Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Tai, Shang Kai ^a   Wu, GuanI ^a   Yuan, Shinsheng ^a   Li, Ker Chau ^a,b  

^a INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CHEA KINASE; CHEMOTAXIS A1 PROTEIN; CYTOCHROME C; MAGNESIUM TRANSPORTER PROTEIN E1; NITRATE REDUCTASE; NITROUS OXIDE; PROTEIN CHEA 3 PROTEIN; PROTEIN GSPF; PROTEIN MTRA; PROTEIN MTRB; PROTEIN OMCA; PROTEIN OMCB; TRANSCRIPTION FACTOR NRF1; UNCLASSIFIED DRUG; ANTIPORTER; CYTOCHROME C OXIDASE; MGTE PROTEIN, BACTERIA;

AEROMONAS HYDROPHILA; ARTICLE; CHEMOTAXIS; COMPLEX FORMATION; CONTROLLED STUDY; ELECTRICITY; ELECTRON TRANSPORT; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME ANALYSIS; MICROARRAY ANALYSIS; NONHUMAN; OPEN READING FRAME; PROTEIN ANALYSIS; PROTEIN FUNCTION; SHEWANELLA ONEIDENSIS; TRANSCRIPTION REGULATION; BACTERIAL GENE; BACTERIAL GENOME; CYTOLOGY; GENETICS; GENOMICS; METABOLISM; SHEWANELLA;

SHEWANELLA ONEIDENSIS; SHEWANELLA ONEIDENSIS MR-1;

ANTIPORTERS; BACTERIAL PROTEINS; CHEMOTAXIS; ELECTRON TRANSPORT; ELECTRON TRANSPORT COMPLEX IV; GENE EXPRESSION PROFILING; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; NITROUS OXIDE; SHEWANELLA;

EID: 77952460504     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-319     Document Type: Article

References (53)

1. Myers CR, Nealson KH. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 1988, 240:1319-1321. 10.1126/science.240.4857.1319, 17815852.
2. Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ. Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat Struct Biol 1999, 6:1113-1117. 10.1038/70051, 10581551.
3. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, Ringelberg DB, White DC, Nishijima M, Sano H, Burghardt J, Stackebrandt E, Nealson KH. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 1999, 49:705-724. 10.1099/00207713-49-2-705, 10319494.
4. Tang YJ, Meadows AL, Kirby J, Keasling JD. Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling. J Bacteriol 2007, 189:894-901. 10.1128/JB.00926-06, 1797319, 17114268.
5. Nealson KH, Saffarini D. Iron and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Annu Rev Microbiol 1994, 48:311-343. 10.1146/annurev.mi.48.100194.001523, 7826009.
6. Abdelouas A, Lu Y, Lutze W, Nuttall EH. Reduction of U(VI) to U(IV) by indigenous bacteria in contaminated ground water. J Contam Hydrol 1998, 35:217-233.
7. 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, et al. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 2002, 20:1118-1123. 10.1038/nbt749, 12368813.
8. Brown SD, Thompson MR, Verberkmoes NC, Chourey K, Shah M, Zhou J, Hettich RL, Thompson DK. Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics 2006, 5:1054-1071. 10.1074/mcp.M500394-MCP200, 16524964.
9. Boukhalfa H, Icopini GA, Reilly SD, Neu MP. Plutonium(IV) reduction by the metal-reducing bacteria Geobacter metallireducens GS15 and Shewanella oneidensis MR1. Appl Environ Microbiol 2007, 73:5897-5903. 10.1128/AEM.00747-07, 2074912, 17644643.
10. Liu C, Jeon BH, Zachara JM, Wang Z. Influence of calcium on microbial reduction of solid phase uranium(VI). Biotechnol Bioeng 2007, 97:1415-1422. 10.1002/bit.21357, 17274063.
11. Ross DE, Ruebush SS, Brantley SL, Hartshorne RS, Clarke TA, Richardson DJ, Tien M. Characterization of protein-protein interactions involved in iron reduction by Shewanella oneidensis MR-1. Appl Environ Microbiol 2007, 73:5797-5808. 10.1128/AEM.00146-07, 2074908, 17675441.
12. Shi L, Squier TC, Zachara JM, Fredrickson JK. Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Mol Microbiol 2007, 65:12-20. 10.1111/j.1365-2958.2007.05783.x, 1974784, 17581116.
13. Bretschger O, Obraztsova A, Sturm CA, Chang IS, Gorby YA, Reed SB, Culley DE, Reardon CL, Barua S, Romine MF, Zhou J, Beliaev AS, Bouhenni R, Saffarini D, Mansfeld F, Kim BH, Fredrickson JK, Nealson KH. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl Environ Microbiol 2007, 73:7003-7012. 10.1128/AEM.01087-07, 2074945, 17644630.
14. Myers CR, Myers JM. MtrB is required for proper incorporation of the cytochromes OmcA and OmcB into the outer membrane of Shewanella putrefaciens MR-1. Appl Environ Microbiol 2002, 68:5585-5594. 10.1128/AEM.68.11.5585-5594.2002, 129928, 12406753.
15. Shi L, Chen B, Wang Z, Elias DA, Mayer MU, Gorby YA, Ni S, Lower BH, Kennedy DW, Wunschel DS, Mottaz HM, Marshall MJ, Hill EA, Beliaev AS, Zachara JM, Fredrickson JK, Squier TC. Isolation of a high-affinity functional protein complex between OmcA and MtrC: two outer membrane decaheme c-type cytochromes of Shewanella oneidensis MR-1. J Bacteriol 2006, 188:4705-4714. 10.1128/JB.01966-05, 1483021, 16788180.
16. Myers CR, Myers JM. The outer membrane cytochromes of Shewanella oneidensis MR-1 are lipoproteins. Lett Appl Microbiol 2004, 39:466-470. 10.1111/j.1472-765X.2004.01611.x, 15482439.
17. Gorby YA, Yanina S, McLean JS, Rosso KM, Moyles D, Dohnalkova A, Beveridge TJ, Chang IS, Kim BH, Kim KS, Culley DE, Reed SB, Romine MF, Saffarini DA, Hill EA, Shi L, Elias DA, Kennedy DW, Pinchuk G, Watanabe K, Ishii S, Logan B, Nealson KH, Fredrickson JK. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc Natl Acad Sci USA 2006, 103:11358-11363. 10.1073/pnas.0604517103, 1544091, 16849424.
18. Py B, Loiseau L, Barras F. An inner membrane platform in the type II secretion machinery of Gram-negative bacteria. EMBO Rep 2001, 2:244-248. 10.1093/embo-reports/kve042, 1083838, 11266368.
19. Stern S, Dror T, Stolovicki E, Brenner N, Braun E. Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge. Mol Syst Biol 2007, 3:106. 10.1038/msb4100147, 1865588, 17453047.
20. Karlebach G, Shamir R. Modelling and analysis of gene regulatory networks. Nature Rev Mol Cell Biol 2008, 9:770-780.
21. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297. 25624, 9843569.
22. Li KC. Genome-wide coexpression dynamics: theory and application. Proc Natl Acad Sci USA 2002, 99:16875-16880. 10.1073/pnas.252466999, 139237, 12486219.
23. Lin LH, Lee HC, Li WH, Chen BS. A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics 2007, 8:473. 10.1186/1471-2105-8-473, 2257980, 18067669.
24. Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol 2007, 3:153. 10.1038/msb4100194, 2174627, 18091724.
25. GEO: Gene Expression Omnibus. , http://www.ncbi.nlm.nih.gov/geo/
26. Li KC, Liu CT, Sun W, Yuan S, Yu T. A system for enhancing genome-wide coexpression dynamics study. Proc Natl Acad Sci USA 2004, 101:15561-15566. 10.1073/pnas.0402962101, 524832, 15492223.
27. Li KC, Yuan S. A functional genomic study on NCI's anticancer drug screen. Pharmacogenomics J 2004, 4:127-135. 10.1038/sj.tpj.6500235, 14993929.
28. Li KC, Palotie A, Yuan S, Bronnikov D, Chen D, Wei X, Choi OW, Saarela J, Peltonen L. Finding disease candidate genes by liquid association. Genome Biol 2007, 8:R205. 10.1186/gb-2007-8-10-r205, 2246280, 17915034.
29. Liu CT, Yuan S, Li KC. Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae. Nucleic Acids Res 2009, 37:526-532. 10.1093/nar/gkn972, 2632914, 19056822.
30. McCarter LL. Polar flagellar motility of the Vibrionaceae. Microbiol Mol Biol Rev 2001, 65:445-462. 10.1128/MMBR.65.3.445-462.2001, 99036, 11528005.
31. Li J, Romine MF, Ward MJ. Identification and analysis of a highly conserved chemotaxis gene cluster in Shewanella species. FEMS Microbiol Lett 2007, 273:180-186. 10.1111/j.1574-6968.2007.00810.x, 17590227.
32. Baker MD, Wolanin PM, Stock JB. Signal transduction in bacterial chemotaxis. Bioessays 2006, 28:9-22. 10.1002/bies.20343, 16369945.
33. Nealson KH, Moser DP, Saffarini DA. Anaerobic electron acceptor chemotaxis in Shewanella putrefaciens. Appl Environ Microbiol 1995, 61:1551-1554. 167410, 11536689.
34. Bencharit S, Ward MJ. Chemotactic responses to metals and anaerobic electron acceptors in Shewanella oneidensis MR-1. J Bacteriol 2005, 187:5049-5053. 10.1128/JB.187.14.5049-5053.2005, 1169517, 15995227.
35. Thompson MR, Thompson DK, Hettich RL. Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of Shewanella oneidensis to chromate exposure. J Proteome Res 2008, 7:648-658. 10.1021/pr070531n, 18171020.
36. Baraquet C, Théraulaz L, Iobbi-Nivol C, Méjean V, Jourlin-Castelli C. Unexpected chemoreceptors mediate energy taxis towards electron acceptors in Shewanella oneidensis. Mol Microbiol 2009, 73:278-290. 10.1111/j.1365-2958.2009.06770.x, 19555457.
37. Hau HH, Gilbert A, Coursolle D, Gralnick JA. Mechanism and consequences of anaerobic respiration of cobalt by Shewanella oneidensis strain MR-1. Appl Environ Microbiol 2008, 74:6880-6886. 10.1128/AEM.00840-08, 2583509, 18836009.
38. Pham CA, Jung SJ, Phung NT, Lee J, Chang IS, Kim BH, Yi H, Chun J. A novel electrochemically active and Fe(III)-reducing bacterium phylogenetically related to Aeromonas hydrophila, isolated from a microbial fuel cell. FEMS Microbiol Lett 2003, 223:129-134. 10.1016/S0378-1097(03)00354-9, 12799011.
39. Merino S, Gavín R, Altarriba M, Izquierdo L, Maguire ME, Tomás JM. The MgtE Mg2+ transport protein is involved in Aeromonas hydrophila adherence. FEMS Microbiol Lett 2001, 198:189-195. 10.1111/j.1574-6968.2001.tb10641.x, 11430413.
40. Burkart M, Toguchi A, Harshey RM. The chemotaxis system, but not chemotaxis, is essential for swarming motility in Escherichia coli. Proc Natl Acad Sci USA 1998, 95:2568-2573. 10.1073/pnas.95.5.2568, 19416, 9482927.
41. Saffarini DA, Schultz R, Beliaev A. Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis. J Bacteriol 2003, 185:3668-3671. 10.1128/JB.185.12.3668-3671.2003, 156221, 12775705.
42. Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics 2009, 10:131. 10.1186/1471-2164-10-131, 2667191, 19321007.
43. McLean JS, Pinchuk GE, Geydebrekht OV, Bilskis CL, Zakrajsek BA, Hill EA, Saffarini DA, Romine MF, Gorby YA, Fredrickson JK, Beliaev AS. Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1. Environ Microbiol 2008, 10:1861-1876. 10.1111/j.1462-2920.2008.01608.x, 18412550.
44. Cruz-García C, Murray AE, Klappenbach JA, Stewart V, Tiedje JM. Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J Bacteriol 2007, 189:656-662. 10.1128/JB.01194-06, 1797406, 17098906.
45. Du Z, Li H, Gu T. A state of the art review on microbial fuel cells: A promising technology for wastewater treatment and bioenergy. Biotechnol Adv 2007, 25:464-482. 10.1016/j.biotechadv.2007.05.004, 17582720.
46. Yuan S, Li KC. Context-dependent clustering for dynamic cellular state modeling of microarray gene expression. Bioinformatics 2007, 23:3039-3047. 10.1093/bioinformatics/btm457, 17846037.
47. Sun W, Yuan S, Li KC. Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC Genomics 2008, 9:242. 10.1186/1471-2164-9-242, 2432080, 18498664.
48. Ho YY, Cope L, Louis TA, Parmigiani G. Generalized liquid association. Working paper 183 2009, Johns Hopkins University, Department of Biostatistics.
49. Qiu X. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J Bacteriol 2006, 188:1199-1204. 10.1128/JB.188.3.1199-1204.2006, 1347324, 16428429.
50. Gao H, Yang ZK, Wu L, Thompson DK, Zhou J. Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J Bacteriol 2006, 188:4560-4569. 10.1128/JB.01908-05, 1482949, 16740962.
51. Gao H, Wang X, Yang ZK, Palzkill T, Zhou J. Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses. BMC Genomics 2008, 9:42. 10.1186/1471-2164-9-42, 2262068, 18221523.
52. Liquid Association Website. , http://kiefer.stat2.sinica.edu.tw/LAP3/index.php
53. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet 2000, 25:25-29. 10.1038/75556, 10802651.