1
|
Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MC, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185:345-360.e28. [PMID: 35063075 PMCID: PMC9985924 DOI: 10.1016/j.cell.2021.12.025] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/01/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023]
Abstract
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.
Collapse
Affiliation(s)
- Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David M. Bianchi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler M. Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo C.R. Melo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nataliya Safronova
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - James P. Sáenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | | | - Kim S. Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | | | | | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NSF Center for the Physics of Living Cells, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.
| |
Collapse
|
2
|
Proteases as Secreted Exoproteins in Mycoplasmas from Ruminant Lungs and Their Impact on Surface-Exposed Proteins. Appl Environ Microbiol 2019; 85:AEM.01439-19. [PMID: 31540994 DOI: 10.1128/aem.01439-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022] Open
Abstract
Many mycoplasma species are isolated from the ruminant lungs as either saprophytes or true pathogens. These wall-less bacteria possess a minimal genome and reduced metabolic capabilities. Accordingly, they rely heavily on their hosts for the supply of essential metabolites and, notably, peptides. Seven of 13 ruminant lung-associated Mycoplasma (sub)species were shown to possess caseinolytic activity when grown in rich media and assessed with a quantitative fluorescence test. For some species, this activity was detected in spent medium, an indication that proteases were secreted outside the mycoplasma cells. To identify these proteases, we incubated concentrated washed cell pellets in a defined medium and analyzed the supernatants by tandem mass spectrometry. Secreted-protease activity was detected mostly in the species belonging to the Mycoplasma mycoides cluster (MMC) and, to a lesser extent, in Mycoplasma bovirhinis Analyzing a Mycoplasma mycoides subsp. capri strain, chosen as a model, we identified 35 expressed proteases among 55 predicted coding genes, of which 5 were preferentially found in the supernatant. Serine protease S41, acquired by horizontal gene transfer, was responsible for the caseinolytic activity, as demonstrated by zymography and mutant analysis. In an M. capricolum mutant, inactivation of the S41 protease resulted in marked modification of the expression or secretion of 17 predicted surface-exposed proteins. This is an indication that the S41 protease could have a role in posttranslational cleavage of surface-exposed proteins and ectodomain shedding, whose physiological impacts still need to be explored.IMPORTANCE Few studies pertaining to proteases in ruminant mycoplasmas have been reported. Here, we focus on proteases that are secreted outside the mycoplasma cell using a mass spectrometry approach. The most striking result is the identification, within the Mycoplasma mycoides cluster, of a serine protease that is exclusively detected outside the mycoplasma cells and is responsible for casein digestion. This protease may also be involved in the posttranslational processing of surface proteins, as suggested by analysis of mutants showing a marked reduction in the secretion of extracellular proteins. By analogy, this finding may help increase understanding of the mechanisms underlying this ectodomain shedding in other mycoplasma species. The gene encoding this protease is likely to have been acquired via horizontal gene transfer from Gram-positive bacteria and sortase-associated surface proteases. Whether this protease and the associated ectodomain shedding are related to virulence has yet to be ascertained.
Collapse
|
3
|
Bastos PAD, da Costa JP, Vitorino R. A glimpse into the modulation of post-translational modifications of human-colonizing bacteria. J Proteomics 2016; 152:254-275. [PMID: 27888141 DOI: 10.1016/j.jprot.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/22/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.
Collapse
Affiliation(s)
- Paulo André Dias Bastos
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Chemistry, University of Aveiro, Portugal
| | | | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
| |
Collapse
|
4
|
Daubenspeck JM, Liu R, Dybvig K. Rhamnose Links Moonlighting Proteins to Membrane Phospholipid in Mycoplasmas. PLoS One 2016; 11:e0162505. [PMID: 27603308 PMCID: PMC5014317 DOI: 10.1371/journal.pone.0162505] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/23/2016] [Indexed: 11/18/2022] Open
Abstract
Many proteins that have a primary function as a cytoplasmic protein are known to have the ability to moonlight on the surface of nearly all organisms. An example is the glycolytic enzyme enolase, which can be found on the surface of many types of cells from bacteria to human. Surface enolase is not enzymatic because it is monomeric and oligomerization is required for glycolytic activity. It can bind various molecules and activate plasminogen. Enolase lacks a signal peptide and the mechanism by which it attaches to the surface is unknown. We found that treatment of whole cells of the murine pathogen Mycoplasma pulmonis with phospholipase D released enolase and other common moonlighting proteins. Glycostaining suggested that the released proteins were glycosylated. Cytoplasmic and membrane-bound enolase was isolated by immunoprecipitation. No post-translational modification was detected on cytoplasmic enolase, but membrane enolase was associated with lipid, phosphate and rhamnose. Treatment with phospholipase released the lipid and phosphate from enolase but not the rhamnose. The site of rhamnosylation was identified as a glutamine residue near the C-terminus of the protein. Rhamnose has been found in all species of mycoplasma examined but its function was previously unknown. Mycoplasmas are small bacteria with have no peptidoglycan, and rhamnose in these organisms is also not associated with polysaccharide. We suggest that rhamnose has a central role in anchoring proteins to the membrane by linkage to phospholipid, which may be a general mechanism for the membrane association of moonlighting proteins in mycoplasmas and perhaps other bacteria.
Collapse
Affiliation(s)
- James M. Daubenspeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Runhua Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Kevin Dybvig
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
- * E-mail:
| |
Collapse
|
5
|
Schäffer C, Messner P. Emerging facets of prokaryotic glycosylation. FEMS Microbiol Rev 2016; 41:49-91. [PMID: 27566466 DOI: 10.1093/femsre/fuw036] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/17/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N- and O-glycosylation, can be found in all three domains of life-the Eukarya, Bacteria and Archaea-thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N- and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes.
Collapse
Affiliation(s)
- Christina Schäffer
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
| |
Collapse
|
6
|
Daubenspeck JM, Jordan DS, Simmons W, Renfrow MB, Dybvig K. General N-and O-Linked Glycosylation of Lipoproteins in Mycoplasmas and Role of Exogenous Oligosaccharide. PLoS One 2015; 10:e0143362. [PMID: 26599081 PMCID: PMC4657876 DOI: 10.1371/journal.pone.0143362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022] Open
Abstract
The lack of a cell wall, flagella, fimbria, and other extracellular appendages and the possession of only a single membrane render the mycoplasmas structurally simplistic and ideal model organisms for the study of glycoconjugates. Most species have genomes of about 800 kb and code for few proteins predicted to have a role in glycobiology. The murine pathogens Mycoplasma arthritidis and Mycoplasma pulmonis have only a single gene annotated as coding for a glycosyltransferase but synthesize glycolipid, polysaccharide and glycoproteins. Previously, it was shown that M. arthritidis glycosylated surface lipoproteins through O-linkage. In the current study, O-linked glycoproteins were similarly found in M. pulmonis and both species of mycoplasma were found to also possess N-linked glycans at residues of asparagine and glutamine. Protein glycosylation occurred at numerous sites on surface-exposed lipoproteins with no apparent amino acid sequence specificity. The lipoproteins of Mycoplasma pneumoniae also are glycosylated. Glycosylation was dependent on the glycosidic linkages from host oligosaccharides. As far as we are aware, N-linked glycoproteins have not been previously described in Gram-positive bacteria, the organisms to which the mycoplasmas are phylogenetically related. The findings indicate that the mycoplasma cell surface is heavily glycosylated with implications for the modulation of mycoplasma-host interactions.
Collapse
Affiliation(s)
- James M. Daubenspeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David S. Jordan
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Warren Simmons
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Kevin Dybvig
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
7
|
Schieck E, Lartigue C, Frey J, Vozza N, Hegermann J, Miller RA, Valguarnera E, Muriuki C, Meens J, Nene V, Naessens J, Weber J, Lowary TL, Vashee S, Feldman MF, Jores J. Galactofuranose in Mycoplasma mycoides is important for membrane integrity and conceals adhesins but does not contribute to serum resistance. Mol Microbiol 2015; 99:55-70. [PMID: 26354009 DOI: 10.1111/mmi.13213] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 12/20/2022]
Abstract
Mycoplasma mycoides subsp. capri (Mmc) and subsp. mycoides (Mmm) are important ruminant pathogens worldwide causing diseases such as pleuropneumonia, mastitis and septicaemia. They express galactofuranose residues on their surface, but their role in pathogenesis has not yet been determined. The M. mycoides genomes contain up to several copies of the glf gene, which encodes an enzyme catalysing the last step in the synthesis of galactofuranose. We generated a deletion of the glf gene in a strain of Mmc using genome transplantation and tandem repeat endonuclease coupled cleavage (TREC) with yeast as an intermediary host for the genome editing. As expected, the resulting YCp1.1-Δglf strain did not produce the galactofuranose-containing glycans as shown by immunoblots and immuno-electronmicroscopy employing a galactofuranose specific monoclonal antibody. The mutant lacking galactofuranose exhibited a decreased growth rate and a significantly enhanced adhesion to small ruminant cells. The mutant was also 'leaking' as revealed by a β-galactosidase-based assay employing a membrane impermeable substrate. These findings indicate that galactofuranose-containing polysaccharides conceal adhesins and are important for membrane integrity. Unexpectedly, the mutant strain showed increased serum resistance.
Collapse
Affiliation(s)
- Elise Schieck
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Carole Lartigue
- UMR 1332 Biologie du Fruit et Pathologie, The French National Institute for Agricultural Research, INRA-Université Bordeaux, Segalen, 71, avenue Edouard Bourlaux, CS20032, F-33882, Villenave D'Ornon CEDEX, Bordeaux, France.,UMR 1332 de Biologie du Fruit et Pathologie, Université Bordeaux, F-33140, Villenave d'Ornon, Bordeaux, France
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, CH-3001, Bern, Switzerland
| | - Nicolas Vozza
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Ezequiel Valguarnera
- Department of Molecular Microbiology, Washington University School of Medicine St Louis, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Cecilia Muriuki
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Vish Nene
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Jan Naessens
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Johann Weber
- Center for Integrative Genomics, Lausanne Genomic Technologies Facility,University of Lausanne, Lausanne, Switzerland
| | - Todd L Lowary
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Sanjay Vashee
- J. Craig Venter Institute, 9704 Medical Center Drive, MD 20850, Rockville, USA
| | - Mario F Feldman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.,Department of Molecular Microbiology, Washington University School of Medicine St Louis, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Joerg Jores
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya.,Institute of Veterinary Bacteriology, University of Bern, CH-3001, Bern, Switzerland
| |
Collapse
|
8
|
Iverson-Cabral SL, Wood GE, Totten PA. Analysis of the Mycoplasma genitalium MgpB Adhesin to Predict Membrane Topology, Investigate Antibody Accessibility, Characterize Amino Acid Diversity, and Identify Functional and Immunogenic Epitopes. PLoS One 2015; 10:e0138244. [PMID: 26381903 PMCID: PMC4575044 DOI: 10.1371/journal.pone.0138244] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/27/2015] [Indexed: 12/23/2022] Open
Abstract
Mycoplasma genitalium is a sexually transmitted pathogen and is associated with reproductive tract disease that can be chronic in nature despite the induction of a strong antibody response. Persistent infection exacerbates the likelihood of transmission, increases the risk of ascension to the upper tract, and suggests that M. genitalium may possess immune evasion mechanism(s). Antibodies from infected patients predominantly target the MgpB adhesin, which is encoded by a gene that recombines with homologous donor sequences, thereby generating sequence variation within and among strains. We have previously characterized mgpB heterogeneity over the course of persistent infection and have correlated the induction of variant-specific antibodies with the loss of that particular variant from the infected host. In the current study, we examined the membrane topology, antibody accessibility, distribution of amino acid diversity, and the location of functional and antigenic epitopes within the MgpB adhesin. Our results indicate that MgpB contains a single transmembrane domain, that the majority of the protein is surface exposed and antibody accessible, and that the attachment domain is located within the extracellular C-terminus. Not unexpectedly, amino acid diversity was concentrated within and around the three previously defined variable regions (B, EF, and G) of MgpB; while nonsynonymous mutations were twice as frequent as synonymous mutations in regions B and G, region EF had equal numbers of nonsynonymous and synonymous mutations. Interestingly, antibodies produced during persistent infection reacted predominantly with the conserved C-terminus and variable region B. In contrast, infection-induced antibodies reacted poorly with the N-terminus, variable regions EF and G, and intervening conserved regions despite the presence of predicted B cell epitopes. Overall, this study provides an important foundation to define how different segments of the MgpB adhesin contribute to functionality, variability, and immunogenicity during persistent M. genitalium infection.
Collapse
Affiliation(s)
- Stefanie L. Iverson-Cabral
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, WA, United States of America
| | - Gwendolyn E. Wood
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, WA, United States of America
| | - Patricia A. Totten
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, WA, United States of America
- Department of Global Health, Pathobiology Interdisciplinary Program, University of Washington, Seattle, WA, United States of America
| |
Collapse
|
9
|
Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K. Comparative genome analysis of Mycoplasma pneumoniae. BMC Genomics 2015; 16:610. [PMID: 26275904 PMCID: PMC4537597 DOI: 10.1186/s12864-015-1801-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/29/2015] [Indexed: 12/30/2022] Open
Abstract
Background Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England. Results Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99 % identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes. Conclusions These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1801-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Li Xiao
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Travis Ptacek
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - John D Osborne
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Donna M Crabb
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Warren L Simmons
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Elliot J Lefkowitz
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Ken B Waites
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - T Prescott Atkinson
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Kevin Dybvig
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| |
Collapse
|