Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232
详细信息 查看全文
- 作者：Ken Pendarvis (29) (32)
Matthew P Padula (30) (31)
Jessica L Tacchi (30)
Andrew C Petersen (28)
Steven P Djordjevic (30) (31)
Shane C Burgess (29) (32)
F Chris Minion (28)
29. School of Animal and Comparative Biomedical Sciences ; University of Arizona ; Tucson ; AZ ; USA
32. Bio5 Institute ; School of Animal and Comparative Biomedical Sciences ; University of Arizona ; Tucson ; AZ ; USA
30. ithree institute ; University of Technology ; Sydney ; Australia
31. Proteomics Core Facility ; Faculty of Science ; University of Technology ; Sydney ; Australia
28. Department of Veterinary Microbiology and Preventive Medicine ; Iowa State University ; Ames ; IA ; USA - 关键词：Mycoplasma hyopneumoniae ; Proteome ; Swine pathogen ; Proteogenomic ; Mapping ; Mass spectrometry
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：287 KB
- 参考文献：1. Ross, R (1992) Diseases of swine. Dis Swine. Iowa State University Press, Ames, Iowa, U.S.A, pp. 537-551
2. Pointon, AM, Byrt, D, Heap, P (1985) Effect of enzootic pneumonia of pigs on growth performance. Aust Vet J 62: pp. 13-18
3. Adams, C, Pitzer, J, Minion, FC (2005) In vivo expression analysis of the P97 and P102 paralog families of Mycoplasma hyopneumoniae. Infect Immun 73: pp. 7784-7787 lass="external" href="http://dx.doi.org/10.1128/IAI.73.11.7784-7787.2005" target="_blank" title="It opens in new window">CrossRef
4. Madsen, ML, Nettleton, D, Thacker, EL, Edwards, R, Minion, FC (2006) Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect Immun 74: pp. 160-166 lass="external" href="http://dx.doi.org/10.1128/IAI.74.1.160-166.2006" target="_blank" title="It opens in new window">CrossRef
5. Madsen, ML, Nettleton, D, Thacker, EL, Minion, FC (2006) Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152: pp. 937-944 lass="external" href="http://dx.doi.org/10.1099/mic.0.28674-0" target="_blank" title="It opens in new window">CrossRef
6. Schafer, ER, Oneal, MJ, Madsen, ML, Minion, FC (2007) Global transcriptional analysis of Mycoplasma hyopneumoniae following exposure to hydrogen peroxide. Microbiology 153: pp. 3785-3790 lass="external" href="http://dx.doi.org/10.1099/mic.0.2007/011387-0" target="_blank" title="It opens in new window">CrossRef
7. Madsen, ML, Puttamreddy, S, Thacker, EL, Carruthers, MD, Minion, FC (2008) Transcriptome changes in Mycoplasma hyopneumoniae during infection. Infect Immun 76: pp. 658-663 lass="external" href="http://dx.doi.org/10.1128/IAI.01291-07" target="_blank" title="It opens in new window">CrossRef
8. Oneal, MJ, Schafer, ER, Madsen, ML, Minion, FC (2008) Global transcriptional analysis of Mycoplasma hyopneumoniae following exposure to norepinephrine. Microbiology 154: pp. 2581-2588 lass="external" href="http://dx.doi.org/10.1099/mic.0.2008/020230-0" target="_blank" title="It opens in new window">CrossRef
9. Gardner, SW, Minion, FC (2010) Detection and quantification of intergenic transcription in Mycoplasma hyopneumoniae. Microbiology 156: pp. 2305-2315 lass="external" href="http://dx.doi.org/10.1099/mic.0.038760-0" target="_blank" title="It opens in new window">CrossRef
10. Minion, FC, Lefkowitz, EJ, Madsen, ML, Cleary, BJ, Swartzell, SM, Mahairas, GG (2004) The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol 186: pp. 7123-7133 lass="external" href="http://dx.doi.org/10.1128/JB.186.21.7123-7133.2004" target="_blank" title="It opens in new window">CrossRef
11. Vasconcelos, ATR, Ferreira, HB, Bizarro, CV, Bonatto, SL, Carvalho, MO, Pinto, PM, Almeida, DF, Almeida, LGP, Almeida, R, Alves-Filho, L, Assun莽茫o, EN, Azevedo, VAC, Bogo, MR, Brigido, MM, Brocchi, M, Burity, HA, Camargo, AA, Camargo, SS, Carepo, MS, Carraro, DM, De Mattos Cascardo, JC, Castro, LA, Cavalcanti, G, Chemale, G, Collevatti, RG, Cunha, CW, Dallagiovanna, B, Dambr贸s, BP, Dellagostin, OA, Falc茫o, C (2005) Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol 187: pp. 5568-5577 lass="external" href="http://dx.doi.org/10.1128/JB.187.16.5568-5577.2005" target="_blank" title="It opens in new window">CrossRef
12. Liu, W, Feng, Z, Fang, L, Zhou, Z, Li, Q, Li, S, Luo, R, Wang, L, Chen, H, Shao, G, Xiao, S (2011) Complete genome sequence of Mycoplasma hyopneumoniae strain 168. J Bacteriol 193: pp. 1016-1017 lass="external" href="http://dx.doi.org/10.1128/JB.01305-10" target="_blank" title="It opens in new window">CrossRef
13. Craig, R, Beavis, RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20: pp. 1466-1467 lass="external" href="http://dx.doi.org/10.1093/bioinformatics/bth092" target="_blank" title="It opens in new window">CrossRef
14. Geer, LY, Markey, SP, Kowalak, JA, Wagner, L, Xu, M, Maynard, DM, Yang, X, Shi, W, Bryant, SH (2004) Open mass spectrometry search algorithm. J Proteome Res 3: pp. 958-964 lass="external" href="http://dx.doi.org/10.1021/pr0499491" target="_blank" title="It opens in new window">CrossRef
15. Pinto, PM, Chemale, G, De Castro, LA, Costa, APM, Kich, JD, Vainstein, MH, Zaha, A, Ferreira, HB (2007) Proteomic survey of the pathogenic Mycoplasma hyopneumoniae strain 7448 and identification of novel post-translationally modified and antigenic proteins. Vet Microbiol 121: pp. 83-93 lass="external" href="http://dx.doi.org/10.1016/j.vetmic.2006.11.018" target="_blank" title="It opens in new window">CrossRef
16. Pinto, PM, Klein, CS, Zaha, A, Ferreira, HB (2009) Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae. Proteome Sci 7: pp. 45 lass="external" href="http://dx.doi.org/10.1186/1477-5956-7-45" target="_blank" title="It opens in new window">CrossRef
17. Jaffe, JD, Berg, HC, Church, GM (2004) Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4: pp. 59-77 lass="external" href="http://dx.doi.org/10.1002/pmic.200300511" target="_blank" title="It opens in new window">CrossRef
18. Yuan, C, Yang, X, Yang, Z, Zhu, N, Zheng, S, Hou, P, Gu, X, Ye, C, Yao, C, Zhu, J, Cui, L, Hua, X (2010) Proteomic study of Mycoplasma suis using the gel-based shotgun strategy. Vet Microbiol 142: pp. 303-308 lass="external" href="http://dx.doi.org/10.1016/j.vetmic.2009.10.022" target="_blank" title="It opens in new window">CrossRef
19. Trimpin, S, Brizzard, B (2009) Analysis of insoluble proteins. Biotechniques 46: pp. 321-326 lass="external" href="http://dx.doi.org/10.2144/000113135" target="_blank" title="It opens in new window">CrossRef
20. Schlosser, A, Vanselow, JT, Kramer, A (2005) Mapping of phosphorylation sites by a multi-protease approach with specific phosphopeptide enrichment and NanoLC-MS/MS analysis. Anal Chem 77: pp. 5243-5250 lass="external" href="http://dx.doi.org/10.1021/ac050232m" target="_blank" title="It opens in new window">CrossRef
21. Wu, CC, MacCoss, MJ, Howell, KE, Yates, JR (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21: pp. 532-538 lass="external" href="http://dx.doi.org/10.1038/nbt819" target="_blank" title="It opens in new window">CrossRef
22. Mare, CJ, Switzer, WP (1965) New Species: Mycoplasma hyopneumoniae; a causative agent of virus pig pneumonia. Vet Med Small Anim Clin 60: pp. 841-846
23. Friis, NF (1975) Some recommendations concerning primary isolation of Mycoplasma suipneumoniae and Mycoplasma flocculare a survey. Nord Vet Med 27: pp. 337-339
24. McCarthy, FM, Burgess, SC, van den Berg, BHJ, Koter, MD, Pharr, GT (2005) Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics. J Proteome Res 4: pp. 316-324 lass="external" href="http://dx.doi.org/10.1021/pr049842d" target="_blank" title="It opens in new window">CrossRef
25. Deutscher, AT, Jenkins, C, Minion, FC, Seymour, LM, Padula, MP, Dixon, NE, Walker, MJ, Djordjevic, SP (2010) Repeat regions R1 and R2 in the P97 paralogue Mhp271 of Mycoplasma hyopneumoniae bind heparin, fibronectin and porcine cilia. Mol Microbiol 78: pp. 444-458 lass="external" href="http://dx.doi.org/10.1111/j.1365-2958.2010.07345.x" target="_blank" title="It opens in new window">CrossRef
26. Gatlin, CL, Kleemann, GR, Hays, LG, Link, AJ, Yates, JR (1998) Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal Biochem 263: pp. 93-101 lass="external" href="http://dx.doi.org/10.1006/abio.1998.2809" target="_blank" title="It opens in new window">CrossRef
27. Hyatt, D, Chen, G-L, Locascio, PF, Land, ML, Larimer, FW, Hauser, LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: pp. 119 lass="external" href="http://dx.doi.org/10.1186/1471-2105-11-119" target="_blank" title="It opens in new window">CrossRef
28. Vizca铆no, JA, C么t茅, RG, Csordas, A, Dianes, JA, Fabregat, A, Foster, JM, Griss, J, Alpi, E, Birim, M, Contell, J, O鈥橩elly, G, Schoenegger, A, Ovelleiro, D, P茅rez-Riverol, Y, Reisinger, F, R铆os, D, Wang, R, Hermjakob, H (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41: pp. D1063-D1069 lass="external" href="http://dx.doi.org/10.1093/nar/gks1262" target="_blank" title="It opens in new window">CrossRef - 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
文摘
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.