Classification of the genus Bacillus based on MALDI-TOF MS analysis of ribosomal proteins coded in S10 and spc operons

Journal of Agricultural and Food Chemistry

Volumn 59, Issue 10, 2011, Pages 5222-5230

  Hotta, Yudai ^a   Sato, Jun ^a   Sato, Hiroaki ^b   Hosoda, Akifumi ^a   Tamura, Hiroto ^a  

^a MEIJO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Bacterial identification; MALDI TOF MS; Ribosomal protein; S10 GERMS; S10 spc alpha operon

Indexed keywords

BACTERIAL IDENTIFICATIONS; MALDI-TOF MS; RIBOSOMAL PROTEIN; S10-GERMS; S10-SPC-ALPHA OPERON;

BACILLI; BACTERIOLOGY; BIOMARKERS; DESORPTION; GENES; MASS SPECTROMETERS; MASS SPECTROMETRY; POLYACRYLATES; RNA;

PROTEINS;

BACTERIAL DNA; BACTERIAL PROTEIN; RIBOSOME PROTEIN; RNA 16S;

ARTICLE; BACILLUS; BACILLUS SUBTILIS; CHEMISTRY; CLASSIFICATION; GENETICS; MASS SPECTROMETRY; OPERON; PHYLOGENY;

BACILLUS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; DNA, BACTERIAL; OPERON; PHYLOGENY; RIBOSOMAL PROTEINS; RNA, RIBOSOMAL, 16S; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

BACILLUS (BACTERIUM); BACILLUS SUBTILIS SUBSP. SPIZIZENII; BACILLUS SUBTILIS SUBSP. SUBTILIS; BACTERIA (MICROORGANISMS); LACTOBACILLUS CASEI; POSIBACTERIA;

EID: 79957952174     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf2004095     Document Type: Article

References (30)

1. Fenselau, C.; Demirev, P. A. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 2001, 20, 157-171. (Pubitemid 34151741)
2. Lay, J. O., Jr. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 2001, 20, 172-194.
3. Mellmann, A.; Cloud, J.; Maier, T.; Keckevoet, U.; Ramminger, I.; Iwen, P.; Dunn, J.; Hall, G.; Wilson, D.; Lasala, P.; Kostrzewa, M.; Harmsen, D. A. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J. Clin. Microbiol. 2008, 46, 1946-1954. (Pubitemid 351831825)
4. Welham, K. J.; Domin, M. A.; Scannell, D. E.; Cohen, E.; Ashton, D. S. The characterization of micro-organisms by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1998, 12, 176-180. (Pubitemid 28118253)
5. Arnold, R J.; Reilly, J. P. Fingerprint matching of E. coli strains with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach. Rapid Commun. Mass Spectrom. 1998, 12, 630-636. (Pubitemid 28222706)
6. Jarman, K. H.; Daly, D. S.; Petersen, C. E.; Saenz, A. J.; Valentine, N. B.; Wahl, K. L. Extracting and visualizing matrix-assisted laser desorption/ionization time-of-flight mass spectral fingerprints. Rapid Commun. Mass Spectrom. 1999, 13, 1586-1594. (Pubitemid 29365787)
7. Fagerquist, C. K.; Miller, W. G.; Harden, L. A.; Bates, A. H.; Vensel, W. H.; Wang, G.; Mandrell, R E. Genomic and proteomic identification of a DNA-binding protein used in the "fingerprinting" of campylobacter species and strains by MALDI-TOF-MS protein biomarker analysis. Anal. Chem. 2005, 77, 4897-4907. (Pubitemid 41076681)
8. Erhard, M.; Hipler, U. C.; Burmester, A.; Brakhage, A. A.; Wostemeyer, J. Identification of dermatophyte species causing onychomycosis and tinea pedis by MALDI-TOF mass spectrometry. Exp. Dermatol. 2008, 17, 356-361. (Pubitemid 351338680)
9. Cherkaoui, A.; Hibbs, J.; Emonet, S.; Tangomo, M.; Girard, M.; Francois, P.; Schrenzel, J. Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J. Clin. Microbiol. 2010, 48, 1169-1175.
10. Demirev, P. A.; Ho, Y.-P.; Ryzhov, V.; Fenselau, C. Microorganism identification by mass spectrometry and protein database searches. Anal. Chem. 1999, 71, 2732-2738. (Pubitemid 29340461)
11. Pineda, F. J.; Antoine, M. D.; Demirev, P. A.; Feldman, A. B.; Jackman, J.; Longenecker, M.; Lin, J. S. Microorganism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers. Anal. Chem. 2003, 75, 3817-3822. (Pubitemid 36962116)
12. Fagerquist, C. K.; Garbus, B. R.; Miller, W. G.; Williams, K. E.; Yee, E.; Bates, A. H.; Boyle, S.; Harden, L. A.; Cooley, M. B.; Mandrell, R E. Rapid identification of protein biomarkers of Escherichia coli O157: H7 by matrix-assisted laser desorption ionization-time-of-flight-timeof-flight mass spectrometry and top-down proteomics. Anal. Chem. 2010, 82, 2717-2725.
13. Teramoto, K.; Sato, H.; Sun, L.; Torimura, M.; Tao, H.; Yoshikawa, H.; Hotta, Y.; Hosoda, A.; Tamura, H. Phylogenetic classification of Pseudomonas putida strains by MALDI-MS using ribosomal subunit proteins as biomarkers. Anal. Chem. 2007, 79, 8712-8719. (Pubitemid 350171384)
14. Hotta, Y.; Teramoto, K.; Sato, H.; Yoshikawa, H.; Hosoda, A.; Tamura, H. Classification of genus Pseudomonas by MALDI-TOF MS based on ribosomal protein coding in S10-spc-alpha operon at strain level. J. Proteome Res. 2010, 9, 6722-6728.
15. Yamada, S.; Ohashi, E.; Agata, N.; Venkateswaran, K. Cloning and nucleotide sequence analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and their application to the detection of B. cereus in rice. Appl. Environ. Microbiol. 1999, 65, 1483-1490. (Pubitemid 29173675)
16. Schnepf, E.; Crickmore, N.; Van Rie, J.; Lereclus, D.; Baum, J.; Feitelson, J.; Zeigler, D. R.; Dean, D. H. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol. Mol. Biol. Rev. 1998, 62, 775-806. (Pubitemid 28415553)
17. Meerak, J.; Yukphan, P.; Miyashita, M.; Sato, H.; Nakagawa, Y.; Tahara, Y. Phylogeny of γ-polyglutamic acid-producing Bacillus strains isolated from a fermented locust bean product manufactured in West Africa. J. Gen. Appl. Microbiol. 2008, 54, 159-166.
18. Thompson, J. M.; Dodd, C. E. R.; Waites, W. M. Spoilage of bread by Bacillus. Int. Biodeterior. Biodegrad. 1993, 32, 55-66.
19. Sun, L.; Teramoto, K.; Sato, H.; Torimura, M.; Tao, H.; Shintani, T. Characterization of ribosomal proteins as biomarkers for matrix-assisted laser desorption/ionization mass spectral identification of Lactobacillus plantarum. Rapid Commun. Mass Spectrom. 2006, 20, 3789-3798. (Pubitemid 44935333)
20. Teramoto, K.; Kitagawa, W.; Sato, H.; Torimura, M.; Tamura, T.; Tao, H. Phylogenetic analysis of Rhodococcus erythropolis based on the variation of ribosomal proteins as observed by matrix-assisted laser desorption ionization-mass spectrometry without using genome information. J. Biosci. Bioeng. 2009, 108, 348-353.
21. Sherman, F.; Stewart, J. W.; Tsunasawa, S. Methionine or not methionine at the beginning of a protein. Bioessays 1985, 3, 27-31.
22. Tompson, J. D.; Gibson, T. J.; Plewniak, F.; Jeanmougin, F.; Higgins, D. G. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876-4882. (Pubitemid 28022245)
23. Kumar, S.; Tamura, K.; Nei, M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings Bioinf. 2004, 5, 150-163.
24. Lauber, M. A.; Running, W. E.; Reilly, J. P. B. subtilis ribosomal proteins: structural homology and post-translational modifications. J. Proteome Res. 2009, 8, 4193-4206.
25. Fritze, D. Taxonomy of the genus bacillus and related genera: the aerobic endospore-forming bacteria. Phytopathology 2004, 94, 1245-1248. (Pubitemid 39448203)
26. Noguchi, H.; Uchino, M.; Shida, O.; Takano, K.; Nakamura, L. K.; Komagata, K. Bacillus vietnamensis sp. nov, a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce. Int. J. Syst. Evol. Microbiol. 2004, 54, 2117-2120. (Pubitemid 39585397)
27. Cerritos, R.; Vinuesa, P.; Eguiarte, L. E.; Herrera-Estrella, L.; Alcaraz-Peraza, L. D.; Arvizu-Gomez, J. L.; Olmedo, G.; Ramirez, E.; Siefert, J. L.; Souza, V. Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Cienegas Valley in Coahuila, Mexico. Int. J. Syst. Evol. Microbiol. 2008, 58, 919-923.
28. Nakamura, L. K.; Roberts, M. S.; Cohan, F. M. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov, and Bacillus subtilis subsp. spizizenii subsp. nov. Int. J. Syst. Bacteriol. 1999, 49, 1211-1215.
29. Rooney, A. P.; Price, N. P.; Ehrhardt, C.; Swezey, J. L.; Bannan, J. D. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int. J. Syst. Evol. Microbiol. 2009, 59, 2429-2436.
30. Wang, L. T.; Lee, F. L.; Tai, C. J.; Kuo, H. P. Bacillus velezensis is a later heterotypic synonym of Bacillus amyloliquefaciens. Int. J. Syst. Evol. Microbiol. 2008, 58, 671-675.