Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches

Journal of Proteomics

Volumn 83, Issue , 2013, Pages 99-118

  Shabbiri, Khadija ^a,b   Botting, Catherine H ^a   Adnan, Ahmad ^b   Fuszard, Matthew ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b GC UNIVERSITY   (Pakistan)

Author keywords

Actinobacteria; B. linens; Cellular proteome; De novo sequencing; Extracellular proteome; NLC MS MS

Indexed keywords

CELL PROTEIN;

ARTICLE; BREVIBACTERIUM LINENS; CELL CULTURE; CELL GROWTH; GENE SEQUENCE; GENOME; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE HOMOLOGY;

BACTERIAL PROTEINS; BREVIBACTERIUM; GENOME, BACTERIAL; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

ACTINOBACTERIA; BREVIBACTERIUM LINENS;

EID: 84876463512     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.02.029     Document Type: Article

References (30)

1. Rattray F.P., Fox P.F. Aspects of enzymology and biochemical properties of Brevibacterium linens relevant to cheese ripening: a review. J Dairy Sci 1999, 82:891-909.
2. Onraedt A., Soetaert W., Vandamme E. Industrial importance of the genus Brevibacterium. Biotechnol Lett 2005, 27:527-533.
3. Oberreuter H., Charzinski J., Scherer S. Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. Microbiology 2002, 148:1523-1532.
4. Bott M., Niebisch A. The respiratory chain of Corynebacterium glutamicum. J Biotechnol 2003, 104:129-153.
5. Domon B., Aebersold R. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
6. Shirran S.L., Botting C.H. A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods. J Proteomics 2010, 73:1391-1403.
7. Hahne H., Wolff S., Hecker M., Becher D. From complementarity to comprehensiveness-targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 2008, 8:4123-4136.
8. Frohlich T., Arnold G.J., Fritsch R., Mayr T., Laforsch C. LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia. BMC Genomics 2009, 10:171.
9. Fu Z., Sun Y., Xia L., Ding X., Mo X., Li X., et al. Assessment of protoxin composition of Bacillus thuringiensis strains by use of polyacrylamide gel block and mass spectrometry. Appl Microbiol Biotechnol 2008, 79:875-880.
10. Junqueira M., Spirin V., Balbuena T.S., Thomas H., Adzhubei I., Sunyaev S., et al. Protein identification pipeline for the homology-driven proteomics. J Proteomics 2008, 71:346-356.
11. Asryants R.A., Duszenkova I.V., Nagradova N.K. Determination of Sepharose-bound protein with Coomassie brilliant blue G-250. Anal Biochem 1985, 151:571-574.
12. Nandakumar M.P., Cheung A., Marten M.R. Proteomic analysis of extracellular proteins from Escherichia coli W3110. J Proteome Res 2006, 5:1155-1161.
13. Thippeswamy S., Girigowda K., Mulimani V.H. Isolation and identification of alpha-amylase producing Bacillus sp. from dhal industry waste. Indian J Biochem Biophys 2006, 43:295-298.
14. Shevchenko A., Wilm M., Vorm O., Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996, 68:850-858.
15. Ahmad W., Shabbiri K., Adnan A. Exploration of respiratory chain of Nocardia asteroides: purification of succinate quinone oxidoreductase. J Membr Biol 2012, 245:89-95.
16. Schagger H., von Jagow G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100kDa. Anal Biochem 1987, 166:368-379.
17. Habermann B., Oegema J., Sunyaev S., Shevchenko A. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics 2004, 3:238-249.
18. Len A.C., Cordwell S.J., Harty D.W., Jacques N.A. Cellular and extracellular proteome analysis of Streptococcus mutans grown in a chemostat. Proteomics 2003, 3:627-646.
19. Cobos R., Barreiro C., Mateos R.M., Coque J.J. Cytoplasmic- and extracellular-proteome analysis of Diplodia seriata: a phytopathogenic fungus involved in grapevine decline. Proteome Sci 2010, 8:46.
20. Ventura M., Canchaya C., Tauch A., Chandra G., Fitzgerald G.F., Chater K.F., et al. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 2007, 71:495-548.
21. Birrell G.W., Earl S., Masci P.P., de Jersey J., Wallis T.P., Gorman J.J., et al. Molecular diversity in venom from the Australian brown snake, Pseudonaja textilis. Mol Cell Proteomics 2006, 5:379-389.
22. Xu C., Ma B. Software for computational peptide identification from MS-MS data. Drug Discov Today 2006, 11:595-600.
23. Tannu N.S., Hemby S.E. De novo protein sequence analysis of Macaca mulatta. BMC Genomics 2007, 8:270.
24. Yergey A.L., Coorssen J.R., Backlund P.S., Blank P.S., Humphrey G.A., Zimmerberg J., et al. De novo sequencing of peptides using MALDI/TOF-TOF. J Am Soc Mass Spectrom 2002, 13:784-791.
25. Banu S., Honore N., Saint-Joanis B., Philpott D., Prevost M.C., Cole S.T. Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens?. Mol Microbiol 2002, 44:9-19.
26. Delogu G., Brennan M.J. Comparative immune response to PE and PE_PGRS antigens of Mycobacterium tuberculosis. Infect Immun 2001, 69:5606-5611.
27. Lykidis A., Mavromatis K., Ivanova N., Anderson I., Land M., DiBartolo G., et al. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol 2007, 189:2477-2486.
28. Wang D.Z., Li C., Xie Z.X., Dong H.P., Lin L., Hong H.S. Homology-driven proteomics of dinoflagellates with unsequenced genomes using MALDI-TOF/TOF and automated de novo sequencing. Evid Based Complement Alternat Med 2011, 2011:471020.
29. Wei N., Deng X.W. Making sense of the COP9 signalosome. A regulatory protein complex conserved from Arabidopsis to human. Trends Genet 1999, 15:98-103.
30. Liska A.J., Shevchenko A. Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications. Proteomics 2003, 3:19-28.