Importance of c-type cytochromes for U(VI) reduction by Geobacter sulfurreducens

BMC Microbiology

Volumn 7, Issue , 2007, Pages

  Shelobolina, Evgenya S ^a   Coppi, Maddalena V ^a   Korenevsky, Anton A ^b   DiDonato, Laurie N ^a   Sullivan, Sara A ^a   Konishi, Hiromi ^c   Xu, Huifang ^c   Leang, Ching ^a   Butler, Jessica E ^a   Kim, Byoung Chan ^a   Lovley, Derek R ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b UNIVERSITY OF GUELPH   (Canada)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; CYTOCHROME C; FERRIC HYDROXIDE; FERRIC ION; IRON CHELATE; URANIUM;

ARTICLE; CELL SUBPOPULATION; COMPARATIVE STUDY; CORRELATION ANALYSIS; CYTOPLASM; ELECTRON; ELECTRON TRANSPORT; GENE DELETION; GEOBACTER; GEOBACTER SULFURREDUCENS; MEMBRANE TRANSPORT; NONHUMAN; NUCLEOTIDE SEQUENCE; OUTER MEMBRANE; WILD TYPE;

BIODEGRADATION, ENVIRONMENTAL; CYTOCHROME C GROUP; FERRIC COMPOUNDS; GEOBACTER; MICROSCOPY, ELECTRON, TRANSMISSION; MUTATION; OXIDATION-REDUCTION; PERIPLASM; URANIUM;

GEOBACTER SULFURREDUCENS; LEPIDIUM MEYENII;

EID: 33947408357     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-7-16     Document Type: Article

References (57)

1. Radioactivity and the 20th century. RC Ewing, Uranium: Mineralogy, Geochemistry and the Environment Mineralogical Society of America, Washington, DC, FR Burns PC, 1999 38 1 21
2. Radionuclides in the geosphere: sources, mobility, reactions in natural waters and interactions with solids. KH Lieser, Radiochimica Acta 1995 70/71 355 375
3. Geomicrobiology of uranium. Y Suzuki JF Banfield, Uranium: Mineralogy, Geochemistry and the Environment Mineralogical Society of America, Washington, DC, FR Burns PC, 1999 38 393 432
4. Enzymology of electron transport: energy generation with geochemical consequences. TJ DiChristina JK Fredrickson JM Zachara, Molecular Geomicrobiology Mineralogical Society of America, JF Banfield, Cervini-Silva J, Nealson KH, 2005 27 52
5. Microbial reduction of uranium. DR Lovley EJP Phillips YA Gorby ER Landa, Nature 1991 350 413 416 10.1038/350413a0
6. Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. DE Holmes KT Finneran RA O'Neil DR Lovley, Appl Environ Microbiol 2002 68 2300 2306 11976101 10.1128/AEM.68.5.2300-2306.2002
7. Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate. N North S Dollhopf L Petrie J Istok D Balkwill J Kostka, Appl Environ Microbiol 2004 70 4911 4920 15294831 10.1128/AEM.70.8.4911-4920.2004
8. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. HA Vrionis RT Anderson I-Bernad Ortiz KR O'Neill CT Resch AD Peacock R Dayvault DC White PE Long DR Lovley, Appl Environ Microbiol 2005 71 6308 6318 16204552 10.1128/AEM.71.10.6308-6318.2005
9. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. RT Anderson HA Vrionis I Ortiz-Bernard CT Resch PE Long R Dayvault K Karp S Marutzky DR Metzler A Peacock DC White M Lowe DR Lovley, Appl Environ Microbiol 2003 69 5884 5891 14532040 10.1128/AEM.69.10.5884-5891.2003
10. Uranium reduction. JD Wall L Krumholz, Annu Rev Microbiol 2006 60 149 166 10.1146/annurev.micro.59.030804.121357 16704344
11. Reduction of uranium by cytochrome c 3 of Desulfovibrio vulgaris. DR Lovley PK Widman JC Woodward EJP Phillips, Appl Environ Microbiol 1993 59 3572 3576 8285665
12. Uranium Reduction by Desulfovibrio desulfuricans Strain G20 and a cytochrome c3 mutant. RB Payne DM Gentry BJ Rapp-Giles L Casalot JD Wall, Appl Environ Microbiol 2002 68 3129 3132 12039777 10.1128/AEM.68.6.3129-3132.2002
13. Interaction between uranium and the cytochrome c3 of Desulfovibrio desulfuricans strain G20. RB Payne L Casalot T Rivere J Terry L Larsen BJ Giles JD Wall, Arch Microbiol 2004 181 398 406 10.1007/s00203-004-0671-7 15114437
14. 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. DR Lovley SJ Giovannoni DC White JE Champine EJP Phillips YA Gorby S Goodwin, Arch Microbiol 1993 159 336 344 10.1007/BF00290916 8387263
15. c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis. MJ Marshall AS Beliaev AC Dohnalkova DW Kennedy L Shi Z Wang MI Boyanov B Lai KM Kemner JS McLean SB Reed DE Culley VL Bailey CJ Simonson DA Saffarini MF Romine JM Zachara JK Fredrickson, PLoS Biology 2006 4 1324 1333 10.1371/journal.pbio.0040268
16. Enzymatic uranium precipitation. YA Gorby DR Lovley, Environ Sci Technol 1992 26 205 207 10.1021/es00025a026
17. Dissimilatory Fe(III) and Mn(IV) Reduction. DR Lovley DE Holmes KP Nevin, Advances in Microbial Physiology 2004 49 219 286 15518832
18. Reduction of uranium by Desulfovibrio desulfuricans. DR Lovley EJP Phillips, Appl Environ Microbiol 1992 58 850 856 1575486
19. Bioremediation of uranium contamination with enzymatic uranium reduction. DR Lovley EJP Phillips, Environ Sci Technol 1992 26 2228 2234 10.1021/es00035a023
20. Radionuclide contamination - nanometer-size products of uranium bioreduction. Y Suzuki SD Kelly KM Kemner JF Banfield, Nature 2002 419 6903 134 134 10.1038/419134a 12226656
21. Reduction of actinides and fission products by Fe(III)-reducing bacteria. JR Lloyd J Chesnes S Glasauer DJ Bunker FR Livens DR Lovley, Geomicrobiol J 2002 19 103 120 10.1080/014904502317246200
22. Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments. B Methé K Nelson J Eisen I Paulsen W Nelson J Heidelberg D Wu M Wu N Ward M Beanan R Dodson R Madupu L Brinkac S Daugherty R DeBoy A Durkin M Gwinn J Kolonay S Sullivan D Haft J Selengut T Davidsen N Zafar O White B Tran C Romero H Forberger J Weidman H Khouri T Feldblyum T Utterback S Van Aken D Lovley C Fraser, Science 2003 302 1967 1969 10.1126/science.1088727 14671304
23. Development of a genetic system for Geobacter sulfurreducens. MV Coppi C Leang SJ Sandler DR Lovley, Appl Environ Microbiol 2001 67 3180 3187 11425739 10.1128/AEM.67.7.3180-3187.2001
24. OmcF, a putative c-type monoheme outer membrane cytochrome required for the expression of outer membrane cytochromes in Geobacter sulfurreducens. B-C Kim C Leang YR Ding RH Glaven MV Coppi DR Lovley, J Bacteriol 2005 187 4505 4513 15968061 10.1128/JB.187.13.4505-4513.2005
25. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. C Leang MV Coppi DR Lovley, J Bacteriol 2003 185 2096 2103 12644478 10.1128/JB.185.7.2096-2103.2003
26. MacA, a diheme c-type cytochrome involved in Fe(III) reduction by Geobacter sulfurreducens. JE Butler F Kaufmann MV Coppi C Núnez DR Lovley, J Bacteriol 2004 186 4042 4045 15175321 10.1128/JB.186.12.4042-4045.2004
27. Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. JR Lloyd C Leang AL Hodges Myerson MV Coppi S Cuifo B Methe SJ Sandler DR Lovley, Biochem J 2003 369 153 161 12356333 10.1042/BJ20020597
28. Increased Fe(III) reduction rates in two c7-type cytochrome mutants. LN DiDonato RJ DiDonato ES Shelobolina KP Nevin TL Woodward SA Sullivan B Postier DR Lovley, 2003
29. The periplasmic 9.6-kilodalton c-type cytochrome of Geobacter sulfurreducens is not an electron shuttle to Fe(III). JR Lloyd EL Blunt-Harris DR Lovley, J Bacteriol 1999 181 7647 7649 10601229
30. Bioreduction of uranium: environmental implications of a pentavalent intermediate. JC Renshaw LJC Butchins FR Livens I May JM Charnock JR Lloyd, Environ Sci Technol 2005 39 5657 5660 10.1021/es048232b 16124300
31. A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria. S Seeliger R Cord-Ruwisch B Schink, J Bacteriol 1998 180 3686 3691 9658015
32. Proteome Analyst Specialized Subcellular Localization Server v2.5. http://www.cs.ualberta.ca/∼bioinfo/PA/Sub/
33. Predicting subcellular localization of proteins using machine-learned classifiers. Z Lu D Szafron R Greiner P Lu DS Wishart B Poulin J Anvik C Macdonell R Eisner, Bioinformatics 2004 20 547 556 10.1093/bioinformatics/btg447 14990451
34. Isolation and characterization of an Fe(III) citrate-adapted strain of the Geobacter sulfurreducens ppcA mutant. LN DiDonato RJ DiDonato KP Nevin B Postier TL Woodard DR Lovley, 2004
35. Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. T Mehta MV Coppi SE Childers DR Lovley, Appl Environ Microbiol 2005 71 8634 8641 16332857 10.1128/AEM.71.12.8634-8641. 2005
36. Topological localization and distribution of OmcB and OmpB proteins involved in Fe(III) reduction in Geobacter sulfurreducens. X Qian G Reguera T Mester DR Lovley, 2005
37. Family of cytochrome c7-type proteins from Geobacter sulfurreducens: structure of one cytochrome c7 at 1.45 A resolution. PR Pokkuluri YY Londer NE Duke WC Long M Schiffer, Biochemistry 2004 43 849 859 14744127
38. Structure of cytochrome c7 from Desulfuromonas acetoxidans at 1.9 A resolution. M Czjzek P Arnoux R Haser W Shepard, Acta Crystallogr D Biol Crystallogr 2001 57 670 678 10.1107/S0907444901003481 11320307
39. Lanthanide accumulation in the periplasmic space of Escherihia coli. ME Bayer MH Bayer, J Bacteriol 1991 173 141 149 1987113
40. Direct epifluourescence enumeration of native aquatic bacteria: uses, limitations and comparative accuracy. RJ Daley, Native Aquatic Bacteria: Enumeration, Activity and Ecology ASTM, Philadelphia, Costerton JW, Colwell RR, 1979 29 45
41. Copper uptake and its compartmentalization in Pseudomonas aeruginosa strains: Chemical nature of cellular metal. SK Kazy P Sar RK Asthana SP Singh, World Journal of Microbiology and Biotechnology 1999 15 599 605 10.1023/A:1008997718811
42. Intracellular nickel accumulation by Pseudomonas aeruginosa and its chemical nature. P Sar SK Kazy SP Singh, Letters in Applied Microbiology 2001 32 257 261 10.1046/j.1472-765X.2001.00878.x 11298937
43. Molecular cloning: a laboratory manual. J Sambrook JE Fritsch T Maniatis, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 2 1989
44. PCR-mediated gene replacement in Escherichia coli. KC Murphy KG Campellone AR Poteete, Gene 2000 246 321 330 10.1016/S0378-1119(00)00071-8 10767554
45. Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors. MV Coppi RA O'Neil Lovley DR, J Bacteriol 2004 186 3022 3028 15126463 10.1128/JB.186.10.3022-3028.2004
46. pBBR1MCS: a broad-host-range cloning vector. ME Kovach RW Phillips PH Elzer RM n Roop KM Peterson, Biotechniques 1994 16 800 802 8068328
47. New shuttle vectors for the introduction of cloned DNA in Desulfovibrio. M Rousset L Casalot BJ Rapp-Giles Z Dermoun P de Philip JP Belaich JD Wall, Plasmid 1998 39 114 122 10.1006/plas.1997.1321 9514705
48. Use of nuclepore filters for counting bacteria by fluorescence microscopy. JE Hobbie RJ Daley S Jasper, Appl Environ Microbiol 1977 33 1225 1228 327932
49. Organic matter mineralization with reduction of ferric iron in anaerobic sediments. D Lovley E Phillips, Appl Environ Microbiol 1986 51 683 689 16347032
50. Enzymatic iron and uranium reduction by sulfate-reducing bacteria. DR Lovley EE Roden EJP Phillips JC Woodward, Marine Geol 1993 113 41 53 10.1016/0025-3227(93)90148-O
51. Transmission Electron Microscopy. DB Williams CB Carter, Plenum, New York 1996
52. Interstratification and other reaction microstructures in the chlorite-berthierine series. H Xu DR Veblen, Contrib Mineral Petrol 1996 124 291 301 10.1007/s004100050192
53. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. F Caccavo DJ Lonergan DR Lovley M Davis JF Stolz MJ McInerney, Appl Environ Microbiol 1994 60 3752 3759 7527204
54. Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens. C Leang DR Lovley, Microbiology 2005 151 1761 1767 10.1099/mic.0.27870-0 15941985
55. Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae. B Yan BA Methe DR Lovley J Krushkal, J Theor Biol 2004 230 133 144 10.1016/j.jtbi.2004.04.022 15276006
56. Expert system for predicting protein localization sites in gram-negative bacteria. K Nakai M Kanehisa, Proteins 1991 11 95 110 10.1002/prot.340110203 1946347
57. PSORT Prediction. http://psort.nibb.ac.jp/form.html