Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Cruz García, Claribel ^a,i   Murray, Alison E ^a,j   Rodrigues, Jorge L M ^c   Gralnick, Jeffrey A ^d   McCue, Lee Ann ^e   Romine, Margaret F ^e   Löffler, Frank E ^f,g,h   Tiedje, James M ^a,b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b University of Texas at Arlington ^*  (United States)

^c UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^f UNIVERSITY OF TENNESSEE   (United States)

^g University of Tennessee   (United States)

^h OAK RIDGE NATIONAL LABORATORY   (United States)

ⁱ Georgia Institute of Technology   (United States)

^j DESERT RESEARCH INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ACETATE KINASE; ACETATE PHOSPHOENOL PYRUVATE CARBOXYLASE; ALCOHOL DEHYDROGENASE; ALDEHYDE ALCOHOL DEHYDROGENASE; BACTERIAL PROTEIN; CYMA PROTEIN; CYTOCHROME C OXIDASE; CYTOCHROME D UBIQUINOL OXIDASE I; CYTOCHROME D UBIQUINOL OXIDASE II; DIMETHYL SULFOXIDE; DIMETHYL SULFOXIDE REDUCTASE; ELECTRON TRANSFERRING FLAVOPROTEIN; ELECTRON TRANSPORT REGULATOR PROTEIN A; FORMATE DEHYDROGENASE; FUMARATE AND NITRATE REDUCTION REGULATOR; FUMARATE REDUCTASE; HCP PROTEIN; LACTATE PERMEASE; MTRB PROTEIN; NAPD PROTEIN; NITRATE; NRFA PROTEIN; PHOSPHATE ACETYLTRANSFERASE; PHOSPHOENOLPYRUVATE CARBOXYLASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE); SUCCINATE DEHYDROGENASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; UNINDEXED DRUG; ETRA PROTEIN, SHEWANELLA;

ANAEROBIC GROWTH; ANAEROBIC METABOLISM; ARTICLE; DOWN REGULATION; ENERGY METABOLISM; GENE CONTROL; GENE DELETION; GENE EXPRESSION; KNOCKOUT GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PROTEIN BINDING; SHEWANELLA ONEIDENSIS; UPREGULATION; WILD TYPE; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGY; SHEWANELLA;

PSEUDOMONAS AERUGINOSA; SHEWANELLA; SHEWANELLA ONEIDENSIS; SHEWANELLA ONEIDENSIS MR-1;

ANAEROBIOSIS; BACTERIAL PROTEINS; ENERGY METABOLISM; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; NITRATES; SEQUENCE ANALYSIS, DNA; SHEWANELLA; TRANSCRIPTION FACTORS;

EID: 79953115195     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-64     Document Type: Article

References (64)

1. The magnificent seven. M Holden S Bentley M Sebaihia N Thompson A Cerdẽo-Trraga J Parkhill, Trends Microbiol 2003 11 12 14.22 10.1016/S0966-842X(02)00009-4 12526849
2. Shewanella-the environmentally versatile genome. JM Tiedje, Nat Biotechnol 2002 20 1093 1094 10.1038/nbt1102-1093 12410251
3. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. JF Heidelberg IT Paulsen KE Nelson EJ Gaidos WC Nelson TD Read JA Eisen R Seshadri N Ward B Methe RA Clayton T Meyer A Tsapin J Scott M Beanan L Brinkac S Daugherty RT DeBoy RJ Dodson Durkin DH Haft JF Kolonay R Madupu JD Peterson LA Umayam O White AM Wolf J Vamathevan J Weidman M Impraim K Lee K Berry C Lee J Mueller H Khouri J Gill TR Utterback LA McDonald TV Feldblyum HO Smith JC Venter KH Nealson CM Fraser, Nat Biotechnol 2002 20 1118 1123 10.1038/nbt749 12368813 (Pubitemid 35285440)
4. Anaerobic regulation by an atypical Arc system in Shewanella oneidensis. JA Gralnick CT Brown DK Newman, Mol Microbiol 2005 56 1347 1357 10.1111/j.1365-2958.2005.04628.x 15882425 (Pubitemid 40756015)
5. Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis. DA Saffarini R Schultz A Beliaev, J Bacteriol 2003 185 3668 3671 10.1128/JB.185.12.3668-3671.2003 12775705 (Pubitemid 36676434)
6. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. AS Beliaev DK Thompson MW Fields L Wu DP Lies KH Nealson J Zhou, J Bacteriol 2002 184 4612 4616 10.1128/JB.184.16.4612-4616.2002 12142431 (Pubitemid 34832589)
7. Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: reassessment of the role of EtrA. TM Maier CR Myers, J Bacteriol 2001 183 4918 4926 10.1128/JB.183.16.4918-4926.2001 11466298 (Pubitemid 32717247)
8. Fnr, NarP, and NarL regulation of E. coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. AJ Darwin EC Ziegelhoffer PJ Kiley V Stewart, J Bacteriol 1998 180 4192 4198 9696769 (Pubitemid 28373525)
9. Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of E. coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site. AJ Darwin V Stewart, J Mol Biol 1997 251 15 29 10.1006/jmbi.1995.0412
10. Anaerobically expressed Escherichia coli genes identified by operon fusion techniques. M Choe WS Reznikoff, J Bacteriol 1991 173 6139 6146 1917846
11. Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions. S Shalel-Levanon KY San GN Bennett, Metab Eng 2005 7 445 456 10.1016/j.ymben.2005.07.001 16143552
12. Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. Y Kang KD Weber Y Qiu PJ Kiley FR Blattner, J Bacteriol 2005 187 1135 1160 10.1128/JB.187.3.1135- 1160.2005 15659690 (Pubitemid 40189786)
13. Mechanism of oxygen sensing by the bacterial transcription factor fumarate-nitrate reduction (FNR). J Crack J Green AJ Thomson, J Biol Chem 2004 279 9278 9286 10.1074/jbc.M309878200 14645253 (Pubitemid 38295991)
14. Iron-sulfur clusters as oxygen-responsive molecular switches. FW Outten, Nat Chem Biol 2007 3 206 207 10.1038/nchembio0407-206 17372605 (Pubitemid 46440535)
15. Regulation of FNR dimerization by subunit charge repulsion. LJ Moore EL Mettert PJ Kiley, J Biol Chem 2006 281 33268 33275 10.1074/jbc.M608331200 16959764 (Pubitemid 46036709)
16. Sequence and genetic characterization of etrA, an fnr analog that regulates anaerobic respiration in Shewanella putrefaciens MR-1. DA Saffarini KH Nealson, J Bacteriol 1993 175 7938 7944 8253682 (Pubitemid 24004401)
17. Involvement of a membrane-bound class III adenylate cyclase in regulation of anaerobic respiration in Shewanella oneidensis MR-1. MA Charania KL Brockman Y Zhang A Banerjee GE Pinchuk JK Fredrickson AS Beliaev DA Saffarini, J Bacteriol 2009 191 4298 4306 10.1128/JB.01829-08 19395492
18. The ArsR repressor mediates arsenite-dependent regulation of arsenate respiration and detoxification operons of Shewanella sp. Strain ANA-3. JN Murphy CW Saltikov, J Bacteriol 2009 191 6722 6731 10.1128/JB.00801-09 19717602
19. Functional roles of arcA, etrA, cyclic AMP (cAMP)-cAMP receptor protein, and cya in the arsenate respiration pathway in Shewanella sp. strain ANA-3. JN Murphy KJ Durbin CW Saltikov, J Bacteriol 2009 191 1035 1043 10.1128/JB.01293-08 19060154
20. Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology. TW Overton L Griffiths MD Patel JL Hobman CW Penn JA Cole C Constantinidou, Biochem Soc T 2006 34 104 107 10.1042/BST0340104 (Pubitemid 43235545)
21. Role of the tetraheme cytochrome CymA in anaerobic electron transport in cells of Shewanella putrefaciens MR-1 with normal levels of menaquinone. CR Myers JM Myers, J Bacteriol 2000 182 67 75 10.1128/JB.182.1.67-75.2000 10613864 (Pubitemid 30004559)
22. Genome-assisted analysis of dissimilatory metal-reducing bacteria. JK Fredrickson MF Romine, Curr Opin Biotechnol 2005 16 269 274 10.1016/j.copbio. 2005.04.001 15961027 (Pubitemid 40806463)
23. Sequencing and the alignment of structural genes in the nqr operon encoding the Na(+)-translocating NADH-quinone reductase from Vibrio alginolyticus. M Hayashi K Hirai T Unemoto, FEBS Lett 1995 363 75 77 10.1016/0014-5793(95)00283-F 7729558
24. Transcriptional regulation of a hybrid cluster (prismane) protein. NA Filenko DF Browning JA Cole, Biochem Soc Trans 2005 33 195 197 10.1042/BST0330195 15667305 (Pubitemid 40313800)
25. Hydroxylamine assimilation by Rhodobacter capsulatus E1F1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction. P Cabello C Pino MF Olmo-Mira F Castillo MD Roldn C Moreno-Vivin, J Biol Chem 2004 279 45485 45494 10.1074/jbc.M404417200 15322098 (Pubitemid 39491534)
26. Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli. MT Wolfe J Heo JS Garavelli PW Ludden, J Bacteriol 2002 184 5898 5902 10.1128/JB.184.21.5898-5902.2002 12374823 (Pubitemid 35168238)
27. The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]. WA van den Berg WR Hagen WM van Dongen, Eur J Biochem 2000 267 666 676 10.1046/j.1432-1327.2000.01032.x 10651802 (Pubitemid 30082378)
28. The htx and ptx operons of Pseudomonas stutzeri WM88 are new members of the pho regulon. AK White WW Metcalf, J Bacteriol 2004 186 5876 5882 10.1128/JB.186.17.5876-5882.2004 15317793 (Pubitemid 39128661)
29. Isolation and biochemical characterization of hypophosphite/2- oxoglutarate dioxygenase. A novel phosphorus-oxidizing enzyme from Pseudomonas stutzeri WM88. AK White WW Metcalf, J Biol Chem 2002 277 38262 38271 10.1074/jbc.M204605200 12161433 (Pubitemid 35154681)
30. Rate of occurrence and pathogenic effect of enteroaggregative Escherichia coli virulence factors in international travelers. ZD Jiang D Greenberg JP Natarro R Stephen HL DuPont, J Clin Microbiol 2002 40 4185 4190 10.1128/JCM.40.11.4185-4190.2002 12409395 (Pubitemid 35285810)
31. Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2. W Jiang WW Metcalf KS Lee BL Wanner, J Bacteriol 1995 177 6411 6421 7592415
32. Mutational analysis of the role of the first helix region 4.2 of the sigma 70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB. SK Kim K Makino M Amemura A Nakata H Shinagawa, Mol Gen Genet 1995 248 1 8 10.1007/BF02456607 7651320
33. Structural basis for the function of stringent starvation protein a as a transcription factor. AM Hansen Y Gu M Li M Andrykovitch DS Waugh DJ Jin X Ji, J Biol Chem 2005 280 17380 17391 10.1074/jbc.M501444200 15735307 (Pubitemid 41389208)
34. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. G Jovanovic L Weiner P Model, J Bacteriol 1996 178 1936 1945 8606168 (Pubitemid 26110537)
35. Survival and stress induced expression of groEL and rpoD of Campylobacter jejuni from different growth phases. A Klancnik N Bottledoorn L Herman SS Mozina, Int J Food Microbiol 2006 112 200 207 10.1016/j.ijfoodmicro.2006.03.015 16782221 (Pubitemid 44708384)
36. Deletion of the putative effector region of Era, an essential GTP-binding protein in Escherichia coli, causes a dominant-negative phenotype. RC Pillutla J Ahnn M Inouye, FEMS Microbiol Lett 1996 143 47 55 10.1111/j.1574-6968.1996. tb08460.x 8807801 (Pubitemid 26292652)
37. Purification and characterization of the Escherichia coli RecO protein. C Luisi-DeLuca R Kolodner, J Mol Biol 1994 236 124 138 10.1006/jmbi.1994.1123 8107098
38. Oxygen, nitrate and molybdenum regulation of dmsABC genes expression in Escherichia coli. PA Cotter RP Gunsalus, J Bacteriol 1989 171 3817 3823 2544558 (Pubitemid 19174155)
39. Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12. V Stewart PJ Bledsoe SB Williams, J Bacteriol 2003 185 5862 5870 10.1128/JB.185.19.5862-5870.2003 13129959 (Pubitemid 37176499)
40. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. X Qiu GW Sundin L Wu J Zhou JM Tiedje, J Bacteriol 2005 187 3556 3564 10.1128/JB.187.10.3556-3564.2005 15866945 (Pubitemid 40628714)
41. Structural basis for the interaction of Escherichia coli NusA with protein N of phage lambda. I Bonin R Muhlberger GP Bourenkov R Huber A Bacher G Richter WC Wahl, Proc Natl Acad Sci USA 2004 101 13762 13767 10.1073/pnas.0405883101 15365170 (Pubitemid 39298481)
42. In vivo effect of NusB and NusG on rRNA transcription antitermination. M Torres JM Balada M Zellars C Squires C Squires, J Bacteriol 2004 186 1304 1310 10.1128/JB.186.5.1304-1310.2004 14973028 (Pubitemid 38248719)
43. The biology of viruses. BA Voyles, Mosby-Year Book, Inc., St. Louis, MO 1993
44. Respiratory Nitrate Ammonification by Shewanella oneidensis MR-1. C Cruz-García AE Murray NJA Klappenbach V Stewart JM Tiedje, J Bacteriol 2007 189 656 662 17098906 (Pubitemid 46106399)
45. New approach to the cultivation of methanogenic bacteria: 2-mercaptoethanesulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressureized atmosphere. WE Balch RS Wolfe, Appl Environ Microbiol 1976 32 781 791 827241 (Pubitemid 8008043)
46. Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. CJ Marx ME Lidstrom, Biotechniques 2002 33 1062 1067 12449384 (Pubitemid 35285540)
47. Determination of ammonium in KCl extracts of soils by the salicylate method. DW Nelson, Comm Soil Sci Plant Anal 1983 14 1051 1062 10.1080/00103628309367431
48. Techniques in Microbial Ecology. RS Burlage R Atlas D Stahl G Gessey G Sayler, Oxford University Press US, New York, NY 1988
49. Novel Mode of Microbial Energy Metabolism: Organic Carbon oxidation Coupled to Dissimilatory Reduction of Iron or Manganese. DR Lovley EJP Phillips, Appl Environ Microbiol 1988 54 1472 1480 16347658
50. Availability of Ferric Iron Microbial Reduction in Bottom Sediments of the Freshwater Tidal Potomac River. DR Lovley EJP Phillips, Appl Environ Microbiol 1986 52 751 757 16347168
51. Complete Detoxification of Vinyl Chloride by an Anaerobic Enrichment Culture and Identification of the Reductively Dechlorinating Population as a Dehalococcoides species. J He RM Ritalahti MR Aiello FE Löffler, Appl Environ Microbiol 2003 69 996 1003 10.1128/AEM.69.2.996-1003.2003 12571022 (Pubitemid 36204828)
52. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs. JLM Rodrigues OV Maltseva TV Tsoi RR Helton JF Quensen III M Fukuda JM Tiedje, Environ Sci Technol 2001 35 663 668 10.1021/es001308t 11349275 (Pubitemid 32173701)
53. Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria. FE Löffler JE Champine KM Ritalahti SJ Sprague JM Tiedje, Appl Environ Microbiol 1997 63 2870 2875 16535654 (Pubitemid 27292889)
54. Molecular Cloning: A Laboratory Manual. J Sambrook DW Russell, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 2001
55. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. H Gao Y Wang X Liu T Yan L Wu E Alm A Arkin DK Thompson J Zhou, J Bacteriol 2004 186 7796 7803 10.1128/JB.186.22.7796-7803.2004 15516594 (Pubitemid 39463746)
56. Improved quantitation and reproducibility in Mycobacterium tuberculosis DNA microarrays. RG Schroeder LM Peterson RD Fleischmann, J Mol Microbiol Biotechnol 2002 4 123 126 11873907 (Pubitemid 34182868)
57. A concise guide to cDNA microarray analysis. P Hedge R Qi K Abernathy C Gay S Dharap R Gaspard J Earlehughes E Snesrud N Lee J Quackenbush, BioTechniques 2000 29 548 562 10997270
58. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. AE Murray D Lies G Li KH Nealson J Zhou JM Tiedje, Proc Natl Acad Sci 2001 98 9853 9858 10.1073/pnas.171178898 11493693 (Pubitemid 32769393)
59. The Gibbs centroid sampler. WA Thompson LA Newberg S Conlan L McCue CE Lawrence, Nucleic Acids Res 2007 35 232 237 10.1093/nar/gkm265 17483517
60. Bayesian inference on biopolymer models. JS Liu CE Lawrence, Bioinformatics 1999 15 38 52 10.1093/bioinformatics/15.1.38 10068691 (Pubitemid 29101197)
61. A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncP) conjugative machineries and their cognate Escherichia coli host strains. G Demarre AM Guérout C Matsumoto-Mashimo DA Rowe-Magnus P Marlière D Mazel, Res Microbiol 2005 156 245 255 15748991 (Pubitemid 40320963)
62. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. CR Myers KH Nealson, Science 1988 240 1319 1321 10.1126/science.240.4857.1319 17815852 (Pubitemid 19301162)
63. Development of versatile broad-host-range vectors for use in methylotrophs and other gram-negative bacteria. CJ Marx L Chistoserdova, Microbiology 2001 147 2065 2075 11495985 (Pubitemid 32785488)
64. The pKNOCK series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria. MF Alexeyev, BioTechniques 1999 26 824 828 10337469