclease. Comparison of a ⌬mnuA mutant with wild-type M. bovis on native and denatured DNA gels and in digestion assays using double-stranded phage DNA and closed circular plasmid DNA demonstrated that inactivation of this gene abolishes most of the cellular exonuclease and endonuclease activity of M. bovis. This activity could be fully restored by complementation with the wild-type mnuA gene, demonstrating that MnuA is the major cellular nuclease of M. bovis. IMPORTANCENucleases are thought to be important contributors to virulence and crucial for the maintenance of a nutritional supply of nucleotides in mycoplasmas that are pathogenic in animals. This study demonstrates for the first time that of the three annotated cell surface nuclease genes in an important pathogenic mycoplasma, the homologue of the thermostable nuclease identified in Gram-positive bacteria is responsible for the majority of the nuclease activity detectable in vitro.A lthough the complete genomes of many Mycoplasma species are now available, the scarcity of tools for exploring their molecular biology has resulted in an understanding of the function of their genes more rudimentary than that which is available for many other prokaryotes. The genomes of three strains of the important bovine pathogen Mycoplasma bovis, the type strain PG45, the Hubei-1 strain, and the HB0801 strain, have been sequenced and published recently (1-3), but apart from several reports on phase switching in M. bovis (4-7), few studies have examined the molecular mechanisms underlying their pathogenicity and virulence or the metabolic functions of the products of their genes.Mycoplasmas evolved from Clostridium-like bacteria by a process of reductive evolution and are believed to have retained only the regulatory and ...

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The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria: amino acid, purine and pyrimidine metabolism in mollicutes

Cited by 15 publications

References 65 publications

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

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

Disruption of the Membrane Nuclease Gene (MBOVPG45_0215) of Mycoplasma bovis Greatly Reduces Cellular Nuclease Activity

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