Proteotyping: Proteomic characterization, classification and identification of microorganisms - A prospectus

Systematic and Applied Microbiology

Volumn 38, Issue 4, 2015, Pages 246-257

  Karlsson, Roger ^a,b   Gonzales Siles, Lucia ^c   Boulund, Fredrik ^d   Svensson Stadler, Liselott ^a,c   Skovbjerg, Susann ^a,c   Karlsson, Anders ^b   Davidson, Max ^b   Hulth, Stefan ^e   Kristiansson, Erik ^d   Moore, Edward R B ^a,c,e  

^a SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^b NANOXIS CONSULTING AB   (Sweden)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

^d CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^e UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Mass spectrometry; Microbial systematics; Proteomics; Proteotyping

Indexed keywords

AMINO ACID SEQUENCE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BIOINFORMATICS; CELL FRACTIONATION; ION EXCHANGE CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROBIAL GENOME; MICROORGANISM DETECTION; NONHUMAN; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; SEQUENCE DATABASE; TANDEM MASS SPECTROMETRY; TAXONOMY; BACTERIUM; CHEMISTRY; CLASSIFICATION; MASS SPECTROMETRY;

BACTERIA (MICROORGANISMS);

BACTERIAL PROTEIN; PROTEOME;

BACTERIA; BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; MASS SPECTROMETRY; PROTEOME; PROTEOMICS;

EID: 84999491367     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2015.03.006     Document Type: Review

References (90)

1. Al-Shahib A., Misra R., Ahmod N., Fang M., Shah H., Gharbia S. Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics. BMC Bioinform. 2010, 11:437.
2. Armengaud J. A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr. Opin. Microbiol. 2009, 12:292-300.
3. Armengaud J. Microbiology and proteomics, getting the best of both worlds!. Environ. Microbiol. 2013, 15:12-23.
4. Arrigo K.R. Marine microorganisms and global nutrient cycles. Nature 2005, 437:349-355.
5. Awdeh Z.L., Williamson A.R., Askonas B.A. Isoelectric focusing in polyacrylamide gel and its application to immunoglobulins. Nature 1968, 219:66-67.
6. Backert S., Kwok T., Schmid M., Selbach M., Moese S., Peek R.M., Konig W., Meyer T.F., Jungblut P.R. Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proteomics 2005, 5:1331-1345.
7. Banks C.A.S., Lakshminarasimhan M., Washburn M.P. Shotgun Proteomics 2014, John Wiley & Sons, Ltd, Chichester, UK.
8. Biosca E.G., Garay E., Toranzo A.E., Amaro C. Comparison of outer membrane protein profiles of Vibrio vulnificus biotypes 1 and 2. FEMS Microbiol. Lett. 1993, 107:217-222.
9. Bissonnette L., Bergeron M.G. Infectious disease management through point-of-care personalized medicine molecular diagnostic technologies. J. Personalized Med. 2012, 2:50-70.
10. Bizzini A., Jaton K., Romo D., Bille J., Prod'hom G., Greub G. Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-to-identify bacterial strains. J. Clin. Microbiol. 2011, 49:693-696.
11. Cain T., Lubman D.M., Weber W.J. Differentiation of bacteria using protein profiles from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 8:1026-1030.
12. Cash P. Proteomics in the study of the molecular taxonomy and epidemiology of bacterial pathogens. Electrophoresis 2009, 30(Suppl. 1):S133-S141.
13. Chao T.C., Hansmeier N. The current state of microbial proteomics: where we are and where we want to go. Proteomics 2012, 12:638-650.
14. Chi A., Bai D.L., Geer L.Y., Shabanowitz J., Hunt D.F. Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int. J. Mass Spectrom. 2007, 259:197-203.
15. Chooneea D., Karlsson R., Encheva V., Arnold C., Appleton H., Shah H. Elucidation of the outer membrane proteome of Salmonella enterica serovar Typhimurium utilising a lipid-based protein immobilization technique. BMC Microbiol. 2010, 10:44.
16. Christie-Oleza J.A., Fernandez B., Nogales B., Bosch R., Armengaud J. Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J. 2012, 6:124-135.
17. Clements D.A., MacInnes S.J., Gilbert G.L. Outer membrane protein subtypes of Haemophilus influenzae type b isolates causing invasive disease in Victoria, Australia, from 1988 to 1990. J. Clin. Microbiol. 1992, 30:1879-1881.
18. Cohan F.M. What are bacterial species?. Annu. Rev. Microbiol. 2002, 56:457-487.
19. Costas M. Numerical analysis of sodium dodecyl sulphate-polyacrylamide gel electrophoretic protein patterns for the classification, identification and typing of medically important bacteria. Electrophoresis 1990, 11:382-391.
20. Costello C.E. Time, life . . . and mass spectrometry. New techniques to address biological questions. Biophys. Chem. 1997, 68:173-188.
21. Delahunty C.M., Yates J.R. MudPIT: multidimensional protein identification technology. BioTechniques 2007, 43:563. 565, 567 passim.
22. Devol A.H. Nitrogen cycle: solution to a marine mystery. Nature 2003, 422:575-576.
23. Dumas E., Desvaux M., Chambon C., Hebraud M. Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics 2009, 9:3136-3155.
24. Dworzanski J.P., Deshpande S.V., Chen R., Jabbour R.E., Snyder A.P., Wick C.H., Li L. Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification. J. Proteome Res. 2006, 5:76-87.
25. Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
26. Fagerquist C.K., Bates A.H., Heath S., King B.C., Garbus B.R., Harden L.A., Miller W.G. Sub-speciating Campylobacter jejuni by proteomic analysis of its protein biomarkers and their post-translational modifications. J. Proteome Res. 2006, 5:2527-2538.
27. Felitsyn N., Pescheke M., Kebarle P. Origin and number of charges observed on multiply-protonated native proteins produced by ESI. Int. J. Mass Spectrom. 2002, 219:39-62.
28. Fenn J.B., Mann M., Meng C.K., Wong S.F., Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246:64-71.
29. Fournier M.L., Gilmore J.M., Martin-Brown S.A., Washburn M.P. Multidimensional separations-based shotgun proteomics. Chem. Rev. 2007, 107:3654-3686.
30. Gupta N., Tanner S., Jaitly N., Adkins J.N., Lipton M., Edwards R., Romine M., Osterman A., Bafna V., Smith R.D., Pevzner P.A. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007, 17:1362-1377.
31. Hebraud M. Analysis of Listeria monocytogenes subproteomes. Methods Mol. Biol. 2014, 1157:109-128.
32. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 1993, 90:5011-5015.
33. Hillenkamp F., Karas M., Beavis R.C., Chait B.T. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 1991, 63:1193A-1203A.
34. Holland R.D., Wilkes J.G., Rafii F., Sutherland J.B., Persons C.C., Voorhees K.J., Lay J.O. Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10:1227-1232.
35. Hu Q., Noll R.J., Li H., Makarov A., Hardman M., Graham Cooks R. The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 2005, 40:430-443.
36. Issaq H.J., Chan K.C., Janini G.M., Conrads T.P., Veenstra T.D. Multidimensional separation of peptides for effective proteomic analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2005, 817:35-47.
37. Jabbour R.E., Deshpande S.V., Wade M.M., Stanford M.F., Wick C.H., Zulich A.W., Skowronski E.W., Snyder A.P. Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics. Appl. Environ. Microbiol. 2010, 76:3637-3644.
38. Jabbour R.E., Wade M.M., Deshpande S.V., Stanford M.F., Wick C.H., Zulich A.W., Snyder A.P. Identification of Yersinia pestis and Escherichia coli strains by whole cell and outer membrane protein extracts with mass spectrometry-based proteomics. J. Proteome Res. 2010, 9:3647-3655.
39. Jetten M.S., Niftrik L., Strous M., Kartal B., Keltjens J.T., Op den Camp H.J. Biochemistry and molecular biology of anammox bacteria. Crit. Rev. Biochem. Mol. Biol. 2009, 44:65-84.
40. Jolley K.A., Maiden M.C. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform. 2010, 11:595.
41. Kallow W., Erhard M., Shah H.N., Raptakis E., Welker M. MALDI-TOF MS for microbial identification: years of experimental development to an established protocol. Mass Spectrometry for Microbial Proteomics 2010, 255-276. John Wiley & Sons, Ltd. H.N. Shah, S.E. Gharbia (Eds.).
42. Karlsson R., Chooneea D., Carlsohn E., Encheva V., Shah H.N. Characterization of bacterial membrane proteins using a novel combination of a lipid based protein immobilization technique with Mass Spectrometry. Mass Spectrometry for Microbial Proteomics 2010, 157-174. John Wiley & Sons, Ltd. H.N. Shah, S.E. Gharbia (Eds.).
43. Karlsson R., Davidson M., Svensson-Stadler L., Karlsson A., Olesen K., Carlsohn E., Moore E.R. Strain-level typing and identification of bacteria using mass spectrometry-based proteomics. J. Proteome Res. 2012, 11:2710-2720.
44. Karlsson R., Karlsson A., Backman O., Johansson B.R., Hulth S. Identification of key proteins involved in the anammox reaction. FEMS Microbiol. Lett. 2009, 297:87-94.
45. Karlsson R., Karlsson A., Backman O., Johansson B.R., Hulth S. Subcellular localization of an ATPase in anammox bacteria using proteomics and immunogold electron microscopy. FEMS Microbiol. Lett. 2014, 354:10-18.
46. Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74:5383-5392.
47. Klein C., Aivaliotis M., Olsen J.V., Falb M., Besir H., Scheffer B., Bisle B., Tebbe A., Konstantinidis K., Siedler F., Pfeiffer F., Mann M., Oesterhelt D. The low molecular weight proteome of Halobacterium salinarum. J. Proteome Res. 2007, 6:1510-1518.
48. Konstantinidis K.T., Tiedje J.M. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 2005, 187:6258-6264.
49. Kossmehl S., Wohlbrand L., Druppel K., Feenders C., Blasius B., Rabus R. Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395. Proteomics 2013, 13:2743-2760.
50. Krishnamurthy T., Ross P.L., Rajamani U. Detection of pathogenic and non-pathogenic bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10:883-888.
51. Li W., Raoult D., Fournier P.E. Bacterial strain typing in the genomic era. FEMS Microbiol. Rev. 2009, 33:892-916.
52. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., Yates J.R. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17:676-682.
53. Lopez-Campistrous A., Semchuk P., Burke L., Palmer-Stone T., Brokx S.J., Broderick G., Bottorff D., Bolch S., Weiner J.H., Ellison M.J. Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol. Cell. Proteomics 2005, 4:1205-1209.
54. Macek B., Waanders L.F., Olsen J.V., Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics 2006, 5:949-958.
55. Maiden M.C., Jansen van Rensburg M.J., Bray J.E., Earle S.G., Ford S.A., Jolley K.A., McCarthy N.D. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol. 2013, 11:728-736.
56. McDonald W.H., Yates J.R. Shotgun proteomics: integrating technologies to answer biological questions. Curr. Opin. Mol. Ther. 2003, 5:302-309.
57. McLafferty F.W., Breuker K., Jin M., Han X., Infusini G., Jiang H., Kong X., Begley T.P. Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 2007, 274:6256-6268.
58. Meyer B., Papasotiriou D.G., Karas M. 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino acids 2011, 41:291-310.
59. Moore E.R., Mihaylova S.A., Vandamme P., Krichevsky M.I., Dijkshoorn L. Microbial systematics and taxonomy: relevance for a microbial commons. Res. Microbiol. 2010, 161:430-438.
60. Munoz R., Lopez-Lopez A., Urdiain M., Moore E.R., Rossello-Mora R. Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments. Syst. Appl. Microbiol. 2011, 34:69-75.
61. Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75:4646-4658.
62. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250:4007-4021.
63. Oganization W.H. Antimicrobial Resistance: Global Report on Surveillance 2014, WHO Press, Geneva, Switzerland.
64. Ogorzalek Loo R.R., Hayes R., Yang Y., Hung F., Ramachandran P., Kim N., Gunsalus R., Loo J.A. Topdown, bottom-up, and side-to-side proteomics with virtual 2-D gels. Int. J. Mass Spectrom. 2005, 240:317-325.
65. Olaya-Abril A., Jimenez-Munguia I., Gomez-Gascon L., Rodriguez-Ortega M.J. Surfomics: shaving live organisms for a fast proteomic identification of surface proteins. J. Proteomics 2014, 97:164-176.
66. Olsen J.V., Ong S.E., Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3:608-614.
67. Ornstein L. Disc electrophoresis. I. Background and theory. Ann. N.Y. Acad. Sci. 1964, 121:321-349.
68. Palys T., Nakamura L.K., Cohan F.M. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 1997, 47:1145-1156.
69. Perez-Riverol Y., Wang R., Hermjakob H., Muller M., Vesada V., Vizcaino J.A. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim. Biophys. Acta 2014, 1844:63-76.
70. Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
71. Pieper R., Huang S.T., Robinson J.M., Clark D.J., Alami H., Parmar P.P., Perry R.D., Fleischmann R.D., Peterson S.N. Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis. Microbiology 2009, 155:498-512.
72. Poulik M.D., Smithies O. Comparison and combination of the starch-gel and filter-paper electrophoretic methods applied to human sera: two-dimensional electrophoresis. Biochem. J. 1958, 68:636-643.
73. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25:39-67.
74. Sabat A.J., Budimir A., Nashev D., Sa-Leao R., van Dijl J., Laurent F., Grundmann H., Friedrich A.W., ESCMID Study Group of Epidemiological Markers (ESGEM) Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013, 18:20380.
75. Sauer S., Kliem M. Mass spectrometry tools for the classification and identification of bacteria. Nat. Rev. Microbiol. 2010, 8:74-82.
76. Schilling O., auf dem Keller U., Overall C.M. Protease specificity profiling by tandem mass spectrometry using proteome-derived peptide libraries. Methods Mol. Biol. 2011, 753:257-272.
77. Smithies O. Zone electrophoresis in starch gels: group variations in the serum proteins of normal human adults. Biochem. J. 1955, 61:629-641.
78. Solis N., Cordwell S.J. Current methodologies for proteomics of bacterial surface-exposed and cell envelope proteins. Proteomics 2011, 11:3169-3189.
79. Strous M., Fuerst J.A., Kramer E.H., Logemann S., Muyzer G., van de Pas-Schoonen K.T., Webb R., Kuenen J.G., Jetten M.S. Missing lithotroph identified as new planctomycete. Nature 1999, 400:446-449.
80. Swaney D.L., Wenger C.D., Coon J.J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 2010, 9:1323-1329.
81. Thelen J.J., Miernyk J.A. The proteomic future: where mass spectrometry should be taking us. Biochem. J. 2012, 444:169-181.
82. Tindall B.J., Rossello-Mora R., Busse H.J., Ludwig W., Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 2010, 60:249-266.
83. van Baar B.L. Characterisation of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry. FEMS Microbiol. Rev. 2000, 24:193-219.
84. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 1996, 60:407-438.
85. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19:242-247.
86. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., Stackebrandt E., Starr M.P., Trüper H.G. Report of the Ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. System. Bacteriol. 1987, 37:463-464.
87. Welker M. Proteomics for routine identification of microorganisms. Proteomics 2011, 11:3143-3153.
88. Welker M., Moore E.R. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst. Appl. Microbiol. 2011, 34:2-11.
89. Williams T.L., Monday S.R., Feng P.C., Musser S.M. Identifying new PCR targets for pathogenic bacteria using top-down LC/MS protein discovery. J. Biomol. Tech. 2005, 16:134-142.
90. Yates J.R., Ruse C.I., Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 2009, 11:49-79.