Application of Proteomics in Bioremediation

Peter Chovanec; Partha Basu; John F. Stolz

doi:10.1128/9781555817190.ch13

Chapter 13 : Application of Proteomics in Bioremediation

Authors: Peter Chovanec¹, Partha Basu², John F. Stolz³

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Affiliations: 1: Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282; 2: Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282; 3: Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282

Content Type: Monograph

Publication Year: 2011

Category: Applied and Industrial Microbiology; Environmental Microbiology

Book DOI: 10.1128/9781555817190

Chapter DOI: 10.1128/9781555817190.ch13

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Abstract:

This chapter reviews proteomics in the context of bioremediation by presenting how this approach has helped elucidate mechanisms of survival in contaminated and extreme environments, the transformation of toxic compounds, and the metabolic pathways and enzymes involved in these processes. It provides a brief review of the techniques and approaches for protein separation and identification that are employed. The chapter includes case studies of microbial community proteomics and the transformation of metals and metalloids in pure cultures. Proteomics is especially useful for examining organisms that possess a wide variety of metabolic and energetic pathways. The application of this approach to an environmental sample, “environmental proteomics,” can provide information on the proteome of the dominant microbial species or the metaproteome of the microbial community under specific environmental conditions. Gel-to-gel variation, which can impair this alignment, has been overcome through the use of precast gels and differential in gel electrophoresis (DIGE) analysis. The isolation and characterization of bacteria from contaminated environments is often the starting point for proteomic analyses. With more rapid development of analytical tools and bioinformatics comes the promise of identifying novel biomarkers relevant to bioremediation. In addition to further improvements in mass spectrometry, development of more efficient and cost-effective methods for protein extraction from microbial communities and improvement in bioinformatics tools will be needed for more accurate identification of proteins from shotgun proteomics.

Citation: Chovanec P, Basu P, Stolz J. 2011. Application of Proteomics in Bioremediation, p 247-259. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch13

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Application of Proteomics in Bioremediation

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FIGURE 1

Application of “-omic” approaches to both pure cultures and microbial communities for assessing the bioremediation of contaminated environments. 10.1128/9781555817190.ch13.f1

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FIGURE 1

Application of “-omic” approaches to both pure cultures and microbial communities for assessing the bioremediation of contaminated environments. 10.1128/9781555817190.ch13.f1

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FIGURE 2

Workflow of MS-driven proteomics in bioremediation studies. Gel (1D and 2D separation) versus gel-free separation of proteins followed by tryptic digestion and MS analyses (MALDI-TOF/MS, LC-MS/MS, multidimensional protein identification technology [MudPIT] coupled with tandem MS). 10.1128/9781555817190.ch13.f2

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FIGURE 2

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FIGURE 3

Two-dimensional gel electrophoresis (18 cm, pH 3 to 11) of proteins from nitrate grown cultures of Desulfovibrio desulfuricans (250 μg of cell lysate) and visualized with Coomassie brilliant blue. The proteins are first separated by charge through isoelectric focusing (first dimension), then by molecular weight using sodium dodecyl sulfate polyacrylamide gel electrophoresis (second dimension). Several hundreds of individual proteins can be resolved and quantified, including posttranslationally modified isoforms. 10.1128/9781555817190.ch13.f3

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FIGURE 3

References

/content/book/10.1128/9781555817190.ch13

1. Bansal, R.,, L. A. Deobald,, R. L. Crawford, and, A. J. Paszczynski. 2009. Proteomic detection of proteins involved in perchlorate and chlorate metabolism. Biodegradation 20: 603– 620.

2. Bencheikh-Latmani, R.,, S. M. Williams,, L. Haucke,, C. S. Criddle,, L. Wu,, J. Zhou, and, B. M. Tebo. 2005. Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl. Environ. Microbiol. 71: 7453– 7460.

3. Benndorf, D.,, G. U. Balcke,, H. Harms, and, M. von Bergen. 2007. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 1: 224– 234.

4. Benndorf, D.,, C. Vogt,, N. Jehmlich,, Y. Schmidt,, H. Thomas,, G. Woffendin,, A. Shevchenko,, H. H. Richnow, and, M. von Bergen. 2009. Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 20: 737– 750.

5. Cao, B.,, A. Geng, and, K. C. Loh. 2008. Induction of ortho-and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes. Appl. Microbiol. Biotechnol. 81: 99– 107.

6. Caraux, G.,, and S. Pinloche. 2005. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 21: 1280– 1281.

7. Chain, P. S.,, V. J. Denef,, K. T. Konstantinidis,, L. M. Vergez,, L. Agulló,, V. L. Reyes,, L. Hauser,, M. Córdova,, L. Gómez,, M. González,, M. Land,, V. Lao,, F. Larimer,, J. J. LiPuma,, E. Mahenthiralingam,, S. A. Malfatti,, C. J. Marx,, J. J. Parnell,, A. Ramette,, P. Richardson,, M. Seeger,, D. Smith,, T. Spilker,, W. J. Sul,, T. V. Tsoi,, L. E. Ulrich,, I. B. Zhulin, and, J. M. Tiedje. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc. Natl. Acad. Sci. USA 103: 15280– 15287.

8. Chourey, K.,, M. R. Thompson,, M. Shah,, B. Zhang,, N. C. Verberkmoes,, D. K. Thompson, and, R. L. Hettich. 2009. Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation. J. Proteome Res. 8: 59– 71.

9. Chovanec, P.,, P. Basu, and, J. F. Stolz. 2010. A proteome investigation of roxarsone degradation by Alkaliphilus oremlandii strain OhILAs. Metallomics 2: 133– 139.

10. De Vriendt, K.,, S. Theunissen,, W. Carpentier,, L. De Smet,, B. Devreese, and, J. Van Beeumen. 2005. Proteomics of Shewanella oneidensis MR-1 biofilm reveals differentially expressed proteins, including AggA and RibB. Proteomics 5: 1308– 1316.

11. Ding, Y. H.,, K. K. Hixson,, M. A. Aklujkar,, M. S. Lipton,, R. D. Smith,, D. R. Lovley, and, T. Mester. 2008. Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as electron acceptor. Biochim. Biophys. Acta 1784: 1935– 1941.

12. Dopson, M.,, C. Baker-Austin, and, P. L. Bond. 2004. First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships. J. Microbiol. Methods 58: 297– 302.

13. Dowling, V. A.,, and D. Sheehan. 2006. Proteomics as a route to identification of toxicity targets in environmental toxicology. Proteomics 6: 5597– 5604.

14. Dworzanski, J. P.,, and A. P. Snyder. 2005. Classification and identification of bacteria using mass spectrometry-based proteomics. Expert Rev. Proteomics 2: 863– 878.

15. Elias, D. A.,, M. E. Monroe,, M. J. Marshall,, M. F. Romine,, A. S. Belieav,, J. K. Fredrickson,, G. A. Anderson,, R. D. Smith, and, M. S. Lipton. 2005. Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics. Proteomics 5: 3120– 3130.

16. Feng, L.,, W. Wang,, J. Cheng,, Y. Ren,, G. Zhao,, C. Gao,, Y. Tang,, X. Liu,, W. Han,, X. Peng,, R. Liu, and, L. Wang. 2007. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc. Natl. Acad. Sci. USA 104: 5602– 5607.

17. Fenselau, C.,, and P. A. Demirev. 2001. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20: 157– 171.

18. Goltsman, D. S.,, V. J. Denef,, S. W. Singer,, N. C. VerBerkmoes,, M. Lefsrud,, R. S. Mueller,, G. J. Dick,, C. L. Sun,, K. E. Wheeler,, A. Zemla,, B. J. Baker,, L. Hauser,, M. Land,, M. B. Shah,, M. P. Thelen,, R. L. Hettich, and, J. F. Banfield. 2009. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing “ Leptospirillum rubarum” (Group II) and “ Leptospirillum ferrodiazotrophum” (Group III) bacteria in acid mine drainage biofilms. Appl. Environ. Microbiol. 75: 4599– 4615.

19. Gorby, Y. A.,, F. Caccavo, Jr., and, H. Bolton, Jr. 1998. Microbial reduction of cobalt III EDTA - in the presence and absence of manganese (IV) oxide. Environ. Sci. Technol. 32: 244– 250.

20. Heidelberg, J. F.,, I. T. Paulsen,, K. E. Nelson,, E. J. Gaidos,, W. C. Nelson,, T. D. Read,, J. A. Eisen,, R. Seshadri,, N. Ward,, B. Methe,, R. A. Clayton,, T. Meyer,, A. Tsapin,, J. Scott,, M. Beanan,, L. Brinkac,, S. Daugherty,, R. T. DeBoy,, R. J. Dodson,, A. S. Durkin,, D. H. Haft,, J. F. Kolonay,, R. Madupu,, J. D. Peterson,, L. A. Umayam,, O. White,, A. M. Wolf,, J. Vamathevan,, J. Weidman,, M. Impraim,, K. Lee,, K. Berry,, C. Lee,, J. Mueller,, H. Khouri,, J. Gill,, T. R. Utterback,, L. A. McDonald,, T. V. Feldblyum,, H. O. Smith,, J. C. Venter,, K. H. Nealson, and, C. M. Fraser. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20: 1118– 1123.

21. Heidelberg, J. F.,, R. Seshadri,, S. A. Haveman,, C. L. Hemme,, I. T. Paulsen,, J. F. Kolonay,, J. A. Eisen,, N. Ward,, B. Methe,, L. M. Brinkac,, S. C. Daugherty,, R. T. Deboy,, R. J. Dodson,, A. S. Durkin,, R. Madupu,, W. C. Nelson,, S. A. Sullivan,, D. Fouts,, D. H. Haft,, J. Selengut,, J. D. Peterson,, T. M. Davidsen,, N. Zafar,, L. Zhou,, D. Radune,, G. Dimitrov,, M. Hance,, K. Tran,, H. Khouri,, J. Gill,, T. R. Utterback,, T. V. Feldblyum,, J. D. Wall,, G. Voordouw, and, C. M. Fraser. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol. 22: 554– 559.

22. Jennings, L. K.,, M. M. Chartrand,, G. Lacrampe-Couloume,, B. S. Lollar,, J. C. Spain, and, J. M. Gossett. 2009. Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp. strain JS666. Appl. Environ. Microbiol. 75: 3733– 3744.

23. Kabiri, M.,, M. A. Amoozegar,, M. Tabebordbar,, K. Gilany, and, G. H. Salekdeh. 2009. Effects of selenite and tellurite on growth, physiology, and proteome of a moderately halophilic bacterium. J. Proteome Res. 8: 3098– 3108.

24. Kan, J.,, T. E. Hanson,, J. M. Ginter,, K. Wang, and, F. Chen. 2005. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst. 1: 7.

25. Keller, M.,, and R. Hettich. 2009. Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol. Mol. Biol. Rev. 73: 62– 70.

26. Kim, S. I.,, J. S. Choi, and, H. Y. Kahng. 2007. A proteomics strategy for the analysis of bacterial biodegradation pathways. OMICS 11: 280– 294.

27. Kim, S. I.,, S. Y. Song,, K. W. Kim,, E. M. Ho, and, K. H. Oh. 2003. Proteomic analysis of the benzoate degradation pathway in Acinetobacter sp. KS-1. Res. Microbiol. 154: 697– 703.

28. Kim, S. J.,, R. C. Jones,, C. J. Cha,, O. Kweon,, R. D. Edmondson, and, C. E. Cerniglia. 2004. 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 4: 3899– 3908.

29. Kim, S. J.,, O. Kweon, and, C. E. Cerniglia. 2009. Proteomic applications to elucidate bacterial aromatic hydrocarbon metabolic pathways. Curr. Opin. Microbiol. 12: 301– 309.

30. Kim, Y. H.,, K. Cho,, S. H. Yun,, J. Y. Kim,, K. H. Kwon,, J. S. Yoo, and, S. I. Kim. 2006. 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 6: 1301– 1318.

31. Kolker, E.,, A. F. Picone,, M. Y. Galperin,, M. F. Romine,, R. Higdon,, K. S. Makarova,, N. Kolker,, G. A. Anderson,, X. Qiu,, K. J. Auberry,, G. Babnigg,, A. S. Beliaev,, P. Edlefsen,, D. A. Elias,, Y. A. Gorby,, T. Holzman,, J. A. Klappenbach,, K. T. Konstantinidis,, M. L. Land,, M. S. Lipton,, L. A. McCue,, M. Monroe,, L. Pasa-Tolic,, G. Pinchuk,, S. Purvine,, M. H. Serres,, S. Tsapin,, B. A. Zakrajsek,, W. Zhu,, J. Zhou,, F. W. Larimer,, C. E. Lawrence,, M. Riley,, F. R. Collart,, J. R. Yates III,, R. D. Smith,, C. S. Giometti,, K. H. Nealson,, J. K. Fredrickson, and, J. M. Tiedje. 2005. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc. Natl. Acad. Sci. USA 102: 2099– 2104.

32. Krayl, M.,, D. Benndorf,, N. Loffhagen, and, W. Babel. 2003. Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440. Proteomics 3: 1544– 1552.

33. Kühner, S.,, L. Wöhlbrand,, I. Fritz,, W. Wruck,, C. Hultschig,, P. Hufnagel,, M. Kube,, R. Reinhardt, and, R. Rabus. 2005. Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J. Bacteriol. 187: 1493– 1503.

34. Kumar, R.,, S. Singh, and, O. V. Singh. 2007. Bioremediation of radionuclides: emerging technologies. OMICS 11: 295– 304.

35. Kweon, O.,, S. J. Kim,, R. C. Jones,, J. P. Freeman,, M. D. Adjei,, R. D. Edmondson, and, C. E. Cerniglia. 2007. A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 189: 4635– 4647.

36. Lacerda, C. M.,, L. H. Choe, and, K. F. Reardon. 2007. Metaproteomic analysis of a bacterial community response to cadmium exposure. J. Proteome Res. 6: 1145– 1152.

37. Lacerda, C. M.,, and K. F. Reardon. 2009. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Brief. Funct. Genomic Proteomic 8: 75– 87.

38. Lay, J. O., Jr. 2001. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 20: 172– 194.

39. Lee, B. U.,, S. C. Park,, Y. S. Cho, and, K. H. Oh. 2008. Exopolymer biosynthesis and proteomic changes of Pseudomonas sp. HK-6 under stress of TNT (2,4,6-trinitrotoluene). Curr. Microbiol. 57: 477– 483.

40. Liang, Y.,, D. R. Gardner,, C. D. Miller,, D. Chen,, A. J. Anderson,, B. C. Weimer, and, R. C. Sims. 2006. Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS. Appl. Environ. Microbiol. 72: 7821– 7828.

41. Lo, I.,, V. J. Denef,, N. C. Verberkmoes,, M. B. Shah,, D. Goltsman,, G. DiBartolo,, G. W. Tyson,, E. E. Allen,, R. J. Ram,, J. C. Detter,, P. Richardson,, M. P. Thelen,, R. L. Hettich, and, J. F. Banfield. 2007. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446: 537– 541.

42. López-Barea, J.,, and J. L. Gómez-Ariza. 2006. Environmental proteomics and metallomics. Proteomics 6 (Suppl. 1): S51– S62.

43. Lupi, C. G.,, T. Colangelo, and, C. A. Mason. 1995. Two-dimensional gel electrophoresis analysis of the response of Pseudomonas putida KT2442 to 2-chlorophenol. Appl. Environ. Microbiol. 61: 2863– 2872.

44. Markowitz, V. M.,, I. M. Chen,, K. Palaniappan,, K. Chu,, E. Szeto,, Y. Grechkin,, A. Ratner,, I. Anderson,, A. Lykidis,, K. Mavromatis,, N. N. Ivanova, and, N. C. Kyrpides. 2010. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38: D382– D390.

45. Maron, P. A.,, L. Ranjard,, C. Mougel, and, P. Lemanceau. 2007. Metaproteomics: a new approach for studying functional microbial ecology. Microb. Ecol. 53: 486– 493.

46. Marshall, M. J.,, A. E. Plymale,, D. W. Kennedy,, L. Shi,, Z. Wang,, S. B. Reed,, A. C. Dohnalkova,, C. J. Simonson,, C. Liu,, D. A. Saffarini,, M. F. Romine,, J. M. Zachara,, A. S. Beliaev, and, J. K. Fredrickson. 2008. Hydrogenase-and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1. Environ. Microbiol. 10: 125– 136.

47. Martínez, P.,, L. Agulló,, M. Hernández, and, M. Seeger. 2007. Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400. Arch. Microbiol. 188: 289– 297.

48. Mazzoli, R.,, E. Pessione,, M. G. Giuffrida,, P. Fattori,, C. Barello,, C. Giunta, and, N. D. Lindley. 2007. Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures. Arch. Microbiol. 188: 55– 68.

49. McLeod, M. P.,, R. L. Warren,, W. W. Hsiao,, N. Araki,, M. Myhre,, C. Fernandes,, D. Miyazawa,, W. Wong,, A. L. Lillquist,, D. Wang,, M. Dosanjh,, H. Hara,, A. Petrescu,, R. D. Morin,, G. Yang,, J. M. Stott,, J. E. Schein,, H. Shin,, D. Smailus,, A. S. Siddiqui,, M. A. Marra,, S. J. Jones,, R. Holt,, F. S. Brinkman,, K. Miyauchi,, M. Fukuda,, J. E. Davies,, W. W. Mohn, and, L. D. Eltis. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. USA 103: 15582– 15587.

50. Methé, B. A.,, K. E. Nelson,, J. A. Eisen,, I. T. Paulsen,, W. Nelson,, J. F. Heidelberg,, D. Wu,, M. Wu,, N. Ward,, M. J. Beanan,, R. J. Dodson,, R. Madupu,, L. M. Brinkac,, S. C. Daugherty,, R. T. DeBoy,, A. S. Durkin,, M. Gwinn,, J. F. Kolonay,, S. A. Sullivan,, D. H. Haft,, J. Selengut,, T. M. Davidsen,, N. Zafar,, O. White,, B. Tran,, C. Romero,, H. A. Forberger,, J. Weidman,, H. Khouri,, T. V. Feldblyum,, T. R. Utterback,, S. E. Van Aken,, D. R. Lovley, and, C. M. Fraser. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 302: 1967– 1969.

51. Monsinjon, T.,, and T. Knigge. 2007. Proteomic applications in ecotoxicology. Proteomics 7: 2997– 3009.

52. Nelson, K. E.,, C. Weinel,, I. T. Paulsen,, R. J. Dodson,, H. Hilbert,, V. A. Martins dos Santos,, D. E. Fouts,, S. R. Gill,, M. Pop,, M. Holmes,, L. Brinkac,, M. Beanan,, R. T. DeBoy,, S. Daugherty,, J. Kolonay,, R. Madupu,, W. Nelson,, O. White,, J. Peterson,, H. Khouri,, I. Hance,, P. Chris Lee,, E. Holtzapple,, D. Scanlan,, K. Tran,, A. Moazzez,, T. Utterback,, M. Rizzo,, K. Lee,, D. Kosack,, D. Moestl,, H. Wedler,, J. Lauber,, D. Stjepandic,, J. Hoheisel,, M. Straetz,, S. Heim,, C. Kiewitz,, J. A. Eisen,, K. N. Timmis,, A. Düsterhöft,, B. Tümmler, and, C. M. Fraser. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4: 799– 808.

53. Nesatyy, V. J.,, and M. J. Suter. 2007. Proteomics for the analysis of environmental stress responses in organisms. Environ. Sci. Technol. 41: 6891– 6900.

54. Nesatyy, V. J.,, and M. J. Suter. 2008. Analysis of environmental stress response on the proteome level. Mass Spectrom. Rev. 27: 556– 574.

55. Park, C.,, and R. F. Helm. 2008. Application of metaproteomic analysis for studying extracellular polymeric substances (EPS) in activated sludge flocs and their fate in sludge digestion. Water Sci. Technol. 57: 2009– 2015.

56. Pérez-Pantoja, D.,, R. De la Iglesia,, D. H. Pieper, and, B. González. 2008. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol. Rev. 32: 736– 794.

57. Picardal, F.,, R. G. Arnold, and, B. B. Huey. 1995. Effects of electron donor and acceptor conditions on reductive dehalogenation of tetrachloromethane by Shewanella putrefaciens 200. Appl. Environ. Microbiol. 61: 8– 12.

58. Rabus, R.,, M. Kube,, J. Heider,, A. Beck,, K. Heitmann,, F. Widdel, and, R. Reinhardt. 2005. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch. Microbiol. 183: 27– 36.

59. Ram, R. J.,, N. C. Verberkmoes,, M. P. Thelen,, G. W. Tyson,, B. J. Baker,, R. C. Blake II,, M. Shah,, R. L. Hettich, and, J. F. Banfield. 2005. Community proteomics of a natural microbial bio-film. Science 308: 1915– 1920.

60. Reardon, K. F.,, and K. H. Kim. 2002. Two-dimensional electrophoresis analysis of protein production during growth of Pseudomonas putida F1 on toluene, phenol, and their mixture. Electrophoresis 23: 2233– 2241.

61. Richey, C.,, P. Chovanec,, S. E. Hoeft,, R. S. Oremland,, P. Basu, and, J. F. Stolz. 2009. Respiratory arsenate reductase as a bidirectional enzyme. Biochem. Biophys. Res. Commun. 382: 298– 302.

62. Saltikov, C. W.,, R. A. Wildman, Jr., and, D. K. Newman. 2005. Expression dynamics of arsenic respiration and detoxification in Shewanella sp. strain ANA-3. J. Bacteriol. 187: 7390– 7396.

63. Santos, P. M.,, D. Benndorf, and, I. Sá-Correia. 2004. Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4: 2640– 2652.

64. Santos, P. M.,, V. Roma,, D. Benndorf,, M. von Bergen,, H. Harms, and, I. Sá-Correia. 2007. Mechanistic insights into the global response to phenol in the phenol-biodegrading strain Pseudomonas sp. M1 revealed by quantitative proteomics. OMICS 11: 233– 251.

65. Schneiker, S.,, V. A. Martins dos Santos,, D. Bartels,, T. Bekel,, M. Brecht,, J. Buhrmester,, T. N. Chernikova,, R. Denaro,, M. Ferrer,, C. Gertler,, A. Goesmann,, O. V. Golyshina,, F. Kaminski,, A. N. Khachane,, S. Lang,, B. Linke,, A. C. McHardy,, F. Meyer,, T. Nechitaylo,, A. Pühler,, D. Regenhardt,, O. Rupp,, J. S. Sabirova,, W. Selbitschka,, M. M. Yakimov,, K. N. Timmis,, F. J. Vorhölter,, S. Weidner,, O. Kaiser, and, P. N. Golyshin. 2006. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat. Biotechnol. 24: 997– 1004.

66. Schulze, W. X.,, G. Gleixner,, K. Kaiser,, G. Guggenberger,, M. Mann, and, E. D. Schulze. 2005. A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142: 335– 343.

67. Schweder, T.,, S. Markert, and, M. Hecker. 2008. Proteomics of marine bacteria. Electrophoresis 29: 2603– 2616.

68. Segura, A.,, P. Godoy,, P. van Dillewijn,, A. Hurtado,, N. Arroyo,, S. Santacruz, and, J. L. Ramos. 2005. Proteomic analysis reveals the participation of energy-and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J. Bacteriol. 187: 5937– 5945.

69. Seshadri, R.,, L. Adrian,, D. E. Fouts,, J. A. Eisen,, A. M. Phillippy,, B. A. Methe,, N. L. Ward,, W. C. Nelson,, R. T. Deboy,, H. M. Khouri,, J. F. Kolonay,, R. J. Dodson,, S. C. Daugherty,, L. M. Brinkac,, S. A. Sullivan,, R. Madupu,, K. E. Nelson,, K. H. Kang,, M. Impraim,, K. Tran,, J. M. Robinson,, H. A. Forberger,, C. M. Fraser,, S. H. Zinder, and, J. F. Heidelberg. 2005. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307: 105– 108.

70. Sharma, S.,, C. S. Sundaram,, P. M. Luthra,, Y. Singh,, R. Sirdeshmukh, and, W. N. Gade. 2006. Role of proteins in resistance mechanism of Pseudomonas fluorescens against heavy metal induced stress with proteomics approach. J. Biotechnol. 126: 374– 382.

71. Shevchenko, A.,, S. Sunyaev,, A. Loboda,, A. Shevchenko,, P. Bork,, W. Ens, and, K. G. Standing. 2001. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal. Chem. 73: 1917– 1926.

72. Singh, O. V.,, and N. S. Nagaraj. 2006. Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation. Brief. Funct. Genomic Proteomic 4: 355– 362.

73. Sowell, S. M.,, L. J. Wilhelm,, A. D. Norbeck,, M. S. Lipton,, C. D. Nicora,, D. F. Barofsky,, C. A. Carlson,, R. D. Smith, and, S. J. Giovanonni. 2009. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 3: 93– 105.

74. Streit, W. R.,, and R. A. Schmitz. 2004. Metagenomics—the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492– 498.

75. Tam Le, T.,, C. Eymann,, D. Albrecht,, R. Sietmann,, F. Schauer,, M. Hecker, and, H. Antelmann. 2006. Differential gene expression in response to phenol and catechol reveals different metabolic activities for the degradation of aromatic compounds in Bacillus subtilis. Environ. Microbiol. 8: 1408– 1427.

76. Tomás-Gallardo, L.,, I. Canosa,, E. Santero,, E. Camafeita,, E. Calvo,, J. A. López, and, B. Floriano. 2006. Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB. Proteomics 6 (Suppl. 1): S119– S132.

77. van Baar, B. L. 2000. Characterisation of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry. FEMS Microbiol. Rev. 24: 193– 219.

78. Wall, J. D.,, and L. R. Krumholz. 2006. Uranium reduction. Annu. Rev. Microbiol. 60: 149– 166.

79. Wasinger, V. C.,, S. J. Cordwell,, A. Cerpa-Poljak,, J. X. Yan,, A. A. Gooley,, M. R. Wilkins,, M. W. Duncan,, R. Harris,, K. L. Williams, and, I. Humphery-Smith. 1995. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16: 1090– 1094.

80. Wiatrowski, H. A.,, P. M. Ward, and, T. Barkay. 2006. Novel reduction of mercury (II) by mercurysensitive dissimilatory metal reducing bacteria. Environ. Sci. Technol. 40: 6690– 6696.

81. Wilkins, M. J.,, N. C. Verberkmoes,, K. H. Williams,, S. J. Callister,, P. J. Mouser,, H. Elifantz,, A. L. N’Guessan,, B. C. Thomas,, C. D. Nicora,, M. B. Shah,, P. Abraham,, M. S. Lipton,, D. R. Lovley,, R. L. Hettich,, P. E. Long, and, J. F. Banfield. 2009. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl. Environ. Microbiol. 75: 6591– 6599.

82. Wilmes, P.,, and P. L. Bond. 2004. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 6: 911– 920.

83. Wilmes, P.,, M. Wexler, and, P. L. Bond. 2008a. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3: e1778.

84. Wilmes, P.,, A. F. Andersson,, M. G. Lefsrud,, M. Wexler,, M. Shah,, B. Zhang,, R. L. Hettich,, P. L. Bond,, N. C. VerBerkmoes, and, J. F. Banfield. 2008b. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2: 853– 864.

85. Wilmes, P.,, and P. L. Bond. 2009. Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth’s biogeochemical cycles. Curr. Opin. Microbiol. 12: 310– 317.

86. Wöhlbrand, L.,, B. Kallerhoff,, D. Lange,, P. Hufnagel,, J. Thiermann,, R. Reinhardt, and, R. Rabus. 2007. Functional proteomic view of metabolic regulation in “ Aromatoleum aromaticum” strain EbN1. Proteomics 7: 2222– 2239.

87. Wood, T. K. 2008. Molecular approaches in bioremediation. Curr. Opin. Biotechnol. 19: 572– 578.

88. Zhao, B.,, and C. L. Poh. 2008. Insights into environmental bioremediation by microorganisms through functional genomics and proteomics. Proteomics 8: 874– 881.

89. Zhao, B.,, C. C. Yeo, and, C. L. Poh. 2005. Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867. Proteomics 5: 1868– 1876.

90. Zhao, J. S.,, J. Spain,, S. Thiboutot,, G. Ampleman,, C. Greer, and, J. Hawari. 2004. Phylogeny of cyclic nitramine-degrading psychrophilic bacteria in marine sediment and their potential role in the natural attenuation of explosives. FEMS Microbiol. Ecol. 49: 349– 357.