Applied Microbiology and Biotechnology

, Volume 98, Issue 23, pp 9735–9747 | Cite as

Comparative proteomics reveal the impact of OmcA/MtrC deletion on Shewanella oneidensis MR-1 in response to hexavalent chromium exposure

  • Chao Wang
  • Juan Chen
  • Wen-Jun Hu
  • Ji-Yun Liu
  • Hai-Lei Zheng
  • Feng Zhao
Genomics, transcriptomics, proteomics


Hexavalent chromium [Cr(VI)] is a priority pollutant causing serious environmental issues. Microbial reduction provides an alternative strategy for Cr(VI) remediation. The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, was employed to study Cr(VI) reduction and toxicity in this work. To understand the effect of membrane cytochromes on Cr(VI) response, a comparative protein profile analysis from S. oneidensis MR-1 wild type and its mutant of deleting OmcA and MtrC (△omcA/mtrC) was conducted using two-dimensional electrophoresis (2-DE) technology. The 2-DE patterns were compared, and the proteins with abundant changes of up to twofold in the Cr(VI) treatment were detected. Using mass spectrometry, 38 and 45 differentially abundant proteins were identified in the wild type and the mutant, respectively. Among them, 25 proteins were shared by the two strains. The biological functions of these identified proteins were analyzed. Results showed that Cr(VI) exposure decreased the abundance of proteins involved in transcription, translation, pyruvate metabolism, energy production, and function of cellular membrane in both strains. There were also significant differences in protein expressions between the two strains under Cr(VI) treatment. Our results suggest that OmcA/MtrC deletion might result in the Cr(VI) toxicity to outer membrane and decrease assimilation of lactate, vitamin B12, and cystine. When carbohydrate metabolism was inhibited by Cr(VI), leucine and sulfur metabolism may act as the important compensatory mechanisms in the mutant. Furthermore, the mutant may regulate electron transfer in the inner membrane and periplasm to compensate for the deletion of OmcA and MtrC in Cr(VI) reduction.


Shewanella oneidensis Cr(VI) reduction Proteomics OmcA/MtrC Membrane 



This research was supported financially by the National Natural Science Foundation of China (21322703, 21177122), China Postdoctoral Science Foundations (2012M520411), and Science and Technology Innovation and Collaboration Team Project of the Chinese Academy of Sciences.

Supplementary material

253_2014_6143_MOESM1_ESM.pdf (492 kb)
ESM 1 (PDF 491 kb)


  1. Alekshun MN, Levy SB (1997) Regulation of chromosomally mediated multiple antibiotic resistance: the mar regulon. Antimicrob Agents Chemother 41:2067–2075PubMedCentralPubMedGoogle Scholar
  2. Aubert S, Alban C, Bligny R, Douce R (1996) Induction of β-methylcrotonyl-coenzyme A carboxylase in higher plant cells during carbohydrate starvation: evidence for a role of MCCase in leucine catabolism. FEBS Lett 383:175–180PubMedCrossRefGoogle Scholar
  3. Barabote RD, Saier MH Jr (2005) Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev 69:608–634PubMedCentralPubMedCrossRefGoogle Scholar
  4. Belchik SM, Kennedy DW, Dohnalkova AC, Wang YM, Sevinc PC, Wu H, Lin YH, Lu HP, Fredrickson JK, Shi L (2011) Extracellular reduction of hexavalent chromium by cytochromes MtrC and OmcA of Shewanella oneidensis MR-1. Appl Environ Microbiol 77:4035–4041PubMedCentralPubMedCrossRefGoogle Scholar
  5. Bencheikh-Latmani R, Williams SM, Haucke L, Criddle CS, Wu LY, Zhou JZ, Tebo BM (2005) Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl Environ Microbiol 71:7453–7460PubMedCentralPubMedCrossRefGoogle Scholar
  6. Binder S, Knill T, Schuster J (2007) Branched-chain amino acid metabolism in higher plants. Physiol Plant 129:68–78CrossRefGoogle Scholar
  7. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, Westermeier R, Postel W (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6:317–339PubMedCrossRefGoogle Scholar
  8. Bradford MM (1976) A rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal Biochem 72:248–254PubMedCrossRefGoogle Scholar
  9. Brown SD, Thompson MR, VerBerkmoes NC, Chourey K, Shah M, Zhou JZ, Hettich RL, Thompson DK (2006) Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics 5:1054–1071PubMedCrossRefGoogle Scholar
  10. Bulut H, Moniot S, Licht A, Scheffel F, Gathmann S, Saenger W, Schneider E (2012) Crystal structures of two solute receptors for L-cystine and L-cysteine, respectively, of the human pathogen Neisseria gonorrhoeae. J Mol Biol 415:560–572PubMedCrossRefGoogle Scholar
  11. Cantoni O, Brandi G, Albano A, Cattabeni F (1995) Action of cystine in the cytotoxic response of Escherichia coli cells exposed to hydrogen peroxide. Free Radic Res 22:275–283PubMedCrossRefGoogle Scholar
  12. Carpentier SC, Witters E, Laukens K, Deckers P, Swennen R, Panis B (2005) Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 5:2497–2507PubMedCrossRefGoogle Scholar
  13. Chourey K, Thompson MR, Morrell-Falvey J, VerBerkmoes NC, Brown SD, Shah M, Zhou JZ, Doktycz M, Hettich RL, Thompson DK (2006) Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol 72:6331–6344PubMedCentralPubMedCrossRefGoogle Scholar
  14. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang ZM, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ (2011) Structure of a bacterial cell surface decaheme electron conduit. Proc Natl Acad Sci U S A 108:9384–9389PubMedCentralPubMedCrossRefGoogle Scholar
  15. Cook AM, Denger K (2002) Dissimilation of the C2 sulfonates. Arch Microbiol 179:1–6PubMedCrossRefGoogle Scholar
  16. Coursolle D, Gralnick JA (2010) Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR-1. Mol Microbiol 77:995–1008Google Scholar
  17. Dhal B, Thatoi HN, Das NN, Pandey BD (2013) Chemical and microbial remediation of hexavalent chromium from contaminated soil and mining/metallurgical solid waste: a review. J Hazard Mater 250:272–291PubMedCrossRefGoogle Scholar
  18. Dong JM, Taylor JS, Latour DJ, Iuchi S, Lin ECC (1993) Three overlapping lct genes involved in L-lactate utilization by Escherichia coli. J Bacteriol 175:6671–6678PubMedCentralPubMedGoogle Scholar
  19. Fischer E, Gunter K, Braun V (1989) Involvement of ExbB and TonB in transport across the outer membrane of Escherichia coli: phenotypic complementation of exb mutants by overexpressed tonB and physical stabilization of TonB by ExbB. J Bacteriol 171:5127–5134PubMedCentralPubMedGoogle Scholar
  20. Ge SM, Zhou MH, Dong XJ, Lu Y, Ge SC (2013) Distinct and effective biotransformation of hexavalent chromium by a novel isolate under aerobic growth followed by facultative anaerobic incubation. Appl Microbiol Biotechnol 97:2131–2137PubMedCrossRefGoogle Scholar
  21. Gnanamani A, Kavitha V, Radhakrishnan N, Rajakumar GS, Sekaran G, Mandal AB (2010) Microbial products (biosurfactant and extracellular chromate reductase) of marine microorganism are the potential agents reduce the oxidative stress induced by toxic heavy metals. Colloids Surf B 79:334–339CrossRefGoogle Scholar
  22. Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS (2008) A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng 10:234–245PubMedCrossRefGoogle Scholar
  23. Hayashi M, Nakayama Y, Unemoto T (2001) Recent progress in the Na+-translocating NADH-quinone reductase from the marine Vibrio alginolyticus. BBA-Bioenergetics 1505:37–44PubMedCrossRefGoogle Scholar
  24. Herrmann G, Jayamani E, Mai G, Buckel W (2008) Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J Bacteriol 190:784–791PubMedCentralPubMedCrossRefGoogle Scholar
  25. Horcajo P, de Pedro MA, Cava F (2012) Peptidoglycan plasticity in bacteria: stress-induced peptidoglycan editing by noncanonical D-amino acids. Microb Drug Resist 18:306–313PubMedCrossRefGoogle Scholar
  26. Imanaka H, Yamatsu A, Fukui T, Atomi H, Imanaka T (2006) Phosphoenolpyruvate synthase plays an essential role for glycolysis in the modified Embden-Meyerhof pathway in Thermococcus kodakarensis. Mol Microbiol 61:898–909PubMedCrossRefGoogle Scholar
  27. Leonhartsberger S, Korsa I, Bock A (2002) The molecular biology of formate metabolism in enterobacteria. J Mol Microbiol Biotechnol 4:269–276PubMedGoogle Scholar
  28. Liu HW, Thorson JS (1994) Pathways and mechanisms in the biogenesis of novel deoxysugars by bacteria. Annu Rev Microbiol 48:223–256PubMedCrossRefGoogle Scholar
  29. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. Methods 25:402–408PubMedCrossRefGoogle Scholar
  30. Lovering AL, de Castro LH, Lim D, Strynadka NCJ (2007) Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis. Science 315:1402–1405PubMedCrossRefGoogle Scholar
  31. Martin RG, Rosner JL (2001) The AraC transcriptional activators. Curr Opin Microbiol 4:132–137PubMedCrossRefGoogle Scholar
  32. McCoy AJ, Maurelli AT (2006) Building the invisible wall: updating the chlamydial peptidoglycan anomaly. Trends Microbiol 14:70–77PubMedCrossRefGoogle Scholar
  33. Narayani M, Shetty KV (2013) Chromium-resistant bacteria and their environmental condition for hexavalent chromium removal: a review. Crit Rev Environ Sci Technol 43:955–1009CrossRefGoogle Scholar
  34. Neumann M, Mittelstädt G, Iobbi-Nivol C, Saggu M, Lendzian F, Hildebrandt P, Leimkühler S (2009) A periplasmic aldehyde oxidoreductase represents the first molybdopterin cytosine dinucleotide cofactor containing molybdo-flavoenzyme from Escherichia coli. FEBS J 276:2762–2774PubMedCrossRefGoogle Scholar
  35. Nikaido H (1994) Prevention of drug access to bacterial targets: permeability barriers and active efflux. Science 264:382–388PubMedCrossRefGoogle Scholar
  36. Postle K, Larsen RA (2007) TonB-dependent energy transduction between outer and cytoplasmic membranes. Biometals 20:453–465PubMedCrossRefGoogle Scholar
  37. Ram S, Vajpayee P, Shanker R (2008) Rapid culture-independent quantitative detection of enterotoxigenic Escherichia coli in surface waters by real-time PCR with molecular beacon. Environ Sci Technol 42:4577–4582PubMedCrossRefGoogle Scholar
  38. Rawls KS, Martin JH, Maupin-Furlow JA (2011) Activity and transcriptional regulation of bacterial protein-like glycerol-3-phosphate dehydrogenase of the haloarchaea in Haloferax volcanii. J Bacteriol 193:4469–4476PubMedCentralPubMedCrossRefGoogle Scholar
  39. Robinson C, Matos CFRO, Beck D, Ren C, Lawrence J, Vasisht N, Mendel S (2011) Transport and proofreading of proteins by the twin-arginine translocation (Tat) system in bacteria. BBA-Biomembranes 1808:876–884PubMedCrossRefGoogle Scholar
  40. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (2003) Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem 278:41148–41159PubMedCrossRefGoogle Scholar
  41. Rouviere PE, Gross CA (1996) SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins. Gene Dev 10:3170–3182PubMedCrossRefGoogle Scholar
  42. Shi L, Rosso KM, Clarke TA, Richardson DJ, Zachara JM, Fredrickson JK (2012) Molecular underpinnings of Fe(III) oxide reduction by Shewanella oneidensis MR-1. Front Microbiol 3:50PubMedCentralPubMedGoogle Scholar
  43. Thompson MR, VerBerkmoes NC, Chourey K, Shah M, Thompson DK, Hettich RL (2007) Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challenge. J Proteome Res 6:1745–1757PubMedCrossRefGoogle Scholar
  44. Thompson DK, Chourey K, Wickham GS, Thieman SB, VerBerkmoes NC, Zhang B, McCarthy AT, Rudisill MA, Shah M, Hettich RL (2010) Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge. BMC Genomics 11:311PubMedCentralPubMedCrossRefGoogle Scholar
  45. Urone PF (1955) Stability of colorimetric reagent for chromium, s-diphenylcarbazide, in various solvents. Anal Chem 27:1354–1355CrossRefGoogle Scholar
  46. Wang YT, Shen H (1995) Bacterial reduction of hexavalent chromium. J Ind Microbiol 14:159–163PubMedCrossRefGoogle Scholar
  47. Wang B, Xu MY, Sun GP (2010) Comparative analysis of membranous proteomics of Shewanella decolorationis S12 grown with azo compound or Fe(III) citrate as sole terminal electron acceptor. Appl Microbiol Biotechnol 86:1513–1523PubMedCrossRefGoogle Scholar
  48. Wang CY, Shen RF, Wang C, Wang W (2013a) Root protein profile changes induced by Al exposure in two rice cultivars differing in Al tolerance. J Proteome 78:281–293CrossRefGoogle Scholar
  49. Wang YM, Sevinc PC, Belchik SM, Fredrickson J, Shi L, Lu HP (2013b) Single-cell imaging and spectroscopic analyses of Cr(VI) reduction on the surface of bacterial cells. Langmuir 29:950–956PubMedCentralPubMedCrossRefGoogle Scholar
  50. Wu R, Cui L, Chen L, Wang C, Cao C, Sheng G, Yu H, Zhao F (2013) Effects of bio-Au nanoparticles on electrochemical activity of Shewanella oneidensis wild type and △omcA/mtrC Mutant. Sci Rep 3:3307PubMedCentralPubMedGoogle Scholar
  51. Yang XF, Kang CM, Brody MS, Price CW (1996) Opposing pairs of serine protein kinases and phosphatases transmit signals of environmental stress to activate a bacterial transcription factor. Gene Dev 10:2265–2275PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Chao Wang
    • 1
  • Juan Chen
    • 2
  • Wen-Jun Hu
    • 2
  • Ji-Yun Liu
    • 2
  • Hai-Lei Zheng
    • 2
  • Feng Zhao
    • 1
  1. 1.Key Laboratory of Urban Pollutant Conversion, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
  2. 2.Key Laboratory of the Coastal and Wetland Ecosystems, Ministry of Education, College of the Environment and EcologyXiamen UniversityXiamenChina

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