Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232

Persistent Link:
http://hdl.handle.net/10150/610026
Title:
Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232
Author:
Pendarvis, Ken; Padula, Matthew; Tacchi, Jessica; Petersen, Andrew; Djordjevic, Steven; Burgess, Shane; Minion, F.
Affiliation:
Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA; ithree institute, University of Technology, Sydney, Australia; Proteomics Core Facility, Faculty of Science, University of Technology, Sydney, Australia; Bio5 Institute, School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
Issue Date:
2014
Publisher:
BioMed Central
Citation:
Pendarvis et al. BMC Genomics 2014, 15:576 http://www.biomedcentral.com/1471-2164/15/576
Journal:
BMC Genomics
Rights:
© 2014 Pendarvis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-15-576
Keywords:
Mycoplasma hyopneumoniae; Proteome; Swine pathogen; Proteogenomic; Mapping; Mass spectrometry
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/15/576

Full metadata record

DC FieldValue Language
dc.contributor.authorPendarvis, Kenen
dc.contributor.authorPadula, Matthewen
dc.contributor.authorTacchi, Jessicaen
dc.contributor.authorPetersen, Andrewen
dc.contributor.authorDjordjevic, Stevenen
dc.contributor.authorBurgess, Shaneen
dc.contributor.authorMinion, F.en
dc.date.accessioned2016-05-20T08:56:49Z-
dc.date.available2016-05-20T08:56:49Z-
dc.date.issued2014en
dc.identifier.citationPendarvis et al. BMC Genomics 2014, 15:576 http://www.biomedcentral.com/1471-2164/15/576en
dc.identifier.doi10.1186/1471-2164-15-576en
dc.identifier.urihttp://hdl.handle.net/10150/610026-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/15/576en
dc.rights© 2014 Pendarvis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectMycoplasma hyopneumoniaeen
dc.subjectProteomeen
dc.subjectSwine pathogenen
dc.subjectProteogenomicen
dc.subjectMappingen
dc.subjectMass spectrometryen
dc.titleProteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232en
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USAen
dc.contributor.departmentSchool of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentithree institute, University of Technology, Sydney, Australiaen
dc.contributor.departmentProteomics Core Facility, Faculty of Science, University of Technology, Sydney, Australiaen
dc.contributor.departmentBio5 Institute, School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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