Proteome turnover in bacteria: Current status for Corynebacterium glutamicum and related bacteria

Microbial Biotechnology

Volumn 6, Issue 6, 2013, Pages 708-719

  Trötschel, Christian ^a   Albaum, Stefan P ^b   Poetsch, Ansgar ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEOME;

ACTINOBACTERIA; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GROWTH; CORYNEBACTERIUM GLUTAMICUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROTEOMICS; STREPTOMYCES COELICOLOR;

BACTERIAL PROTEINS; CORYNEBACTERIUM GLUTAMICUM; PROTEOME; PROTEOMICS;

EID: 84885709763     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12035     Document Type: Article

References (56)

1. Aggarwal, K., Choe, L.H., and Lee, K.H. (2006) Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct Genomic Proteomic 5: 112-120.
2. Albaum, S.P., Neuweger, H., Franzel, B., Lange, S., Mertens, D., Trotschel, C., etal. (2009) Qupe - a rich internet application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics 25: 3128-3134.
3. Araki, T. (1992) An analysis of the effect of changes in growth temperature on proteolysis in vivo in the psychrophilic bacterium Vibrio sp. strain ANT-300. J Gen Microbiol 138: 2075-2082.
4. Bandow, J.E., and Hecker, M. (2007) Proteomic profiling of cellular stresses in Bacillus subtilis reveals cellular networks and assists in elucidating antibiotic mechanisms of action. Prog Drug Res 64: 81-101.
5. Becker, J., and Wittmann, C. (2012) Bio-based production of chemicals, materials and fuels - Corynebacterium glutamicum as versatile cell factory. Curr Opin Biotechnol 23: 631-640.
6. Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., etal. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147.
7. Camus, J.C., Pryor, M.J., Medigue, C., and Cole, S.T. (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148: 2967-2973.
8. Cargile, B.J., Bundy, J.L., Grunden, A.M., and Stephenson, J.L., Jr (2004) Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover. Anal Chem 76: 86-97.
9. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372.
10. Dieterich, D.C., Link, A.J., Graumann, J., Tirrell, D.A., and Schuman, E.M. (2006) Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci USA 103: 9482-9487.
11. Doherty, M.K., and Beynon, R.J. (2006) Protein turnover on the scale of the proteome. Expert Rev Proteomics 3: 97-110.
12. Doherty, M.K., Hammond, D.E., Clague, M.J., Gaskell, S.J., and Beynon, R.J. (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J Proteome Res 8: 104-112.
13. Fischer, F., Wolters, D., Rogner, M., and Poetsch, A. (2006) Toward the complete membrane proteome: high coverage of integral membrane proteins through transmembrane peptide detection. Mol Cell Proteomics 5: 444-453.
14. Franzel, B., Trotschel, C., Ruckert, C., Kalinowski, J., Poetsch, A., and Wolters, D.A. (2010) Adaptation of Corynebacterium glutamicum to salt-stress conditions. Proteomics 10: 445-457.
15. Gerth, U., Kock, H., Kusters, I., Michalik, S., Switzer, R.L., and Hecker, M. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190: 321-331.
16. Guan, S., Price, J.C., Prusiner, S.B., Ghaemmaghami, S., and Burlingame, A.L. (2011) A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol Cell Proteomics 10: M111.010728.
17. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97: 9390-9395.
18. Haegler, K., Mueller, N.S., Maccarrone, G., Hunyadi-Gulyas, E., Webhofer, C., Filiou, M.D., etal. (2009) QuantiSpec - quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins. J Proteomics 71: 601-608.
19. Jayapal, K.P., Philp, R.J., Kok, Y.J., Yap, M.G., Sherman, D.H., Griffin, T.J., and Hu, W.S. (2008) Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS ONE 3: e2097.
20. Jayapal, K.P., Sui, S., Philp, R.J., Kok, Y.J., Yap, M.G., Griffin, T.J., and Hu, W.S. (2010) Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. J Proteome Res 9: 2087-2097.
21. Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., etal. (2003) The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol 104: 5-25.
22. Kinoshita, S., Udaka, S., and Shimono, M. (2004) Studies on the amino acid fermentation. Part 1. Production of L-glutamic acid by various microorganisms. J Gen Appl Microbiol 50: 331-343.
23. Kramer, G., Sprenger, R.R., Back, J., Dekker, H.L., Nessen, M.A., van Maarseveen, J.H., etal. (2009) Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Mol Cell Proteomics 8: 1599-1611.
24. Kramer, R., and Morbach, S. (2004) BetP of Corynebacterium glutamicum, a transporter with three different functions: betaine transport, osmosensing, and osmoregulation. Biochim Biophys Acta 1658: 31-36.
25. Larrabee, K.L., Phillips, J.O., Williams, G.J., and Larrabee, A.R. (1980) The relative rates of protein synthesis and degradation in a growing culture of Escherichia coli. J Biol Chem 255: 4125-4130.
26. MacCoss, M.J., Wu, C.C., Liu, H., Sadygov, R., and Yates, J.R., 3rd (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem 75: 6912-6921.
27. Maier, T., Schmidt, A., Guell, M., Kuhner, S., Gavin, A.C., Aebersold, R., and Serrano, L. (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511.
28. Manteca, A., Jung, H.R., Schwammle, V., Jensen, O.N., and Sanchez, J. (2010) Quantitative proteome analysis of Streptomyces coelicolor nonsporulating liquid cultures demonstrates a complex differentiation process comparable to that occurring in sporulating solid cultures. J Proteome Res 9: 4801-4811.
29. Manteca, A., Ye, J., Sanchez, J., and Jensen, O.N. (2011) Phosphoproteome analysis of Streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation. J Proteome Res 10: 5481-5492.
30. Michalik, S., Liebeke, M., Zuhlke, D., Lalk, M., Bernhardt, J., Gerth, U., and Hecker, M. (2009) Proteolysis during long-term glucose starvation in Staphylococcus aureus COL. Proteomics 9: 4468-4477.
31. Michalik, S., Bernhardt, J., Otto, A., Moche, M., Becher, D., Meyer, H., etal. (2012) Life and death of proteins: a case study of glucose-starved Staphylococcus aureus. Mol Cell Proteomics 11: 558-570.
32. Muffler, A., Bettermann, S., Haushalter, M., Horlein, A., Neveling, U., Schramm, M., and Sorgenfrei, O. (2002) Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. J Biotechnol 98: 255-268.
33. Pan, C., Kora, G., McDonald, W.H., Tabb, D.L., VerBerkmoes, N.C., Hurst, G.B., etal. (2006) ProRata: a quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Anal Chem 78: 7121-7131.
34. Pine, M.J. (1972) Turnover of intracellular proteins. Annu Rev Microbiol 26: 103-126.
35. Pratt, J.M., Petty, J., Riba-Garcia, I., Robertson, D.H., Gaskell, S.J., Oliver, S.G., and Beynon, R.J. (2002) Dynamics of protein turnover, a missing dimension in proteomics. Mol Cell Proteomics 1: 579-591.
36. Rao, P.K., Rodriguez, G.M., Smith, I., and Li, Q. (2008a) Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-Fourier transform mass spectrometry. Anal Chem 80: 6860-6869.
37. Rao, P.K., Roxas, B.A., and Li, Q. (2008b) Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-Fourier transform mass spectrometry. Anal Chem 80: 396-406.
38. Rodriguez, G.M., Voskuil, M.I., Gold, B., Schoolnik, G.K., and Smith, I. (2002) ideR, an essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect Immun 70: 3371-3381.
39. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R., and Rajewsky, N. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
40. Shiloh, M.U., and DiGiuseppe Champion, P.A. (2010) To catch a killer. What can mycobacterial models teach us about Mycobacterium tuberculosis pathogenesis?, Curr Opin Microbiol 13: 86-92.
41. Snijders, A.P., de Koning, B., and Wright, P.C. (2005) Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics. J Proteome Res 4: 2185-2191.
42. Sperling, E., Bunner, A.E., Sykes, M.T., and Williamson, J.R. (2008) Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution. Anal Chem 80: 4906-4917.
43. Stackebrandt, E., Rainey, F.A., and Ward-Rainey, N.L. (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47: 479-491.
44. Stone, K.L., DeAngelis, R., LoPresti, M., Jones, J., Papov, V.V., and Williams, K.R. (1998) Use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Electrophoresis 19: 1046-1052.
45. Takahashi, M., and Ono, Y. (2003) Pulse-chase analysis of protein kinase C. Methods Mol Biol 233: 163-170.
46. Timmins, G.S., Master, S., Rusnak, F., and Deretic, V. (2004a) Requirements for nitric oxide generation from isoniazid activation in vitro and inhibition of mycobacterial respiration in vivo. J Bacteriol 186: 5427-5431.
47. Timmins, G.S., Master, S., Rusnak, F., and Deretic, V. (2004b) Nitric oxide generated from isoniazid activation by KatG: source of nitric oxide and activity against Mycobacterium tuberculosis. Antimicrob Agents Chemother 48: 3006-3009.
48. Trotschel, C., Albaum, S.P., Wolff, D., Schroder, S., Goesmann, A., Nattkemper, T.W., and Poetsch, A. (2012) Protein turnover quantification in a multilabeling approach: from data calculation to evaluation. Mol Cell Proteomics 11: 512-526.
49. Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G.F., Chater, K.F., and van Sinderen, D. (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71: 495-548.
50. Voges, R., and Noack, S. (2012) Quantification of proteome dynamics in Corynebacterium glutamicum by (15)N-labeling and selected reaction monitoring. J Proteomics 75: 2660-2669.
51. Voskuil, M.I., Schnappinger, D., Visconti, K.C., Harrell, M.I., Dolganov, G.M., Sherman, D.R., and Schoolnik, G.K. (2003) Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med 198: 705-713.
52. Wang, M., You, J., Bemis, K.G., Tegeler, T.J., and Brown, D.P. (2008) Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 7: 329-339.
53. Washburn, M.P., Wolters, D., and Yates, J.R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19: 242-247.
54. Weinand, M., Kramer, R., and Morbach, S. (2007) Characterization of compatible solute transporter multiplicity in Corynebacterium glutamicum. Appl Microbiol Biotechnol 76: 701-708.
55. Wolters, D.A., Washburn, M.P., and Yates, J.R., 3rd (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73: 5683-5690.
56. Zhang, Y., Reckow, S., Webhofer, C., Boehme, M., Gormanns, P., Egge-Jacobsen, W.M., and Turck, C.W. (2011) Proteome scale turnover analysis in live animals using stable isotope metabolic labeling. Anal Chem 83: 1665-1672.