Skip to main content
SpringerLink
Log in

Biodegradation: gaining insight through proteomics

  • Review Paper
  • Published:
Biodegradation Aims and scope Submit manuscript

Abstract

Biodegradation, a generic term used to describe methodologies to affect cleanup of environmental pollutants, has come up as an improved substitute for ineffective and expensive physico-chemical remediation methods. However, lack of information about the factors controlling the growth and metabolism of microorganisms in the polluted environment often limits its implementation. Recent advances in the understanding of biogeochemical processes and genomics have opened up new perspectives towards new opportunities of pollution abatement. High throughput genomic techniques have revolutionized the remediation process leading to breakthroughs in characterizing proteomes, metabolomes and phenotypes for organisms, communities and populations. These new techniques have allowed us to address longstanding questions regarding the molecular mechanisms that may control the mineralization processes and have an in-depth understanding of microbial community structure and stress responses. In order to explore insights of biodegradation this article discusses ways in which proteomics may be able to meet challenges in biodegradation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198–207

    Article  CAS  PubMed  Google Scholar 

  • Agullo L, Camara B, Martinez P, Latorre V, Seeger M (2007) 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 267(2):167–175

    Article  CAS  PubMed  Google Scholar 

  • Alexander M (1984) Ecological constraints on genetic engineering. Basic Life Sci 28:151–168

    CAS  PubMed  Google Scholar 

  • Al-Tahhan RA, Sandrin TR, Bodour AA, Maier RM (2000) Rhamnolipid-induced removal of lipopolysaccharide from Pseudomonas aeruginosa: effect on cell surface properties and interaction with hydrophobic substrates. Appl Environ Microbiol 66(8):3262–3268

    Article  CAS  PubMed  Google Scholar 

  • Amann R, Fuchs BM, Behrens S (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol 12:231–236

    Article  CAS  PubMed  Google Scholar 

  • Anderson RT (2006) DOE genomics: applications to in situ subsurface bioremediation. Remediat J 17(1):23–38

    Article  Google Scholar 

  • Anderson IC, Cairney JW (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6(8):769–779

    Article  CAS  PubMed  Google Scholar 

  • Arai H, Ohishi T, Chang MY, Kudo T (2000) Arrangement and regulation of the genes for meta-pathway enzymes required for degradation of phenol in Comamonas testosteroni TA441. Microbiology 146(Pt 7):1707–1715

    CAS  PubMed  Google Scholar 

  • Aulenta F, Rossetti S, Majone M, Tandoi V (2004) Detection and quantitative estimation of Dehalococcoides spp. in a dechlorinating bioreactor by a combination of fluorescent in situ hybridisation (FISH) and kinetic analysis. Appl Microbiol Biotechnol 64:206–212

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Benndorf D, Vogt C, Jehmlich N, Schmidt Y, Thomas H, Woffendin G, Shevchenko A, Richnow HH, von Bergen M (2009) Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 20(6):737–750

    Article  CAS  PubMed  Google Scholar 

  • Blackstock WP, Weir MP (1999) Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 17(3):121–127

    Article  CAS  PubMed  Google Scholar 

  • Bleeker EA, Wiegman S, de Voogt P, Kraak M, Leslie HA, de Haas E, Admiraal W (2002) Toxicity of azaarenes. Rev Environ Contam Toxicol 173:39–83

    PubMed  Google Scholar 

  • Bojes HK, Pope PG (2007) Characterization of EPA’s 16 priority pollutant polycyclic aromatic hydrocarbons (PAHs) in tank bottom solids and associated contaminated soils at oil exploration and production sites in Texas. Regul Toxicol Pharmacol 47(3):288–295

    Article  CAS  PubMed  Google Scholar 

  • Breen A, Rope AF, Taylor D, Loper JC, Sferra PR (1995) Application of DNA amplification fingerprinting (DAF) to mixed culture bioreactors. J Ind Microbiol 14:10–16

    Article  CAS  PubMed  Google Scholar 

  • Busse HJ, Denner EB, Lubitz W (1996) Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J Biotechnol 47:3–38

    Article  CAS  PubMed  Google Scholar 

  • Cao B, Nagarajan K, Loh KC (2009) Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 85:207–228

    Article  CAS  PubMed  Google Scholar 

  • Caracciolo AB, Grenni P, Ciccoli R, Di Landa G, Cremisini C (2005) Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization. Pest Manag Sci 61:863–869

    Article  CAS  PubMed  Google Scholar 

  • Cho YS, Park SH, Kim CK, Oh KH (2000) Induction of stress shock proteins DnaK and GroEL by phenoxyherbicide 2,4-D in Burkholderia sp. YK-2 isolated from rice field. Curr Microbiol 41(1):33–38

    Article  CAS  PubMed  Google Scholar 

  • Chuang A, Jin YO, Schmidt LS, Li Y, Fogel S, Smoler D, Mattes TE (2010) Proteomics analysis of ethane enriched ground water microcosms from vinyl chloride contaminated site. Environ Sci Technol 44(5):1594–1601

    Article  CAS  PubMed  Google Scholar 

  • Cohen M (2007) Environmental toxins and health—the health impact of pesticides. Aust Fam Physician 36(12):1002–1014

    PubMed  Google Scholar 

  • Collins G, Kavanagh S, McHugh S, Connaughton S, Kearney A, Rice O, Carrigg C, Scully C, Bhreathnach N, Mahony T, Madden P, Enright AM, O’flaherty V (2006) Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments. J Environ Sci Health A 41:897–922

    CAS  Google Scholar 

  • Cristoni S, Bernardi LR (2003) Development of new methodologies for the mass spectrometry study of bioorganic macromolecules. Mass Spectrom Rev 22(6):369–406

    Article  CAS  PubMed  Google Scholar 

  • Cronan JE, Roughan PG (1987) Fatty acid specificity and selectivity of the chloroplast sn-glycerol 3-phosphate acyltransferase of the chilling sensitive plant, Amaranthus lividus. Plant Physiol 83(3):676–680

    Article  CAS  PubMed  Google Scholar 

  • de Melo Plese LP, Paraiba LC, Foloni LL, Pimentel Trevizan LR (2005) Kinetics of carbosulfan hydrolysis to carbofuran and the subsequent degradation of this last compound in irrigated rice fields. Chemosphere 60(2):149–156

    Article  PubMed  CAS  Google Scholar 

  • DeLong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50:470–478

    Article  CAS  PubMed  Google Scholar 

  • Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF (2009) Proteomics-inferred genome typing (PIGT) demonstrates interpopulation recombination as a strategy for environmental adaptation. Environ Microbiol 11:313–325

    Article  CAS  PubMed  Google Scholar 

  • Deutschbauer AM, Chivian D, Arkin AP (2006) Genomics for environmental microbiology. Curr Opin Biotechnol 17:229–235

    Article  CAS  PubMed  Google Scholar 

  • Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol 7(3):173–180

    CAS  PubMed  Google Scholar 

  • Diaz E, Prieto MA (2000) Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11(5):467–475

    Article  CAS  PubMed  Google Scholar 

  • Donlon BA, Razo-Flores E, Field JA, Lettinga G et al (1995) Toxicity of N-substituted aromatics to acetoclastic methanogenic activity in granular sludge. Appl Environ Microbiol 61(11):3889–3893

    CAS  PubMed  Google Scholar 

  • Donnes P, Hoglund A (2004) Predicting protein subcellular localization: past, present and future. Genomics Proteomics Bioinformatics 2(4):209–215

    PubMed  Google Scholar 

  • Dua M, Singh A, Sethunathan N, Johri AK et al (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59(2–3):143–152

    CAS  PubMed  Google Scholar 

  • Ellis RJ, Morgan P, Weightman AJ, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223–3230

    Article  CAS  PubMed  Google Scholar 

  • Engelmann S, Hecker M (1996) Impaired oxidative stress resistance of Bacillus subtilis sig mutants and the role of katA and katE. FEMS Microbiol Lett 145(1):63–69

    Article  CAS  PubMed  Google Scholar 

  • Favaloro B, Tamburro A, Trofino MA, Bologna L et al (2000) Modulation of the glutathione S-transferase in Ochrobactrum anthropi: function of xenobiotic substrates and other forms of stress. Biochem J 346(Pt 2):553–559

    Article  CAS  PubMed  Google Scholar 

  • Ferrari MD (1996) Biodegradation of polycyclic aromatic hydrocarbons and its application to the bioremediation of contaminated soils and sludges. Rev Argent Microbiol 28:83–98

    CAS  PubMed  Google Scholar 

  • Ficker M, Krastel K, Orlicky S, Edwards E (1999) Molecular characterization of a toluene-degrading methanogenic consortium. Appl Environ Microbiol 65:5576–5585

    CAS  PubMed  Google Scholar 

  • Gage DJ, Neidhardt FC (1993) Adaptation of Escherichia coli to the uncoupler of oxidative phosphorylation 2,4-dinitrophenol. J Bacteriol 175(21):7105–7108

    CAS  PubMed  Google Scholar 

  • Giacomazzi S, Cochet N (2004) Environmental impact of diuron transformation: a review. Chemosphere 56:1021–1032

    Article  CAS  PubMed  Google Scholar 

  • Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF (2009) Community genomic and proteomic analysis of chemoautotrophic, iron-oxidizing “Leptospirillum rubarum” (Group II) and Leptospirillum ferrodiazotrophum (Group III) in acid mine drainage biofilms. Appl Environ Microbiol 75(13):4599–4615

    Article  CAS  PubMed  Google Scholar 

  • González JM, Simó R, Massana R, Covert JS, Casamayor EO, Pedrós-Alió C, Moran MA (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66(10):4237–4246

    Article  PubMed  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nat Biotechnol 17(10):994–999

    Article  CAS  PubMed  Google Scholar 

  • Haggblom M (1990) Mechanisms of bacterial degradation and transformation of chlorinated monoaromatic compounds. J Basic Microbiol 30(2):115–141

    Article  CAS  PubMed  Google Scholar 

  • Halden RU, Colquhoun DR, Wisniewski ES (2005) 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 71(5):2442–2451

    Article  CAS  PubMed  Google Scholar 

  • Hartwig A (1994) Role of DNA repair inhibition in lead- and cadmium-induced genotoxicity: a review. Environ Health Perspect 102(3):45–50

    Article  CAS  PubMed  Google Scholar 

  • Hecker M, Antelmann H, Büttner K, Bernhardt J (2008) Gel-based proteomics of Gram-positive bacteria: a powerful tool to address physiological questions. Proteomics 8(23):4958–4975

    Article  CAS  PubMed  Google Scholar 

  • Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 20:1118–1123

    Article  CAS  PubMed  Google Scholar 

  • Heipieper HJ, Diefenbach R, Keweloh H (1992) Conversion of cis unsaturated fatty acids to trans, a possible mechanism for the protection of phenol-degrading Pseudomonas putida P8 from substrate toxicity. Appl Environ Microbiol 58(6):1847–1852

    CAS  PubMed  Google Scholar 

  • Heipieper HJ, Meulenbeld G, van Oirschot Q, de Bont J (1996) Effect of environmental factors on the trans/cis ratio of unsaturated fatty acids in Pseudomonas putida S12. Appl Environ Microbiol 62(8):2773–2777

    CAS  PubMed  Google Scholar 

  • Hopfgartner G, Varesio E, Tschappat V, Grivet C et al (2004) Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J Mass Spectrom 39(8):845–855

    Article  CAS  PubMed  Google Scholar 

  • Hughes TR, Robinson MD, Mitsakakis N, Johnston M et al (2004) The promise of functional genomics: completing the encyclopedia of a cell. Curr Opin Microbiol 7(5):546–554

    Article  CAS  PubMed  Google Scholar 

  • Hur I, Chun J (2004) A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J Microbiol 42(1):9–13

    CAS  PubMed  Google Scholar 

  • Iwamoto T, Nasu M (2001) Current bioremediation practice and perspective. J Biosci Bioeng 92(1):1–8

    Article  CAS  PubMed  Google Scholar 

  • Jeans C, Singer SW, Chan CS, Verberkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP (2008) Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J 2(5):542–550

    Article  CAS  PubMed  Google Scholar 

  • Junker F, Ramos JL (1999) Involvement of the cis/trans isomerase Cti in solvent resistance of Pseudomonas putida DOT-T1E. J Bacteriol 181(18):5693–5700

    CAS  PubMed  Google Scholar 

  • Kalia A, Gupta RP (2005) Proteomics: a paradigm shift. Crit Rev Biotechnol 25(4):173–198

    Article  CAS  PubMed  Google Scholar 

  • Katsivela E, Moore ER, Maroukli D, Strömpl C, Pieper D, Kalogerakis N (2005) Bacterial community dynamics during in situ bioremediation of petroleum waste sludge in landfarming sites. Biodegradation 16(2):169–180

    Article  CAS  PubMed  Google Scholar 

  • Kim HW, Han BW, Yoon HJ, Yang JK et al (2002) Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase from Pseudomonas aeruginosa. Acta Crystallogr D 58(Pt 10 Pt 2):1874–1875

    Article  PubMed  CAS  Google Scholar 

  • Kim YH, Moody JD, Freeman JP, Brezna B et al (2004) Evidence for the existence of PAH-quinone reductase and catechol-O-methyltransferase in Mycobacterium vanbaalenii PYR-1. J Ind Microbiol Biotechnol 31(11):507–516

    Article  CAS  PubMed  Google Scholar 

  • Kim SIL, Choi J-S, Kahng H-Y (2007) A proteomics strategy for the analysis of bacterial biodegradation pathways. OMICS 11(3):280–294

    Article  CAS  PubMed  Google Scholar 

  • Kitts CL (2001) Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2:17–25

    CAS  PubMed  Google Scholar 

  • Knigge T, Monsinjon T, Andersen OK (2004) Surface-enhanced laser desorption/ionization-time of flight-mass spectrometry approach to biomarker discovery in blue mussels (Mytilus edulis) exposed to polyaromatic hydrocarbons and heavy metals under field conditions. Proteomics 4(9):2722–2727

    Article  CAS  PubMed  Google Scholar 

  • Krivobok S, Kuony S, Meyer C, Louwagie M et al (2003) Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J Bacteriol 185(13):3828–3841

    Article  CAS  PubMed  Google Scholar 

  • Kuhner S, Wohlbrand L, Fritz I, Wruck W et al (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187(4):1493–1503

    Article  PubMed  CAS  Google Scholar 

  • LaBaer J, Ramachandran N (2005) Protein microarrays as tools for functional proteomics. Curr Opin Chem Biol 9(1):14–19

    Article  CAS  PubMed  Google Scholar 

  • Labana S, Pandey G, Paul D, Sharma NK, Basu A, Jain RK (2005) Pot and field studies on bioremediation of pnitrophenol contaminated soil using Arthrobacter protophormiae RKJ100. Environ Sci Technol 39:3330–3337

    Article  CAS  PubMed  Google Scholar 

  • Lacerda CM, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community response to cadmium exposure. J Proteome Res 6(3):1145–1152

    Article  CAS  PubMed  Google Scholar 

  • Lee H, Yi EC, Wen B, Reily TP et al (2004) Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B 803(1):101–110

    Article  CAS  Google Scholar 

  • Leone S, Izzo V, Silipo A, Sturiale L et al (2004) A novel type of highly negatively charged lipooligosaccharide from Pseudomonas stutzeri OX1 possessing two 4,6-O-(1-carboxy)-ethylidene residues in the outer core region. Eur J Biochem 271(13):2691–2704

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Xu J, Tang C, Wu J, Muhammad A, Wang H (2006) Application of 16S rDNA-PCR amplification and DGGE fingerprinting for detection of shift in microbial community diversity in Cu-, Zn-, and Cd-contaminated paddy soils. Chemosphere 62(8):1374–1380

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Ghosh S, Searls DB, Saunders AM, Cossman J, Roses AD (2005) Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery. OMICS 9(4):351–363

    Article  CAS  PubMed  Google Scholar 

  • Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135):537–541

    Article  CAS  PubMed  Google Scholar 

  • Loh K-C, Caoa B (2008) Paradigm in biodegradation using Pseudomonas putida—a review of proteomics studies. Enzyme Microb Technol 43(1):1–12

    Article  CAS  Google Scholar 

  • Magnuson K, Jackowski S, Rock CO, Cronan JE (1993) Regulation of fatty acid biosynthesis in Escherichia coli. J Microbiol Rev 57(3):522–542

    CAS  Google Scholar 

  • Mann M, Hendrickson RC, Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70:437–473

    Article  CAS  PubMed  Google Scholar 

  • Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53(3):486–493

    Article  CAS  PubMed  Google Scholar 

  • Marouga R, David S, Hawkins E (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382(3):669–678

    Article  CAS  PubMed  Google Scholar 

  • Marrero J, Gonzalez LJ, Sanchez A, Ayala M et al (2004) Effect of high concentration of Co (II) on Enterobacter liquefaciens strain C-1: a bacterium highly resistant to heavy metals with an unknown genome. Proteomics 4(5):1265–1279

    Article  CAS  PubMed  Google Scholar 

  • Marsh TL (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2(3):323–327

    Article  CAS  PubMed  Google Scholar 

  • Martín GH, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24:1263–1269

    Google Scholar 

  • Martinez P, Agullo L, Hernandez M, Seeger M (2007) Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400. Arch Microbiol 188(3):289–297

    Article  CAS  PubMed  Google Scholar 

  • Maymo-Gatell X, Schraa G (1997) Engineers and microbiologists: a future together in bioremediation. Microbiologia 13(1):85–87

    CAS  PubMed  Google Scholar 

  • McBurney W, Mangold M, Munro K, Schultz M, Rath HC, Tannock GW (2006) PCR/DGGE and 16S rRNA gene library analysis of the colonic microbiota of HLA-B27/beta2-microglobulin transgenic rats. Lett Appl Microbiol 42(2):165–171

    Article  CAS  PubMed  Google Scholar 

  • McDonald WH, Yates JR III (2003) Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther 5(3):302–309

    CAS  PubMed  Google Scholar 

  • Mergaert J, Anderson C, Wouters A, Swings J, Kersters K (1992) Biodegradation of polyhydroxyalkanoates. FEMS Microbiol Rev 9:317–321

    CAS  PubMed  Google Scholar 

  • Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, Wattiez R (2003) Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27(2–3):385–410

    Article  CAS  PubMed  Google Scholar 

  • Mills DK, Fitzgerald K, Litchfield CD, Gillevet PM (2003) A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. J Microbiol Methods 54(1):57–74

    Article  CAS  PubMed  Google Scholar 

  • Morris RM (2006) Environmental genomics: exploring ecological sequence space. Curr Biol 16(13):R499–R501

    Article  CAS  PubMed  Google Scholar 

  • Morris RM, Fung JM, Rahm BG, Zhang S, Freedman DL, Zinder SH, Richardson RE (2007) Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity. Appl Environ Microbiol 73(1):320–326

    Article  CAS  PubMed  Google Scholar 

  • Nesvizhskii AI, Aebersold R (2004) Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today 9(4):173–181

    Article  CAS  PubMed  Google Scholar 

  • Neumann CA, Krause DS, Carman CV, Das S, Dubey DP, Abraham JL, Bronson RT, Fujiwara Y, Orkin SH, Van Etten RA (2003) Essential role for the peroxiredoxin Prdx1 in erythrocyte antioxidant defence and tumour suppression. Nature 424(6948):561–565

    Article  CAS  PubMed  Google Scholar 

  • Neumann G, Veeranagouda Y, Karegoudar TB, Sahin O, Mäusezahl I, Kabelitz N, Kappelmeyer U, Heipieper HJ (2005) Cells of Pseudomonas putida and Enterobacter sp. adapt to toxic organic compounds by increasing their size. Extremophiles 9(2):163–168

    Article  CAS  PubMed  Google Scholar 

  • Nojiri H, Tsuda M (2005) Functional evolution of bacteria in degradation of environmental pollutants. Tanpakushitsu Kakusan Koso 50(12):1505–1509

    PubMed  Google Scholar 

  • Ogawa N, Miyashita K, Chakrabarty AM (2003) Microbial genes and enzymes in the degradation of chlorinated compounds. Chem Rec 3(3):158–171

    Article  CAS  PubMed  Google Scholar 

  • Okuyama H, Sasaki S, Higashi S, Murata N (1990) A trans-unsaturated fatty acid in a psychrophilic bacterium, Vibrio sp. strain ABE-1. J Bacteriol 172(6):3515–3518

    CAS  PubMed  Google Scholar 

  • Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376–386

    Article  CAS  PubMed  Google Scholar 

  • Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M (2007) Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 74(2):501–510

    Article  CAS  PubMed  Google Scholar 

  • Paul D, Pandey G, Meier C, van der Meer JR, Jain RK (2006) Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation. FEMS Microbiol Ecol 57:116–127

    Article  CAS  PubMed  Google Scholar 

  • Pazos F, Valencia A, de Lorenzo V (2003) The organization of the microbial biodegradation network from a systems-biology perspective. EMBO Rep 4:913

    Article  CAS  Google Scholar 

  • Pedrotta V, Witholt B (1999) Isolation and characterization of the cis-trans-unsaturated fatty acid isomerase of Pseudomonas oleovorans GPo12. J Bacteriol 181(10):3256–3261

    CAS  PubMed  Google Scholar 

  • Pessione E, Giuffrida MG, Prunotto L, Barello C, Mazzoli R et al (2003) Membrane proteome of Acinetobacter radioresistens S13 during aromatic exposure. Proteomics 3(6):1070–1076

    Article  CAS  PubMed  Google Scholar 

  • Płaza G, Ulfig K, Hazen TC, Brigmon RL (2001) Use of molecular techniques in bioremediation. Acta Microbiol Pol 50(3–4):205–218

    PubMed  Google Scholar 

  • Rabus R (2005) Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Appl Microbiol Biotechnol 68(5):580–587

    Article  CAS  PubMed  Google Scholar 

  • Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC II, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308(5730):1915–1920

    Article  CAS  PubMed  Google Scholar 

  • Razin S, Yogev D, Naot Y (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62(4):1094–1156

    CAS  PubMed  Google Scholar 

  • Rieger PG, Meier HM, Gerle M, Vogt U, Groth T, Knackmuss HJ (2002) Xenobiotics in the environment: present and future strategies to obviate the problem of biological persistence. J Biotechnol 94(1):101–123

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Valera F (2004) Environmental genomics, the big picture? FEMS Microbiol Lett 231(2):153–158

    Article  CAS  PubMed  Google Scholar 

  • Rosen R, Buttner K, Schmid R, Hecker M, Ron EZ (2001) Stress-induced proteins of Agrobacterium tumefaciens. FEMS Microbiol Ecol 35(3):277–285

    Article  CAS  PubMed  Google Scholar 

  • Santos PM, Benndorf D, Sa-Correia I (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4(9):2640–2652

    Article  CAS  PubMed  Google Scholar 

  • Schneider T, Riedel K (2010) Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 10(4):785–798

    Article  CAS  PubMed  Google Scholar 

  • Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2005) A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142(3):335–343

    Article  PubMed  Google Scholar 

  • Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF (2005) Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307(5706):105–108

    Article  CAS  PubMed  Google Scholar 

  • Shannon MJ, Unterman R (1993) Evaluating bioremediation: distinguishing fact from fiction. Annu Rev Microbiol 47:715–738

    Article  CAS  PubMed  Google Scholar 

  • Sharma S, Sundaram CS, Luthra PM, Singh Y, Sirdeshmukh R, Gade WN (2006) Role of proteins in resistance mechanism of Pseudomonas fluorescens against heavy metal induced stress with proteomics approach. J Biotechnol 126(3):374–382

    Article  CAS  PubMed  Google Scholar 

  • Sikkema J, de Bont JA, Poolman B (1995) Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59(2):201–222

    CAS  PubMed  Google Scholar 

  • Silbergeld EK, Patrick TE (2005) Environmental exposures, toxicologic mechanisms, and adverse pregnancy outcomes. Am J Obstet Gynecol 192(5 Suppl):S11–S21

    Article  PubMed  Google Scholar 

  • Solyanikova IP, Golovleva LA (2004) Isolation, biochemical and molecular characterization of 2-chlorophenol-degrading Bacillus isolates. J Environ Sci Health B 39(3):333–351

    Article  PubMed  CAS  Google Scholar 

  • Somiari RI, Somiari S, Russell S, Shriver CD (2005) Proteomics of breast carcinoma. J Chromatogr B 815(1–2):215–225

    Article  CAS  Google Scholar 

  • Spain JC (1994) Environmental biotechnology research: an overview. Aviat Space Environ Med 65(5 Suppl):A131–A137

    CAS  PubMed  Google Scholar 

  • Steen H, Mann M (2001) Similarity between condensed phase and gas phase chemistry: fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics. J Am Soc Mass Spectrom 12(2):228–232

    Article  CAS  PubMed  Google Scholar 

  • Stolz A, Knackmuss HJ (1993) Degradation of 2,4-dihydroxybenzoate by Pseudomonas sp. BN9. FEMS Microbiol Lett 108(2):219–224

    Article  CAS  PubMed  Google Scholar 

  • Suutari M, Laakso S (1994) Microbial fatty acids and thermal adaptation. Crit Rev Microbiol 20(4):285–328

    Article  CAS  PubMed  Google Scholar 

  • Svedruzić D, Jónsson S, Toyota CG, Reinhardt LA, Ricagno S, Lindqvist Y, Richards NG (2005) The enzymes of oxalate metabolism: unexpected structures and mechanisms. Arch Biochem Biophys 433(1):176–192

    Article  PubMed  CAS  Google Scholar 

  • Symons ZC, Bruce NC (2006) Bacterial pathways for degradation of nitroaromatics. Nat Prod Rep 23(6):845–850

    Article  CAS  PubMed  Google Scholar 

  • Tamburro A, Robuffo I, Heipieper HJ, Allocati N, Rotilio D, Di Ilio C, Favaloro B (2004) Expression of glutathione S-transferase and peptide methionine sulphoxide reductase in Ochrobactrum anthropi is correlated to the production of reactive oxygen species caused by aromatic substrates. FEMS Microbiol Lett 241(2):151–156

    Article  CAS  PubMed  Google Scholar 

  • Thompson IP, van der Gast CJ, Ciric L, Singer AC et al (2005) Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol 7(7):909–915

    Article  CAS  PubMed  Google Scholar 

  • Timmis KN, Pieper DH (1999) Bacteria designed for bioremediation. Trends Biotechnol 17(5):200–204

    Article  CAS  PubMed  Google Scholar 

  • Trakselis MA, Alley SC, Ishmael FT (2005) Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage and proteomics. Bioconjug Chem 16(4):741–750

    Article  CAS  PubMed  Google Scholar 

  • Tropel D, van der Meer JR (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68(3):474–500

    Article  CAS  PubMed  Google Scholar 

  • Uchiyama H, Shinohara Y, Tomioka N, Kusakabe I (1999) Induction and enhancement of stress proteins in a trichloroethylene degrading methanotrophic bacterium, Methylocystis sp. M. FEMS Microbiol Lett 170(1):125–130

    Article  CAS  PubMed  Google Scholar 

  • Veeranagouda Y, Karegoudar TB, Neumann G, Heipieper HJ (2006) Enterobacter sp. VKGH12 growing with n-butanol as the sole carbon source and cells to which the alcohol is added as pure toxin show considerable differences in their adaptive responses. FEMS Microbiol Lett 254(1):48–54

    Article  CAS  PubMed  Google Scholar 

  • VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009) Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7:196–205

    Google Scholar 

  • Vieth A, Kastner M, Schirmer M, Weiss H, Godeke S, Meckenstock RU, Richnow HH (2005) Monitoring in situ biodegradation of benzene and toluene by stable carbon isotope fractionation. Environ Toxicol Chem 24:51–60

    Article  CAS  PubMed  Google Scholar 

  • Viñas M, Sabaté J, Guasp C, Lalucat J, Solanas AM (2005) Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium. Can J Microbiol 51(11):897–909

    Article  PubMed  Google Scholar 

  • Wall DB, Lubman DM, Flynn SJ (1999) Rapid profiling of induced proteins in bacteria using MALDITOF mass spectrometric detection of nonporous RP-HPLC-separated whole cell lysates. Anal Chem 71(17):3894–3900

    Article  CAS  PubMed  Google Scholar 

  • Wang YX, Yuan YJ (2005) Direct proteomic mapping of Streptomyces luteogriseus strain 103 and cnn1 and insights into antibiotic biosynthesis. J Proteome Res 4(6):1999–2006

    Article  CAS  PubMed  Google Scholar 

  • Washburn MP, Wolters D, Yates JR III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242–247

    Article  CAS  PubMed  Google Scholar 

  • Washburn MP, Koller A, Oshiro G, Ulaszek G, Plouffe D, Deciu C, Winzeler E, Yates JR III (2003) Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 100:3107–3112

    Google Scholar 

  • Watanabe K, Baker PW (2000) Environmentally relevant microorganisms. J Biosci Bioeng 89(1):1–11

    Article  CAS  PubMed  Google Scholar 

  • Weber S, Karbe L (1995) Suitability of the ruffe (Gymnocephalus cernua [L.]) for investigations on activity of hepatic enzymes induced by xenobiotics. Ecotoxicol Environ Saf 32(3):215–218

    Article  CAS  PubMed  Google Scholar 

  • Weber FJ, Ooijkaas LP, Schemen RM, Hartmans S, de Bont JA (1993) Adaptation of Pseudomonas putida S12 to high concentrations of styrene and other organic solvents. Appl Environ Microbiol 59(10):3502–3504

    CAS  PubMed  Google Scholar 

  • Wenderoth DF, Rosenbrock P, Abraham WR, Pieper DH, Höfle MG (2003) Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater. Microb Ecol 46(2):161–176

    Article  CAS  PubMed  Google Scholar 

  • Weston AD, Hood L (2004) Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 3(2):179–196

    Article  CAS  PubMed  Google Scholar 

  • Whyte A, Lafong C, Malone J, Golda BP et al (1999) Contaminated lithium heparin bottles as a source of pseudobacteraemia. J Hosp Infect 42(4):342–343

    Article  CAS  PubMed  Google Scholar 

  • Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N’guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, Banfield JF (2009) Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol 75(20):6591–6599

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14(2):92–97

    Article  CAS  PubMed  Google Scholar 

  • Wilmes P, Bond PL (2009) Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth’s biogeochemical cycles. Curr Opin Microbiol 12(3):310–317

    Article  CAS  PubMed  Google Scholar 

  • Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF (2008a) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2(8):853–864

    Article  CAS  PubMed  Google Scholar 

  • Wilmes P, Wexler M, Bond PL (2008b) Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One 3(3):e1778

    Article  PubMed  CAS  Google Scholar 

  • Winkler J, Timmis KN, Snyder RA (1995) Tracking the response of Burkholderia cepacia G4 5223-PR1 in aquifer microcosms. Appl Environ Microbiol 61:448–455

    CAS  PubMed  Google Scholar 

  • Wolf E, Hiendleder S, Bauersachs S, Fröhlich T, Sinowatz F, Blum H, Arnold GJ (2006) Methods for transcriptome and proteome research: applications for studying the biology of reproduction in cattle. Berl Munch Tierarztl Wochenschr 119(1–2):7–16

    CAS  PubMed  Google Scholar 

  • Wolters DA, Washburn MP, Yates JR III (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73(23):5683–5690

    Article  CAS  PubMed  Google Scholar 

  • Wu XY, Xiao ZQ, Chen ZC, Li C, Li JL, Feng XP, Yi H, Li MY (2004) Improvement of protein preparation methods for bronchial epithelial tissues and establishment of 2-DE profiles from carcinogenic process of human bronchial epithelial tissues. Zhong Nan Da Xue Xue Bao Yi Xue Ban 29(4):376–381

    CAS  PubMed  Google Scholar 

  • Yan F, Subramanian B, Nakeff A, Barder TJ, Parus SJ, Lubman DM (2003) A comparison of drug-treated and untreated HCT-116 human colon adenocarcinoma cells using a 2-D liquid separation mapping method based upon chromatofocusing P1 fractionation. Anal Chem 75(10):2299–2308

    Article  CAS  PubMed  Google Scholar 

  • Yang C, Crowley DE, Menge JA (2001) 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 35(2):129–136

    Article  CAS  PubMed  Google Scholar 

  • Yates JR III (2004) Mass spectrometry as an emerging tool for systems biology. Biotechniques 36(6):917–919

    CAS  PubMed  Google Scholar 

  • Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20(8):2160–2176

    Article  CAS  PubMed  Google Scholar 

  • Zhao B, Poh CL (2008) Insights into environmental bioremediation by microorganisms through functional genomics and proteomics. Proteomics 8:874–881

    Article  CAS  PubMed  Google Scholar 

  • Zhao B, Yeo CC, Poh CL (2005) Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867. Proteomics 5(7):1868–1876

    Article  CAS  PubMed  Google Scholar 

  • Zhao B, Yeo CC, Tan CL, Poh CL (2007) Proteome analysis of heat shock protein expression in Pseudomonas alcaligenes NCIMB 9867 in response to gentisate exposure and elevated growth temperature. Biotechnol Bioeng 97(3):506–514

    Article  CAS  PubMed  Google Scholar 

  • Zhong M, Zhou Q (2002) Molecular-ecological technology of microorganisms and its application to research on environmental pollution. Ying Yong Sheng Tai Xue Bao 13(2):247–251

    CAS  PubMed  Google Scholar 

  • Zhu X, Gibbons J, Garcia-Rivera J, Casadevall A, Williamson PR (2001) Laccase of Cryptococcus neoformans is a cell wall-associated virulence factor. Infect Immun 69(9):5589–5596

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are thankful to Ms. Navdeep Kaur Dhami, Ms. Sangeetha Sukumar and Ms. Kanika Jain for their help in preparing the manuscript. This work is supported, in part, by the Council of Scientific and Industrial Research (CSIR) network project NWP 0019. This is IMTECH Communication number 053/2008. There are no financial/commercial conflicts of interest.

Author information

Authors and Affiliations

  1. Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh, 160036, India

    Archana Chauhan & Rakesh K. Jain

Authors
  1. Archana Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rakesh K. Jain
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rakesh K. Jain.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chauhan, A., Jain, R.K. Biodegradation: gaining insight through proteomics. Biodegradation 21, 861–879 (2010). https://doi.org/10.1007/s10532-010-9361-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10532-010-9361-0

Keywords

Search

Navigation