Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232

Pendarvis, K; Padula, MP; Tacchi, JL; Petersen, AC; Djordjevic, SP; Burgess, SC; Minion, FC

Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232

Pendarvis, K Padula, MP

Tacchi, JL Petersen, AC Djordjevic, SP

Burgess, SC Minion, FC

Permalink

Publication Type:: Journal Article
Citation:: BMC Genomics, 2014, 15 (1)
Issue Date:: 2014-07-08

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Accepted Manuscript VersionAdobe PDF (294.95 kB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Pendarvis, K	en_US
dc.contributor.author	Padula, MP https://orcid.org/0000-0002-8283-0643	en_US
dc.contributor.author	Tacchi, JL	en_US
dc.contributor.author	Petersen, AC	en_US
dc.contributor.author	Djordjevic, SP https://orcid.org/0000-0001-9301-5372	en_US
dc.contributor.author	Burgess, SC	en_US
dc.contributor.author	Minion, FC	en_US
dc.date.available	2014-07-01	en_US
dc.date.issued	2014-07-08	en_US
dc.identifier.citation	BMC Genomics, 2014, 15 (1)	en_US
dc.identifier.uri	http://hdl.handle.net/10453/116059
dc.description.abstract	Background: Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is one of the smallest and best annotated microbial genomes, containing only 728 annotated genes and 691 known proteins. Standard protein databases for mass spectrometry only allow for the identification of known and predicted proteins, which if incorrect can limit our understanding of the biological processes at work. Proteogenomic mapping is a methodology which allows the entire 6-frame genome translation of an organism to be used as a mass spectrometry database to help identify unknown proteins as well as correct and confirm existing annotations. This methodology will be employed to perform an in-depth analysis of the M. hyopneumoniae proteome.Results: Proteomic analysis indicates 483 of 691 (70%) known M. hyopneumoniae strain 232 proteins are expressed under the culture conditions given in this study. Furthermore, 171 of 328 (52%) hypothetical proteins have been confirmed. Proteogenomic mapping resulted in the identification of previously unannotated genes gatC and rpmF and 5-prime extensions to genes mhp063, mhp073, and mhp451, all conserved and annotated in other M. hyopneumoniae strains and Mycoplasma species. Gene prediction with Prodigal, a prokaryotic gene predicting program, completely supports the new genomic coordinates calculated using proteogenomic mapping.Conclusions: Proteogenomic mapping showed that the protein coding genes of the M. hyopneumoniae strain 232 identified in this study are well annotated. Only 1.8% of mapped peptides did not correspond to genes defined by the current genome annotation. This study also illustrates how proteogenomic mapping can be an important tool to help confirm, correct and append known gene models when using a genome sequence as search space for peptide mass spectra. Using a gene prediction program which scans for a wide variety of promoters can help ensure genes are accurately predicted or not missed completely. Furthermore, protein extraction using differential detergent fractionation effectively increases the number of membrane and cytoplasmic proteins identifiable my mass spectrometry. © 2014 Pendarvis et al.; licensee BioMed Central Ltd.	en_US
dc.relation.ispartof	BMC Genomics	en_US
dc.relation.isbasedon	10.1186/1471-2164-15-576	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Mycoplasma hyopneumoniae	en_US
dc.subject.mesh	Bacterial Proteins	en_US
dc.subject.mesh	Proteome	en_US
dc.subject.mesh	Chromosome Mapping	en_US
dc.subject.mesh	Virulence	en_US
dc.subject.mesh	Genome, Bacterial	en_US
dc.subject.mesh	Open Reading Frames	en_US
dc.subject.mesh	Tandem Mass Spectrometry	en_US
dc.subject.mesh	Gene Ontology	en_US
dc.title	Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232	en_US
dc.type	Journal Article
utslib.citation.volume	1	en_US
utslib.citation.volume	15	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	1107 Immunology	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
utslib.for	11 Medical and Health Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.issue	1	en_US
pubs.publication-status	Published	en_US
pubs.volume	15	en_US

Abstract:

Background: Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is one of the smallest and best annotated microbial genomes, containing only 728 annotated genes and 691 known proteins. Standard protein databases for mass spectrometry only allow for the identification of known and predicted proteins, which if incorrect can limit our understanding of the biological processes at work. Proteogenomic mapping is a methodology which allows the entire 6-frame genome translation of an organism to be used as a mass spectrometry database to help identify unknown proteins as well as correct and confirm existing annotations. This methodology will be employed to perform an in-depth analysis of the M. hyopneumoniae proteome.Results: Proteomic analysis indicates 483 of 691 (70%) known M. hyopneumoniae strain 232 proteins are expressed under the culture conditions given in this study. Furthermore, 171 of 328 (52%) hypothetical proteins have been confirmed. Proteogenomic mapping resulted in the identification of previously unannotated genes gatC and rpmF and 5-prime extensions to genes mhp063, mhp073, and mhp451, all conserved and annotated in other M. hyopneumoniae strains and Mycoplasma species. Gene prediction with Prodigal, a prokaryotic gene predicting program, completely supports the new genomic coordinates calculated using proteogenomic mapping.Conclusions: Proteogenomic mapping showed that the protein coding genes of the M. hyopneumoniae strain 232 identified in this study are well annotated. Only 1.8% of mapped peptides did not correspond to genes defined by the current genome annotation. This study also illustrates how proteogenomic mapping can be an important tool to help confirm, correct and append known gene models when using a genome sequence as search space for peptide mass spectra. Using a gene prediction program which scans for a wide variety of promoters can help ensure genes are accurately predicted or not missed completely. Furthermore, protein extraction using differential detergent fractionation effectively increases the number of membrane and cytoplasmic proteins identifiable my mass spectrometry. © 2014 Pendarvis et al.; licensee BioMed Central Ltd.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/116059