c-type cytochromes in Pelobacter carbinolicus

Applied and Environmental Microbiology

Volumn 72, Issue 11, 2006, Pages 6980-6985

  Haveman, Shelley A ^a   Holmes, Dawn E ^a   Ding, Yan Huai R ^a   Ward, Joy E ^a   DiDonato Jr , Raymond J ^a   Lovley, Derek R ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CELLS; ELECTRON TRANSITIONS; ELECTROPHORESIS; GENES; MASS SPECTROMETRY;

C-TYPE CYTOCHROMES; ELECTRON TRANSFER; HEME-STAINED PROTEINS;

PROTEINS;

CYTOCHROME C; FERRIC ION; HEME;

CYTOCHROME; GENE EXPRESSION; GENOME; IRON-REDUCING BACTERIUM;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL METABOLISM; DESULFUROMONAS; ELECTRON TRANSPORT; GEOBACTER; NONHUMAN; OPEN READING FRAME; PELOBACTER; PELOBACTER CARBINOLICUS; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BACTERIAL PROTEINS; CYTOCHROMES C; DELTAPROTEOBACTERIA; HEME; POLYMERASE CHAIN REACTION; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

DESULFUROMONAS; GEOBACTER; GEOBACTER SULFURREDUCENS; GEOBACTERACEAE; PELOBACTER; PELOBACTER CARBINOLICUS;

EID: 33750976399     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01128-06     Document Type: Article

References (53)

1. 7 from the metal-reducing bacterium, Geobacter metallireducens. FEMS Microbiol. Lett. 175:205-210.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. 7 produced in Desulfovibrio desulfuricans retains its metal reductase activity. Appl. Environ. Microbiol. 64:1308-1312.
4. Beckett, C. S., J. A. Loughman, K. A. Karberg, G. M. Donato, W. E. Goldman, and R. G. Kranz. 2000. Four genes are required for the system II cytochrome c biogenesis pathway in Bordetella pertussis, a unique bacterial model. Mol. Microbiol. 38:465-481.
5. Bendtsen, J. D., H. Nielsen, G. von Heijne, and S. Brunak. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340:783-795.
6. Bruschi, M., M. Woudstra, B. Guigliarelli, M. Asso, E. Lojou, Y. Petillot, and C. Abergel. 1997. Biochemical and spectroscopic characterization of two new cytochromes isolated from Desulfuromonas acetoxidans. Biochemistry 36:10601-10608.
7. Buchanan, S. K., B. S. Smith, L. Venkatramani, D. Xia, L. Esser, M. Palnitkar, R. Chakraborty, D. van der Helm, and J. Deisenhofer. 1999. Crystal structure of the outer membrane active transporter FepA from Escherichia coli. Nat. Struct. Biol. 6:56-63.
8. Butler, J. E., F. Kaufmann, M. V. Coppi, C. Nunez, and D. R. Lovley. 2004. MacA, a diheme c-type cytochrome involved in Fe(III) reduction by Geobacter sulfurreducens. J. Bacteriol. 186:4042-4045.
9. Coppi, M. V., C. Leang, S. J. Sandler, and D. R. Lovley. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl. Environ Microbiol. 67:3180-3187.
10. Dailey, H. A. 2002. Terminal steps of haem biosynthesis. Biochem. Soc. Trans. 30:590-595.
11. Francis, R. T., Jr., and R. R. Becker. 1984. Specific indication of hemoproteins in polyacrylamide gels using a double-staining process. Anal. Biochem. 136:509-514.
12. Gardy, J. L., M. R. Laird, F. Chen, S. Rey, C. J. Walsh, M. Ester, and F. S. L. Brinkman. 2005. PSORTb v. 2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21:617-623.
13. Haveman, S. A., E. A. Greene, C. P. Stilwell, J. K. Voordouw, and G. Voordouw. 2004. Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris Hildenborough by nitrite. J. Bacteriol. 186:7944-7950.
14. Hayashi, S., and H. C. Wu. 1990. Lipoproteins in bacteria. J. Bioenerg. Biomembr. 22:451-471.
15. Hofmann, K., and W. Stoffel. 1993. TMbase-a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166.
16. Holmes, D. E., D. R. Bond, R. A. O'Neil, C. E. Reimers, L. R. Tender, and D. R. Lovley. 2004. Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments. Microb. Ecol. 48:178-190.
17. Holmes, D. E., K. P. Nevin, and D. R. Lovley. 2004. In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl. Environ. Microbiol. 70:7251-7259.
18. Holmes, D. E., K. P. Nevin, R. A. O'Neil, J. E. Ward, L. A. Adams, T. L. Woodard, H. A. Vrionis, and D. R. Lovley. 2005. Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes. Appl. Environ. Microbiol. 71:6870-6877.
19. Hua, S., and Z. Sun. 2001. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17:721-728.
20. Kim, B. C., C. Leang, Y. H. Ding, R. H. Glaven, M. V. Coppi, and D. R. Lovley. 2005. OmcF, a putative c-type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens. J. Bacteriol. 187:4505-4513.
21. Kim, B. C., X. Qian, C. Leang, M. V. Coppi, and D. R. Lovley. 2006. Two putative c-type multiheme cytochromes required for the expression of OmcB, an outer membrane protein essential for optimal Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 188:3138-3142.
22. o- reducing bacteria in a sulfate-rich environment. Environ. Microbiol. 8:141-155.
23. Kranz, R. G., C. S. Beckett, and B. S. Goldman. 2002. Genomic analyses of bacterial respiratory and cytochrome c assembly systems: Bordetella as a model for the system II cytochrome c biogenesis pathway. Res. Microbiol. 153:1-6.
24. Kranz, R. G., R. Lill, B. S. Goldman, G. Bonnard, and S. Merchant. 1998. Molecular mechanisms of cytochrome c biogenesis: three distinct systems. Mol. Microbiol. 29:383-396.
25. Leang, C., M. V. Coppi, and D. R. Lovley. 2003. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 185:2096-2103.
26. Le Brun, N. E., J. Bengtsson, and L. Hederstedt. 2000. Genes required for cytochrome c synthesis in Bacillus subtilis. Mol. Microbiol. 36:638-650.
27. Lin, W. C., M. V. Coppi, and D. R. Lovley. 2004. Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor. Appl. Environ. Microbiol. 70:2525-2528.
28. Lloyd, J. R., C. Leang, A. L. Hodges Myerson, M. V. Coppi, S. Cuifo, B. Methe, S. J. Sandler, and D. R. Lovley. 2003. Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. Biochem. J. 369:153-161.
29. Lonergan, D. J., H. L. Jenter, J. D. Coates, E. J. Phillips, T. M. Schmidt, and D. R. Lovley. 1996. Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. J. Bacteriol. 178:2402-2408.
30. Lovley, D. R., S. J. Giovannoni, D. C. White, J. E. Champine, E. J. Phillips, Y. A. Gorby, and S. Goodwin. 1993. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch. Microbiol. 159:336-344.
31. Lovley, D. R., R. C. Greening, and J. G. Ferry. 1984. Rapidly growing rumen methanogenic organism that synthesizes coenzyme M and has a high affinity for formate. Appl. Environ. Microbiol. 48:81-87.
32. Lovley, D. R., D. E. Holmes, and K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219-286.
33. Lovley, D. R., and E. J. Phillips. 1988. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl. Environ. Microbiol. 54:1472-1480.
34. o reduction by Pelobacter carbinolicus. Appl. Environ. Microbiol. 61:2132-2138.
35. Mehta, T., M. V. Coppi, S. E. Childers, and D. R. Lovley. 2005. Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. Appl. Environ. Microbiol. 71:8634-8641.
36. Methe, 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.
37. Mussmann, M., K. Ishii, R. Rabus, and R. Amann. 2005. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol. 7:405-418.
38. Page, M. D., Y. Sambongi, and S. J. Ferguson. 1998. Contrasting routes of c-type cytochrome assembly in mitochondria, chloroplasts and bacteria. Trends Biochem. Sci. 23:103-108.
39. Pereira, I. A., J. LeGall, A. V. Xavier, and M. Teixeira. 2000. Characterization of a heme c nitrite reductase from a non-ammonifying microorganism, Desulfovibrio vulgaris Hildenborough. Biochim. Biophys. Acta 1481:119-130.
40. Reguera, G., K. D. McCarthy, T. Mehta, J. S. Nicoll, M. T. Tuominen, and D. R. Lovley. 2005. Extracellular electron transfer via microbial nanowires. Nature 435:1098-1101.
41. Roden, E. E., and D. R. Lovley. 1993. Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans. Appl. Environ. Microbiol. 59:734-742.
42. 3-type oxidase belonging to the superfamily of heme-copper oxidases. J. Bacteriol. 183:687-699.
43. 2 compounds. Arch. Microbiol. 137:33-41.
44. Schink, B. 1985. Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. Arch. Microbiol. 142:295-301.
45. Schink, B., and N. Pfennig. 1982. Fermentation of trihydroxybenzenes by Pelobacter acidigallici gen. nov. sp. nov., a new strictly anaerobic, non-sporeforming bacterium. Arch. Microbiol. 133:195-201.
46. Schink, B., and M. Stieb. 1983. Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov. Appl. Environ. Microbiol. 45:1905-1913.
47. Schnell, S., A. Brune, and B. Schink. 1991. Degradation of hydroxyhydroquinone by the strictly anaerobic fermenting bacterium Pelobacter massiliensis sp. nov. Arch. Microbiol. 155:511-516.
48. Simon, J. 2002. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol. Rev. 26:285-309.
49. Stevens, J. M., O. Daltrop, J. W. A. Allen, and S. J. Ferguson. 2004. c-type cytochrome formation: chemical and biological enigmas. Acc. Chem. Res. 37:999-1007.
50. Thamdrup, B., R. Rossello-Mora, and R. Amann. 2000. Microbial manganese and sulfate reduction in Black Sea shelf sediments. Appl. Environ. Microbiol. 66:2888-2897.
51. Thomas, P. E., D. Ryan, and W. Levin. 1976. An improved staining procedure for the detection of the peroxidase activity of cytochrome P-450 on sodium dodecyl sulfate polyacrylamide gels. Anal. Biochem. 75:168-176.
52. Vrionis, H. A., R. T. Anderson, I. Ortiz-Bernad, K. R. O'Neill, C. T. Resch, A. D. Peacock, R. Dayvault, D. C. White, P. E. Long, and D. R. Lovley. 2005. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71:6308-6318.
53. Yanyushin, M. F., M. C. del Rosario, D. C. Brune, and R. E. Blankenship. 2005. New class of bacterial membrane oxidoreductases. Biochemistry 44:10037-10045.