Proteomics in environmental and technical microbiology

Engineering in Life Sciences

Volumn 14, Issue 1, 2014, Pages 27-46

  Benndorf, Dirk ^a   Reichl, Udo ^a,b  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

^b MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

Adaptation; Metaproteomics; Microbial communities; MS; Proteomics

Indexed keywords

ADAPTATION; METAPROTEOMICS; MICROBIAL COMMUNITIES; MS; PROTEOMICS;

BIOINFORMATICS; ELECTROPHORESIS; MICROORGANISMS; MOLECULAR BIOLOGY; PLANTS (BOTANY); PROTEINS;

ENVIRONMENTAL MICROBIOLOGY;

BIOGAS;

ADAPTATION; BIOGAS; BIOINFORMATICS; BIOTECHNOLOGY; GENOME; MASS SPECTROMETRY; MICROBIAL COMMUNITY; MICROBIOLOGY; PROTEOMICS; RESEARCH WORK; WASTE FACILITY;

ANALYTIC METHOD; BIOINFORMATICS; BIOTECHNOLOGY; CULTURE TECHNIQUE; HIGH PERFORMANCE MASS SPECTROMETRY; HIGH THROUGHPUT SEQUENCING; MASS SPECTROMETRY; METAPROTEOMICS; MICROBIAL COMMUNITY; MICROBIAL GENOME; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; NONHUMAN; PROTEOMICS; REVIEW; SLUDGE; TWO DIMENSIONAL ELECTROPHORESIS; WASTE WATER TREATMENT PLANT;

EID: 84892498329     PISSN: 16180240     EISSN: 16182863     Source Type: Journal    
DOI: 10.1002/elsc.201200205     Document Type: Review

References (216)

1. Cowen, D. A., The upper temperature of life-where do we draw the line? Trends Microbiol. 2004, 12, 58-60.
2. Baker-Austin, C., Dopson, M., Life in acid: pH homeostasis in acidophiles. Trends Microbiol. 2007, 15, 165-171.
3. Kato, S., Watanabe, K., Ecological and evolutionary interactions in syntrophic methanogenic consortia. Microbes Environ. 2010, 25, 145-151.
4. Wittebolle, L., Marzorati, M., Clement, L., Balloi, A. et al., Initial community evenness favours functionality under selective stress. Nature 2009, 458, 623-626.
5. Amann, R. I., Ludwig, W., Schleifer, K. H., Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59, 143-169.
6. Fearon, W. R., Urease. Part II. The mechanism of the zymolysis of urea. Biochem. J. 1923, 17, 800-812.
7. O'Farrell, P. H., High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 1975, 250, 4007-4021.
8. Anderson, N. L., Anderson, N. G., Proteome and proteomics: New technologies, new concepts, and new words. Electrophoresis 1998, 19, 1853-1861.
9. Banfield, J. F., Verberkmoes, N. C., Hettich, R. L., Thelen, M. P., Proteogenomic approaches for the molecular characterization of natural microbial communities. Omics 2005, 9, 301-333.
10. Schneider, T., Riedel, K., Environmental proteomics: Analysis of structure and function of microbial communities. Proteomics 2010, 10, 785-798.
11. Lacerda, C. M. R., Reardon, K. F., Environmental proteomics: Applications of proteome profiling in environmental microbiology and biotechnology. Brief. Funct. Genomic. Proteomic. 2009, 8, 75-87.
12. Reis, H. E., Wetter, O., Isoelectric fractionation in protein chemistry. Klin. Wochenschr. 1970, 48, 643-650.
13. Laemmli, U. K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227, 680-685.
14. Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. Humangenetik 1975, 26, 231-243.
15. Wilkins, M. R., Sanchez, J. C., Gooley, A. A., Appel, R. D. et al., Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 1996, 13, 19-50.
16. Garrels, J. I., The QUEST system for quantitative-analysis of two-dimensional gels. J. Biol. Chem. 1989, 264, 5269-5282.
17. Appel, R. D., Hochstrasser, D. F., Funk, M., Vargas, J. R. et al., The Melanie project-From a biopsy to automatic protein map interpretation by computer. Electrophoresis 1991, 12, 722-735.
18. Millioni, R., Miuzzo, M., Sbrignadello, S., Murphy, E. et al., Delta2D and Proteomweaver: Performance evaluation of two different approaches for 2-DE analysis. Electrophoresis 2010, 31, 1311-1317.
19. Appel, R., Hochstrasser, D., Roch, C., Funk, M. et al., Automatic classification of two-dimensional gel-electrophoresis pictures by heuristic clustering analysis - a step toward machine learning. Electrophoresis 1988, 9, 136-142.
20. Bjellqvist, B., Pasquali, C., Ravier, F., Sanchez, J. C. et al., A nonlinear wide-range immobilized pH gradient for 2-dimensional electrophoresis and its definition in a relevant pH scale. Electrophoresis 1993, 14, 1357-1365.
21. Unlu, M., Morgan, M. E., Minden, J. S., Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18, 2071-2077.
22. Riederer, B. M., Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. J. Proteomics 2008, 71, 231-244.
23. Neuhoff, V., Arold, N., Taube, D., Ehrhardt, W., Improved staining of proteins in polyacrylamide gels including isoelectric-focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9, 255-262.
24. Blum, H., Beier, H., Gross, H. J., Improved silver staining of plant proteins RNA and DNA in polyacrylamide gels. 1987, 8, 93-99.
25. Edman, P., Method for determination of the amino acid sequence in peptides. Acta Chem. Scand. 1950, 4, 283-293.
26. Eckerskorn, C., Jungblut, P., Mewes, W., Klose, J. et al., Identification of mouse-brain proteins after two-dimensional electrophoresis and electroblotting by microsequence analysis and amino-acid composition analysis. Electrophoresis 1988, 9, 830-838.
27. Pedersen, S., Bloch, P. L., Reeh, S., Neidhardt, F. C., Patterns of protein-synthesis in Escherichia-coli-catalog of amount of 140 individual proteins at different growth-rates. Cell 1978, 14, 179-190.
28. Vanbogelen, R. A., Sankar, P., Clark, R. L., Bogan, J. A. et al., The gene-protein database of Escherichia coli - edition 5. Electrophoresis 1992, 13, 1014-1054.
29. Eckerskorn, C., Lottspeich, F., Internal amino-acid sequence-analysis of proteins separated by gel-electrophoresis after tryptic digestion in polyacrylamide matrix. Chromatographia 1989, 28, 92-94.
30. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F. et al., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
31. Tanaka, K., Waki, H., Ido, Y., Akita, S. et al., Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1988, 2, 151-153.
32. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C. et al., Identifying proteins from 2-dimensional gels by molecular mass searching of peptide-fragments in protein-sequence databases. Proc. Natl. Acad. Sci. USA 1993, 90, 5011-5015.
33. Perkins, D. N., Pappin, D. J. C., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
34. Eng, J., McCormack, A., Yates, J., 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.
35. Schneider, T., Riedel, K., Geomicrobiology: Molecular and Environmental Perspective, Springer-Verlag, Berlin 2010, pp. 91-108.
36. 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.
37. Mann, M., Wilm, M., Error tolerant indentification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66, 4390-4399.
38. Mann, M., Hendrickson, R. C., Pandey, A., Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 2001, 70, 437-473.
39. Frank, A., Pevzner, P., PepNovo: De novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
40. Ma, B., Zhang, K., Hendrie, C., Liang, C. et al., PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2003, 17, 2337-2342.
41. Chait, B. T., Mass spectrometry: Bottom-up or top-down? Science 2006, 314, 65-66.
42. Ong, S.-E., Kratchmarova, I., Mann, M., Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2002, 2, 173-181.
43. Schmidt, A., Kellermann, J., Lottspeich, F., A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005, 5, 4-15.
44. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotech. 1999, 17, 994-999.
45. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
46. Zhang, H. Z., Brown, R. N., Qian, W. J., Monroe, M. E. et al., Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with O-18 labeling. J. Proteome Res. 2010, 9, 2160-2169.
47. Liu, H. B., Sadygov, R. G., Yates, J. R., A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
48. Hecker, M., Antelmann, H., Buettner, K., Bernhardt, J., Gel-based proteomics of gram-positive bacteria: A powerful tool to address physiological questions. Proteomics 2008, 8, 4958-4975.
49. Benndorf, D., Muller, A., Bock, K., Manuwald, O. et al., Identification of spore allergens from the indoor mould Aspergillus versicolor. Allergy 2008, 63, 454-460.
50. Tissiéres, A., Mitchell, H. K., Tracy, U. M., Protein synthesis in salivary glands of Drosophila melanogaster: Relation to chromosome puffs. J. Mol. Biol. 1974, 84, 389-398.
51. Yamamori, T., Ito, K., Nakamura, Y., Yura, T., Transient regulation of protein synthesis in Escherichia coli upon shift-up of growth temperature. J. Bacteriol. 1978, 134, 1133-1140.
52. Craig, E. A., Essential roles of 70kDa heat inducible proteins. Bioessays 1989, 11, 48-52.
53. Krueger, J. H., Walker, G. C., Groel and Dnak genes of Escherichia coli are induced by UV irradiation and nalidixic-acid in an HTPR+dependent fashion. Proc. Natl. Acad. Sci. USA 1984, 81, 1499-1503.
54. Morgan, R. W., Christman, M. F., Jacobson, F. S., Storz, G. et al., Hydrogen peroxide-inducible proteins in Salmonella typhimurium overlap with heat-shock and other stress proteins. Proc. Natl. Acad. Sci. USA 1986, 83, 8059-8063.
55. Spector, M. P., Aliabadi, Z., Gonzalez, T., Foster, J. W., Global control in Salmonella typhimurium: Two-dimensional electrophoretic analysis of starvation-, anaerobiosis-, and heat shock-inducible proteins. J. Bacteriol. 1986, 168, 420-424.
56. Antelmann, H., Bernhardt, J., Schmid, R., Mach, H. et al., First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis. Electrophoresis 1997, 18, 1451-1463.
57. Groat, R. G., Schultz, J. E., Zychlinsky, E., Bockman, A. et al., Starvation proteins in Escherichia-coli-kinetics of synthesis and role in starvation survival. J. Bacteriol. 1986, 168, 486-493.
58. Graumann, P., Schroder, K., Schmid, R., Marahiel, M. A., Cold shock stress-induced proteins in Bacillus subtilis. J. Bacteriol. 1996, 178, 4611-4619.
59. VanBogelen, R. A., Kelley, P. M., Neidhardt, F. C., Differential induction of heat shock, SOS, and oxidation stress regulons and accumulation of nucleotides in Escherichia coli. J. Bacteriol. 1987, 169, 26-32.
60. Tanji, K., Mizushima, T., Natori, S., Sekimizu, K., Induction by psychotropic-drugs and local-anesthetics of DnaK and GroEL proteins in Escherichia coli. Biochim. Biophys. Acta 1992, 1129, 172-176.
61. Ödberg-Ferragut, C., Espigares, M., Dive, D., Stress protein synthesis, a potential toxicity marker in Escherichia coli. Ecotoxicol. Environ. Saf. 1991, 21, 275-282.
62. Blom, A., Harder, W., Matin, A., Unique and overlapping pollutant stress proteins of Escherichia coli. Appl. Environ. Microbiol. 1992, 58, 331-334.
63. Faber, F., Egli, T., Harder, W., Transient repression of the synthesis of Ompf and aspartate transcarbamoylase in Escherichia coli K12 as a response to pollutant stress. FEMS Microbiol. Lett. 1993, 111, 189-195.
64. Gage, D. J., Neidhardt, F. C., Adaptation of Escherichia coli to the uncoupler of oxidative-phosphorylation 2, 4-dinitrophenol. J. Bacteriol. 1993, 175, 7105-7108.
65. Vandyk, T. K., Reed, T. R., Vollmer, A. C., Larossa, R. A., Synergistic induction of the heat-shock response in Escherichia coli by simultaneous treatment with chemical inducers. J. Bacteriol. 1995, 177, 6001-6004.
66. Lupi, C. G., Colangelo, T., Mason, C. A., 2-dimensional gel-electrophoresis analysis of the response of Pseudomonas putida KT2442 to 2-chlorophenol. Appl. Environ. Microbiol. 1995, 61, 2863-2872.
67. Benndorf, D., Loffhagen, N., Babel, W., Chemicals and heat generate different protein patterns in Acinetobacter calcoaceticus. J. Basic Microbiol. 1997, 37, 167-174.
68. Benndorf, D., Loffhagen, N., Babel, W., Induction of heat shock proteins in response to primary alcohols in Acinetobacter calcoaceticus. Electrophoresis 1999, 20, 781-789.
69. Benndorf, D., Loffhagen, N., Babel, W., Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress. FEMS Microbiol. Lett. 2001, 200, 247-252.
70. Benndorf, D., Loffhagen, N., Hartig, C., Babel, W., Growth on phenol at chemostress levels amplifies the expression of the phenol degradation pathway in Acinetobacter calcoaceticus. Eng. Life Sci. 2004, 4, 38-42.
71. Hallsworth, J. E., Heim, S., Timmis, K. N., Chaotropic solutes cause water stress in Pseudomonas putida. Environ. Microbiol. 2003, 5, 1270-1280.
72. Santos, P. M., Benndorf, D., Sa-Correia, I., Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 2004, 4, 2640-2652.
73. Benndorf, D., Thiersch, M., Loffhagen, N., Kunath, C. et al., Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites. Proteomics 2006, 6, 3319-3329.
74. Benndorf, D., Babel, W., Assimilatory detoxification of herbicides by Delftia acidovorans MC1: Induction of two chlorocatechol 1, 2-dioxygenases as a response to chemostress. Microbiology 2002, 148, 2883-2888.
75. Benndorf, D., Davidson, I., Babel, W., Regulation of catabolic enzymes during long-term exposure of Delftia acidovorans MC1 to chlorophenoxy herbicides. Microbiology 2004, 150, 1005-1014.
76. Agullo, L., Camara, B., Martinez, P., Latorre, V. et al., Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress. FEMS Microbiol. Lett. 2007, 267, 167-175.
77. Lacerda, C. M. R., Choe, L. H., Reardon, K. F., Metaproteomic analysis of a bacterial community response to cadmium exposure. J. Proteome Res. 2007, 6, 1145-1152.
78. Kim, S. I., Kim, S. J., Nam, M. H., Kim, S. H. et al., Proteome analysis of aniline-induced proteins in Acinetobacter lwoffii K24. Curr. Microbiol. 2002, 44, 61-66.
79. Krivobok, S., Kuony, S., Meyer, C., Louwagie, M. et al., Identification of pyrene-induced proteins in Mycobacterium sp strain 6PY1: Evidence for two ring-hydroxylating dioxygenases. J. Bacteriol. 2003, 185, 3828-3841.
80. Kim, S. J., Jones, R. C., Cha, C. J., Kweon, O. et al., Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods. Proteomics 2004, 4, 3899-3908.
81. Halden, R. U., Colquhoun, D. R., Wisniewski, E. S., Identification and phenotypic characterization of Sphingomonas wittichii strain RW1 by peptide mass fingerprinting using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 2005, 71, 2442-2451.
82. Kim, Y. H., Cho, K., Yun, S. H., Kim, J. Y. et al., Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 2006, 6, 1301-1318.
83. Kuhner, S., Wohlbrand, L., Fritz, I., Wruck, W. et al., Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J. Bacteriol. 2005, 187, 1493-1503.
84. Rohwerder, T., Breuer, U., Benndorf, D., Lechner, U. et al., The alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway. Appl. Environ. Microbiol. 2006, 72, 4128-4135.
85. Schäfer, F., Breuer, U., Benndorf, D., von Bergen, M. et al., Growth of Aquincola tertiaricarbonis L108 on tert-butyl alcohol leads to the induction of a phthalate dioxygenase-related protein and its associated oxidoreductase subunit. Eng. Life Sci. 2007, 7, 512-519.
86. Ettwig, K. F., Butler, M. K., Le Paslier, D., Pelletier, E. et al., Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 2010, 464, 543-548.
87. Tebbe, A., Schmidt, A., Konstantinidis, K., Falb, M. et al., Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics 2009, 9, 3843-3855.
88. Pessione, E., Giuffrida, M. G., Prunotto, L., Barello, C. et al., Membrane proteome of Acinetobacter radioresistens S13 during aromatic exposure. Proteomics 2003, 3, 1070-1076.
89. Roma-Rodrigues, C., Santos, P. M., Benndorf, D., Rapp, E. et al., Response of Pseudomonas putida KT2440 to phenol at the level of membrane proteome. J. Proteomics 2010, 73, 1461-1478.
90. Antranikian, G., Vorgias, C. E., Bertoldo, C., in: Gal, Y. L., Ulber, R. (Eds.), Marine Biotechnology I, Springer-Verlag, Berlin 2005, pp. 219-262.
91. Hirose, I., Sano, K., Shioda, I., Kumano, M. et al., Proteome analysis of Bacillus subtilis extracellular proteins: A two-dimensional protein electrophoretic study. Microbiology 2000, 146, 65-75.
92. Muddiman, D., Andrews, G., Lewis, D., Notey, J. et al., Part I: Characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2. Anal. Bioanal. Chem. 2010, 398, 377-389.
93. Ravalason, H., Jan, G., Molle, D., Pasco, M. et al., Secretome analysis of Phanerochaete chrysosporium strain CIRM-BRFM41 grown on softwood. Appl. Microbiol. Biotechnol. 2008, 80, 719-733.
94. Kellner, H., Jehmlich, N., Benndorf, D., Hoffmann, R. et al., Detection, quantification and identification of fungal extracellular laccases using polyclonal antibody and mass spectrometry. Enzyme Microb. Technol. 2007, 41, 694-701.
95. Westendorf, A., Benndorf, D., Pribyl, T., Harms, H. et al., Kinetic traits and enzyme form patterns of (R)-2-(2, 4-dichlorophenoxy) propionate/alpha-ketoglutarate dioxygenase (RdpA) after expression in different bacterial strains. Eng. Life Sci. 2006, 6, 552-559.
96. Leibeling, S., Schmidt, F., Jehmlich, N., von Bergen, M. et al., Declining capacity of starving Delftia acidovorans MC1 to degrade phenoxypropionate herbicides correlates with oxidative modification of the initial enzyme. Environ. Sci. Technol. 2010, 44, 3793-3799.
97. Ginsburg, A., Yeh, J., Hennig, S. B., Denton, M. D., Effects of adenylylation on the biosynthetic properties of the glutamine synthetase from Escherichia coli. Biochemistry 1970, 9, 633-649.
98. Kern, A., Tilley, E., Hunter, I. S., Legiša, M. et al., Engineering primary metabolic pathways of industrial micro-organisms. J. Biotechnol. 2007, 129, 6-29.
99. Rossignol, T., Kobi, D., Jacquet-Gutfreund, L., Blondin, B., The proteome of a wine yeast strain during fermentation, correlation with the transcriptome. J. Appl. Microbiol. 2009, 107, 47-55.
100. Schaffer, S., Weil, B., Nguyen, V. D., Dongmann, G. et al., A high-resolution reference map for cytoplasmic and membrane-associated proteins of Corynebacterium glutamicum. Electrophoresis 2001, 22, 4404-4422.
101. Kim, Y. H., Park, J. S., Cho, J. Y., Cho, K. M. et al., Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli. Biochem. J. 2004, 381, 823-829.
102. Wang, W., Sun, J. B., Hartlep, M., Deckwer, W. D. et al., Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol. Bioeng. 2003, 83, 525-536.
103. Mao, S. M., Luo, Y. A. M., Zhang, T. R., Li, J. S. et al., Proteome reference map and comparative proteomic analysis between a wild type Clostridium acetobutylicum DSM 1731 and its mutant with enhanced butanol tolerance and butanol yield. J. Proteome Res. 2010, 9, 3046-3061.
104. Verhoef, S., Wierckx, N., Westerhof, R. G. M., de Winde, J. H., Ruijssenaars, H. J., Bioproduction of p-hydroxystyrene from glucose by the solvent-tolerant bacterium Pseudomonas putida S12 in a two-phase water-decanol fermentation. Appl. Environ. Microbiol. 2009, 75, 931-936.
105. Hesketh, A. R., Chandra, G., Shaw, A. D., Rowland, J. J. et al., Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol. Microbiol. 2002, 46, 917-932.
106. Kim, C. Y., Park, H. J., Kim, E. S., Proteomics-driven identification of putative AfsR2-target proteins stimulating antibiotic biosynthesis in Streptomyces lividans. Biotechnol. Bioprocess Eng. 2005, 10, 248-253.
107. Kiel, J., van den Berg, M. A., Fusetti, F., Poolman, B. et al., Matching the proteome to the genome: The microbody of penicillin-producing Penicillium chrysogenum cells. Funct. Integr. Genomics 2009, 9, 167-184.
108. Taylor, R. D., Saparno, A., Blackwell, B., Anoop, V. et al., Proteomic analyses of Fusarium graminearum grown under mycotoxin-inducing conditions. Proteomics 2008, 8, 2256-2265.
109. Bumpus, S. B., Evans, B. S., Thomas, P. M., Ntai, I. et al., A proteomics approach to discovering natural products and their biosynthetic pathways. Nat. Biotechnol. 2009, 27, 951-956.
110. Poetter, M., Mueller, H., Reinecke, F., Wieczorek, R. et al., The complex structure of polyhydroxybutyrate (PHB) granules: Four orthologous and paralogous phasins occur in Ralstonia eutropha. Microbiology 2004, 150, 2301-2311.
111. Pallerla, S. R., Knebel, S., Polen, T., Klauth, P. et al., Formation of volutin granules in Corynebacterium glutamicum. FEMS Microbiol. Lett. 2005, 243, 133-140.
112. Arakaki, A., Nakazawa, H., Nemoto, M., Mori, T. et al., Formation of magnetite by bacteria and its application. J. R. Soc. Interface 2008, 5, 977-999.
113. Linn, T., Losick, R., Program of protein-synthesis during sporulation in Bacillus subtilis. Cell 1976, 8, 103-114.
114. Liu, H. B., Bergman, N. H., Thomason, B., Shallom, S. et al., Formation and composition of the Bacillus anthracis endospore. J. Bacteriol. 2004, 186, 164-178.
115. Jagtap, P., Michailidis, G., Zielke, R., Walker, A. K. et al., Early events of Bacillus anthracis germination identified by time-course quantitative proteomics. Proteomics 2006, 6, 5199-5211.
116. Lawley, T. D., Croucher, N. J., Yu, L., Clare, S. et al., Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores. J. Bacteriol. 2009, 191, 5377-5386.
117. Dahl, J. L., Tengra, F. K., Dutton, D., Yan, J. Y. et al., Identification of major sporulation proteins of Myxcoccus xanthus using a proteomic approach. J. Bacteriol. 2007, 189, 3187-3197.
118. Ireland, M. M. E., Karty, J. A., Quardokus, E. M., Reilly, J. P. et al., Proteomic analysis of the Caulobacter crescentus stalk indicates competence for nutrient uptake. Mol. Microbiol. 2002, 45, 1029-1041.
119. Trevors, J. T., Viable but non-culturable (VBNC) bacteria: Gene expression in planktonic and biofilm cells. J. Microbiol. Methods 2011, 86, 266-273.
120. Heim, S., Lleo, M. D., Bonato, B., Guzman, C. A. et al., The viable but nonculturable state and starvation are different stress responses of Enterococcus faecalis, as determined by proteome analysis. J. Bacteriol. 2002, 184, 6739-6745.
121. Muela, A., Seco, C., Camafeita, E., Arana, I. et al., Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state. FEMS Microbiol. Ecol. 2008, 64, 28-36.
122. Wiacek, C., Muller, S., Benndorf, D., A cytomic approach reveals population heterogeneity of Cupriavidus necator in response to harmful phenol concentrations. Proteomics 2006, 6, 5983-5994.
123. Junter, G. A., Jouenne, T., Immobilized viable microbial cells: From the process to the proteome. or the cart before the horse. Biotechnol. Adv. 2004, 22, 633-658.
124. Heine, F., Stahl, F., Strauber, H., Wiacek, C. et al., Prediction of flocculation ability of brewing yeast inoculates by flow cytometry, proteome analysis, and mRNA profiling. Cytometry A 2009, 75, 140-147.
125. van Houdt, R., Michiels, C., Biofilm formation and the food industry, a focus on the bacterial outer surface. J. Appl. Microbiol. 2010, 109, 1117-1131.
126. Seneviratne, C. J., Wang, Y., Jin, L. J., Wong, S. S. W. et al., Unraveling the resistance of microbial biofilms: Has proteomics been helpful? Proteomics 2012, 12, 651-665.
127. Oosthuizen, M. C., Steyn, B., Lindsay, D., Brozel, V. S. et al., Novel method for the proteomic investigation of a dairy-associated Bacillus cereus biofilm. FEMS Microbiol. Lett. 2001, 194, 47-51.
128. Steyn, B., Oosthuizen, M. C., MacDonald, R., Theron, J., Brozel, V. S., The use of glass wool as an attachment surface for studying phenotypic changes in Pseudomonas aeruginosa biofilms by two-dimensional gel electrophoresis. Proteomics 2001, 1, 871-879.
129. Petrova, O. E., Sauer, K., A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development. PLoS Pathog. 2009, 5, e1000668.
130. Nigaud, Y., Cosette, P., Collet, A., Song, P. C. T. et al., Biofilm-induced modifications in the proteome of Pseudomonas aeruginosa planktonic cells. Biochim. Biophys. Acta 2010, 1804, 957-966.
131. Eberl, L., Riedel, K., Mining quorum sensing regulated proteins - role of bacterial cell-to-cell communication in global gene regulation as assessed by proteomics. Proteomics 2011, 11, 3070-3085.
132. Callahan, S. M., Dunlap, P. V., LuxR- and acyl-homoserine-lactone-controlled non-lux genes define a quorum-sensing regulon in Vibrio fischeri. J. Bacteriol. 2000, 182, 2811-2822.
133. Arevalo-Ferro, C., Reil, G., Gorg, A., Eberl, L. et al., Biofilm formation of Pseudomonas putida IsoF: The role of quorum sensing as assessed by proteomics. Syst. Appl. Microbiol. 2005, 28, 87-114.
134. Guerreiro, N., Redmond, J. W., Rolfe, B. G., Djordjevic, M. A., New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins. Mol. Plant Microbe Interact. 1997, 10, 506-516.
135. Guerreiro, N., Djordjevic, M. A., Rolfe, B. G., Proteome analysis of the model microsymbiont Sinorhizobium meliloti: Isolation and characterisation of novel proteins. Electrophoresis 1999, 20, 818-825.
136. Sarma, A. D., Emerich, D. W., Global protein expression pattern of Bradyrhizobium japonicum bacteroids: A prelude to functional proteomics. Proteomics 2005, 5, 4170-4184.
137. Delmotte, N., Knief, C., Chaffron, S., Innerebner, G. et al., Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA 2009, 106, 16428-16433.
138. Markert, S., Arndt, C., Felbeck, H., Becher, D. et al., Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 2007, 315, 247-250.
139. Buchmeier, N. A., Heffron, F., Induction of Salmonella stress proteins upon infection of macrophages. Science 1990, 248, 730-732.
140. RafieKolpin, M., Essenberg, R. C., Wyckoff, J. H., Identification and comparison of macrophage-induced proteins and proteins induced under various stress conditions in Brucella abortus. Infect. Immun. 1996, 64, 5274-5283.
141. Shi, L., Adkins, J. N., Coleman, J. R., Schepmoes, A. A. et al., Proteomic analysis of Salmonella enterica serovar Typhimurium isolated from RAW 264.7 macrophages - identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages. J. Biol. Chem. 2006, 281, 29131-29140.
142. Kluge, S., Hoffmann, M., Benndorf, D., Rapp, E. et al., Proteomic tracking and analysis of a bacterial mixed culture. Proteomics 2012, 12, 1893-1901.
143. Cash, P., The application of 2-dimensional polyacrylamide-gel electrophoresis to medical microbiology - molecular epidemiology of viruses and bacteria. Electrophoresis 1991, 12, 592-604.
144. Cash, P., Protein mutations revealed by 2-dimensional electrophoresis. J. Chromatogr. A 1995, 698, 203-224.
145. Madeira, A., Santos, P. M., Coutinho, C. P., Pinto-de-Oliveira, A. et al., Quantitative proteomics (2-D DIGE) reveals molecular strategies employed by Burkholderia cenocepacia to adapt to the airways of cystic fibrosis patients under antimicrobial therapy. Proteomics 2011, 11, 1313-1328.
146. Coiras, M., Camafeita, E., Lopez-Huertas, M. R., Calvo, E. et al., Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents. Proteomics 2008, 8, 852-873.
147. Dori-Bachash, M., Dassa, B., Pietrokovski, S., Jurkevitch, E., Proteome-based comparative analyses of growth stages reveal new cell cycle-dependent functions in the predatory bacterium Bdellovibrio bacteriovorus. Appl. Environ. Microbiol. 2008, 74, 7152-7162.
148. Kan, J., Hanson, T., Ginter, J., Wang, K. et al., Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 2005, 1, 1-13.
149. Wilmes, P., Bond, P. L., The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 2004, 6, 911-920.
150. Ram, R. J., VerBerkmoes, N. C., Thelen, M. P., Tyson, G. W. et al., Community proteomics of a natural microbial biofilm. Science 2005, 308, 1915-1920.
151. Schulze, W. X., Protein analysis in dissolved organic matter: What proteins from organic debris, soil leachate and surface water can tell us - a perspective. Biogeosciences 2005, 2, 75-86.
152. Prosser, J. I., Replicate or lie. Environ. Microbiol. 2010, 12, 1806-1810.
153. Murase, A., Yoneda, M., Ueno, R., Yonebayashi, K., Isolation of extracellular protein from greenhouse soil. Soil Biol. Biochem. 2003, 35, 733-736.
154. Maron, P. A., Ranjard, L., Mougel, C., Lemanceau, P., Metaproteomics: A new approach for studying functional microbial ecology. Microb. Ecol. 2007, 53, 486-493.
155. Schulze, W., Protein analysis in dissolved organic matter: What free proteins from soil leachate and surface water can tell - a perspective. Biogeosciences 2004, 1, 825-853.
156. Benndorf, D., Balcke, G. U., Harms, H., von Bergen, M., Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 2007, 1, 224-234.
157. Renella, G., Landi, L., Nannipieri, P., Hydrolase activities during and after the chloroform fumigation of soil as affected by protease activity. Soil Biol. Biochem. 2002, 34, 51-60.
158. Chen, S. N., Rillig, M. C., Wang, W., Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics 2009, 9, 4970-4973.
159. Chourey, K., Jansson, J., VerBerkmoes, N., Shah, M. et al., Direct cellular lysis/protein extraction protocol for soil metaproteomics. J. Proteome Res. 2010, 9, 6615-6622.
160. Simonart, P., Batistic, L., Mayaudon, J., Isolation of protein from humic acid extracted from soil. Plant Soil 1967, 27, 153-161.
161. Wang, W., Scali, M., Vignani, R., Spadafora, A. et al., Protein extraction for two-dimensional electrophoresis from olive leaf, a plant tissue containing high levels of interfering compounds. Electrophoresis 2003, 24, 2369-2375.
162. Wang, H. B., Zhang, Z. X., Li, H., He, H. B. et al., Characterization of metaproteomics in crop rhizospheric soil. J. Proteome Res. 2011, 10, 932-940.
163. Schneider, T., Gerrits, B., Gassmann, R., Schmid, E. et al., Proteome analysis of fungal and bacterial involvement in leaf litter decomposition. Proteomics 2010, 10, 1819-1830.
164. Schneider, T., Keiblinger, K. M., Schmid, E., Sterflinger-Gleixner, K. et al., Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME J. 2012, 6, 1749-1762.
165. Giagnoni, L., Magherini, F., Landi, L., Taghavi, S. et al., Extraction of microbial proteome from soil: Potential and limitations assessed through a model study. Eur. J. Soil Sci. 2011, 62, 74-81.
166. Tanoue, E., Characterization of the particulate protein in Pacific surface waters. J. Mar. Res. 1996, 54, 967-990.
167. Suzuki, S., Kogure, K., Tanoue, E., Immunochemical detection of dissolved proteins and their source bacteria in marine environments. Mar. Ecol. Prog. Ser. 1997, 158, 1-9.
168. Saijo, S., Tanoue, E., Characterization of particulate proteins in Pacific surface waters. Limnol. Oceanogr. 2004, 49, 953-963.
169. Sowell, S. M., Wilhelm, L. J., Norbeck, A. D., Lipton, M. S. et al., Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 2009, 3, 93-105.
170. Dong, H. P., Wang, D. Z., Dai, M., Chan, L. L. et al., Shotgun proteomics: Tools for analysis of marine particulate proteins. Limnol. Oceanogr. Methods 2009, 7, 865-874.
171. Benndorf, D., Vogt, C., Jehmlich, N., Schmidt, Y. et al., Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 2009, 20, 737-750.
172. Jehmlich, N., Kleinsteuber, S., Vogt, C., Benndorf, D. et al., Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community. J. Appl. Microbiol. 2010, 109, 1937-1945.
173. Klaassens, E. S., de Vos, W. M., Vaughan, E. E., Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 2007, 73, 1388-1392.
174. Rooijers, K., Kolmeder, C., Juste, C., Dore, J. et al., An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 2011, 12, 6.
175. Warnecke, F., Luginbuhl, P., Ivanova, N., Ghassemian, M. et al., Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450, 560-565.
176. Toyoda, A., Iio, W., Mitsumori, M., Minato, H., Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl. Environ. Microbiol. 2009, 75, 1667-1673.
177. Wilmes, P., Andersson, A. F., Lefsrud, M. G., Wexler, M. et al., Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2008, 2, 853-864.
178. Kuhn, R., Benndorf, D., Rapp, E., Reichl, U. et al., Metaproteome analysis of sewage sludge from membrane bioreactors. Proteomics 2011, 11, 2738-2744.
179. Abram, F., Enright, A. M., O'Reilly, J., Botting, C. H. et al., A metaproteomic approach gives functional insights into anaerobic digestion. J. Appl. Microbiol. 2011, 110, 1550-1560.
180. Hanreich, A., Heyer, R., Benndorf, D., Rapp, E. et al., Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can. J. Microbiol. 2012, 58, 917-922.
181. Gagnaire, V., Piot, M., Camier, B., Vissers, J. P. C. et al., Survey of bacterial proteins released in cheese: A proteomic approach. Int. J. Food Microbiol. 2004, 94, 185-201.
182. Jardin, J., Molle, D., Piot, M., Lortal, S. et al., Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening. Int. J. Food Microbiol. 2012, 155, 19-28.
183. Gagnaire, V., Jardin, J., Jan, G., Lortal, S., Invited review: Proteomics of milk and bacteria used in fermented dairy products: From qualitative to quantitative advances. J. Dairy Sci. 2009, 92, 811-825.
184. Rossetti, S., Tomei, M. C., Nielsen, P. H., Tandoi, V., "Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: A review of current knowledge. FEMS Microbiol. Rev. 2005, 29, 49-64.
185. Bott, C. B., Love, N. G., The immunochemical detection of stress proteins in activated sludge exposed to toxic chemicals. Water Res. 2001, 35, 91-100.
186. Denecke, M., Protein extraction from activated sludge. Water Sci. Technol. 2006, 54, 175-181.
187. Abram, F., Gunnigle, E., O'Flaherty, V., Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms. Electrophoresis 2009, 30, 4149-4151.
188. Park, C., Novak, J. T., Helm, R. F., Ahn, Y. O. et al., Evaluation of the extracellular proteins in full-scale activated sludges. Water Res. 2008, 42, 3879-3889.
189. Huang, Y. T., Huang, T. H., Yang, J. H., Damodar, R. A., Identifications and characterizations of proteins from fouled membrane surfaces of different materials. Int. Biodeterior. Biodegrad. 2012, 66, 47-52.
190. Ehlers, M. M., Cloete, T. E., Comparing the protein profiles of 21 different activated sludge systems after SDS-PAGE. Water Res. 1999, 33, 1181-1186.
191. Heyer, R., Kohrs, F., Benndorf, D., Rapp, E. et al., Metaproteome analysis of the microbial communities in agricultural biogas plants. N. Biotechnol. 2013, 30, 614-622.
192. Sabounchi-Schutt, F., Astrom, J., Olsson, I., Eklund, A. et al., An Immobiline DryStrip application method enabling high-capacity two-dimensional gel electrophoresis. Electrophoresis 2000, 21, 3649-3656.
193. Hanreich, A., Schimpf, U., Zakrzewski, M., Schluter, A. et al., Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst. Appl. Microbiol. 2013, 36, 330-338.
194. Hu, Q., Noll, R. J., Li, H., Makarov, A. et al., The Orbitrap: A new mass spectrometer. J. Mass Spectrom. 2005, 40, 430-443.
195. Wiesner, J., Premsler, T., Sickmann, A., Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 2008, 8, 4466-4483.
196. Jehmlich, N., Hubschmann, T., Salazar, M. G., Volker, U. et al., Advanced tool for characterization of microbial cultures by combining cytomics and proteomics. Appl. Microbiol. Biotechnol. 2010, 88, 575-584.
197. Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J. et al., Protein-based stable isotope probing. Nat. Protoc. 2010, 5, 1957-1966.
198. Chey, S., Claus, C., Liebert, U. G., Improved method for simultaneous isolation of proteins and nucleic acids. Anal. Biochem. 2011, 411, 164-166.
199. Ogunseitan, O. A., Direct extraction of catalytic proteins from natural microbial communities. J. Microbiol. Methods 1997, 28, 55-63.
200. Cairo, J., Leonardo, F. C., Alvarez, T. M., Ribeiro, D. A. et al., Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi. Biotechnol. Biofuels 2011, 4, 50.
201. Boja, E. S., Rodriguez, H., Mass spectrometry-based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins. Proteomics 2012, 12, 1093-1110.
202. Welker, M., Proteomics for routine identification of microorganisms. Proteomics 2011, 11, 3143-3153.
203. Lee, C. Y., Hong, Y., Ryu, J., Kim, Y. R. et al., Detection and identification of Vibrio species using whole-cell protein pattern analysis. J. Microbiol. Biotechnol. 2012, 22, 1107-1112.
204. Wu, Y. J., Wang, B., Han, J. X., Zhang, Z. M. et al., RAPD-2100 bio-analyzer and 2DGE methods applied to qualitatively and quantitatively assess grain purity of commercial malting barley. Eur. Food Res. Technol. 2012, 234, 381-390.
205. Helsens, K., Colaert, N., Barsnes, H., Muth, T. et al., Ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics 2010, 10, 1261-1264.
206. Sturm, M., Bertsch, A., Gropl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163.
207. Goh, W. W., Lee, Y. H., Chung, M., Wong, L., How advancement in biological network analysis methods empowers proteomics. Proteomics 2012, 12, 550-563.
208. Muller, T., Schrotter, A., Loosse, C., Helling, S. et al., Sense and nonsense of pathway analysis software in proteomics. J. Proteome Res. 2011, 10, 5398-5408.
209. Weckwerth, W., Green systems biology - from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J. Proteomics 2011, 75, 284-305.
210. Bernhardt, J., Michalik, S., Wollscheid, B., Volker, U. et al., Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information. Curr. Opin. Biotechnol. 2013, 24, 112-119.
211. Taffs, R., Aston, J. E., Brileya, K., Jay, Z. et al., In silico approaches to study mass and energy flows in microbial consortia: A syntrophic case study. BMC Syst. Biol. 2009, 3, 114.
212. Muth, T., Benndorf, D., Reichl, U., Rapp, E. et al., Searching for a needle in a stack of needles: Challenges in metaproteomics data analysis. Mol. Biosyst. 2013, 9, 578-585.
213. Frank, A. M., Bandeira, N., Shen, Z., Tanner, S. et al., Clustering millions of tandem mass spectra. J. Proteome Res. 2008, 7, 113-122.
214. Frank, A. M., Monroe, M. E., Shah, A. R., Carver, J. J. et al., Spectral archives: Extending spectral libraries to analyze both identified and unidentified spectra. Nat. Methods 2011, 8, 587-591.
215. Kolmeder, C. A., de Been, M., Nikkila, J., Ritamo, I. et al., Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One 2012, 7, e29913.
216. Pierre-Alain, M., Christophe, M., Severine, S., Houria, A. et al., Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb. Ecol. 2007, 53, 426-434.