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Volumn 13, Issue 1, 2012, Pages

Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production

Author keywords

Comparative genomics; Extracellular electron transfer; Geobacter sulfurreducens KN400; Microbial fuel cell

Indexed keywords

ADENOSINE TRIPHOSPHATE DEPENDENT PROTEINASE; AMINO ACID; CYTOCHROME; EXCINUCLEASE; MEMBRANE PROTEIN; MISMATCH REPAIR PROTEIN; PROTEIN HISTIDINE KINASE; UNCLASSIFIED DRUG;

EID: 84866006487     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-471     Document Type: Article
Times cited : (37)

References (41)
  • 2
    • 0037337606 scopus 로고    scopus 로고
    • Electricity production by Geobacter sulfurreducens attached to electrodes
    • 10.1128/AEM.69.3.1548-1555.2003, 150094, 12620842
    • Bond DR, Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. Appl Environ Microbiol 2003, 69(3):1548-1555. 10.1128/AEM.69.3.1548-1555.2003, 150094, 12620842.
    • (2003) Appl Environ Microbiol , vol.69 , Issue.3 , pp. 1548-1555
    • Bond, D.R.1    Lovley, D.R.2
  • 3
    • 77953160485 scopus 로고    scopus 로고
    • Microbial fuel cells, a current review
    • Franks AE, Nevin KP. Microbial fuel cells, a current review. Energies 2010, 3:899-919.
    • (2010) Energies , vol.3 , pp. 899-919
    • Franks, A.E.1    Nevin, K.P.2
  • 4
    • 51649118803 scopus 로고    scopus 로고
    • Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells
    • 10.1111/j.1462-2920.2008.01675.x, 18564184
    • Nevin KP, Richter H, Covalla SF, Johnson JP, Woodard TL, Orloff AL, Jia H, Zhang M, Lovley DR. Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells. Environ Microbiol 2008, 10(10):2505-2514. 10.1111/j.1462-2920.2008.01675.x, 18564184.
    • (2008) Environ Microbiol , vol.10 , Issue.10 , pp. 2505-2514
    • Nevin, K.P.1    Richter, H.2    Covalla, S.F.3    Johnson, J.P.4    Woodard, T.L.5    Orloff, A.L.6    Jia, H.7    Zhang, M.8    Lovley, D.R.9
  • 5
    • 67650085480 scopus 로고    scopus 로고
    • Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells
    • 10.1016/j.bios.2009.05.004, 19487117
    • Yi H, Nevin KP, Kim BC, Franks AE, Klimes A, Tender LM, Lovley DR. Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells. Biosens Bioelectron 2009, 24(12):3498-3503. 10.1016/j.bios.2009.05.004, 19487117.
    • (2009) Biosens Bioelectron , vol.24 , Issue.12 , pp. 3498-3503
    • Yi, H.1    Nevin, K.P.2    Kim, B.C.3    Franks, A.E.4    Klimes, A.5    Tender, L.M.6    Lovley, D.R.7
  • 7
    • 77956203114 scopus 로고    scopus 로고
    • De novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads
    • 10.1371/journal.pone.0010922, 2882325, 20544019
    • Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methe BA, Palsson BO, Lovley DR, Barrett CL. De novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One 2010, 5(6):e10922. 10.1371/journal.pone.0010922, 2882325, 20544019.
    • (2010) PLoS One , vol.5 , Issue.6
    • Nagarajan, H.1    Butler, J.E.2    Klimes, A.3    Qiu, Y.4    Zengler, K.5    Ward, J.6    Young, N.D.7    Methe, B.A.8    Palsson, B.O.9    Lovley, D.R.10    Barrett, C.L.11
  • 9
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • 1716718, 17130148
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35(Database issue):D61-D65. 1716718, 17130148.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 10
    • 77954761569 scopus 로고    scopus 로고
    • Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow
    • 10.1038/nrmicro2382, 20601965
    • Wozniak RA, Waldor MK. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010, 8(8):552-563. 10.1038/nrmicro2382, 20601965.
    • (2010) Nat Rev Microbiol , vol.8 , Issue.8 , pp. 552-563
    • Wozniak, R.A.1    Waldor, M.K.2
  • 11
    • 0842309140 scopus 로고    scopus 로고
    • Diversity of structures and properties among catalases
    • 10.1007/s00018-003-3206-5, 14745498
    • Chelikani P, Fita I, Loewen PC. Diversity of structures and properties among catalases. Cell Mol Life Sci 2004, 61(2):192-208. 10.1007/s00018-003-3206-5, 14745498.
    • (2004) Cell Mol Life Sci , vol.61 , Issue.2 , pp. 192-208
    • Chelikani, P.1    Fita, I.2    Loewen, P.C.3
  • 12
    • 0242608621 scopus 로고    scopus 로고
    • Pathways of oxidative damage
    • 10.1146/annurev.micro.57.030502.090938, 14527285
    • Imlay JA. Pathways of oxidative damage. Annu Rev Microbiol 2003, 57:395-418. 10.1146/annurev.micro.57.030502.090938, 14527285.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 395-418
    • Imlay, J.A.1
  • 13
    • 77954948121 scopus 로고    scopus 로고
    • Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus
    • 10.1186/1471-2148-10-230, 2923632, 20667132
    • Aklujkar M, Lovley DR. Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus. BMC Evol Biol 2010, 10(1):230. 10.1186/1471-2148-10-230, 2923632, 20667132.
    • (2010) BMC Evol Biol , vol.10 , Issue.1 , pp. 230
    • Aklujkar, M.1    Lovley, D.R.2
  • 14
    • 79959319829 scopus 로고    scopus 로고
    • CRISPR-based adaptive immune systems
    • 10.1016/j.mib.2011.03.005, 3119747, 21531607
    • Terns MP, Terns RM. CRISPR-based adaptive immune systems. Curr Opin Microbiol 2011, 14(3):321-327. 10.1016/j.mib.2011.03.005, 3119747, 21531607.
    • (2011) Curr Opin Microbiol , vol.14 , Issue.3 , pp. 321-327
    • Terns, M.P.1    Terns, R.M.2
  • 15
    • 33144470047 scopus 로고    scopus 로고
    • Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling
    • 10.1128/AEM.72.2.1558-1568.2006, 1392927, 16461711
    • Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 2006, 72(2):1558-1568. 10.1128/AEM.72.2.1558-1568.2006, 1392927, 16461711.
    • (2006) Appl Environ Microbiol , vol.72 , Issue.2 , pp. 1558-1568
    • Mahadevan, R.1    Bond, D.R.2    Butler, J.E.3    Esteve-Nunez, A.4    Coppi, M.V.5    Palsson, B.O.6    Schilling, C.H.7    Lovley, D.R.8
  • 16
    • 40149105737 scopus 로고    scopus 로고
    • Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens
    • 10.1371/journal.pcbi.0040036, 2233667, 18266464
    • Segura D, Mahadevan R, Juarez K, Lovley DR. Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol 2008, 4(2):e36. 10.1371/journal.pcbi.0040036, 2233667, 18266464.
    • (2008) PLoS Comput Biol , vol.4 , Issue.2
    • Segura, D.1    Mahadevan, R.2    Juarez, K.3    Lovley, D.R.4
  • 17
    • 0028050079 scopus 로고
    • Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism
    • 201883, 7527204
    • Caccavo F, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 1994, 60(10):3752-3759. 201883, 7527204.
    • (1994) Appl Environ Microbiol , vol.60 , Issue.10 , pp. 3752-3759
    • Caccavo, F.1    Lonergan, D.J.2    Lovley, D.R.3    Davis, M.4    Stolz, J.F.5    McInerney, M.J.6
  • 18
    • 80255137210 scopus 로고    scopus 로고
    • Composition and function of cytochrome c biogenesis System II
    • 10.1111/j.1742-4658.2011.08374.x, 21955752
    • Simon J, Hederstedt L. Composition and function of cytochrome c biogenesis System II. FEBS J 2011, 278(22):4179-4188. 10.1111/j.1742-4658.2011.08374.x, 21955752.
    • (2011) FEBS J , vol.278 , Issue.22 , pp. 4179-4188
    • Simon, J.1    Hederstedt, L.2
  • 19
    • 66949152917 scopus 로고    scopus 로고
    • Thermodynamic characterization of the redox centres in a representative domain of a novel c-type multihaem cytochrome
    • 10.1042/BJ20082428, 19351328
    • Morgado L, Fernandes AP, Londer YY, Pokkuluri PR, Schiffer M, Salgueiro CA. Thermodynamic characterization of the redox centres in a representative domain of a novel c-type multihaem cytochrome. Biochem J 2009, 420(3):485-492. 10.1042/BJ20082428, 19351328.
    • (2009) Biochem J , vol.420 , Issue.3 , pp. 485-492
    • Morgado, L.1    Fernandes, A.P.2    Londer, Y.Y.3    Pokkuluri, P.R.4    Schiffer, M.5    Salgueiro, C.A.6
  • 20
    • 77953645311 scopus 로고    scopus 로고
    • Alignment of the c-type cytochrome OmcS along pili of Geobacter sulfurreducens
    • 10.1128/AEM.00023-10, 2893476, 20400557
    • Leang C, Qian X, Mester T, Lovley DR. Alignment of the c-type cytochrome OmcS along pili of Geobacter sulfurreducens. Appl Environ Microbiol 2010, 76(12):4080-4084. 10.1128/AEM.00023-10, 2893476, 20400557.
    • (2010) Appl Environ Microbiol , vol.76 , Issue.12 , pp. 4080-4084
    • Leang, C.1    Qian, X.2    Mester, T.3    Lovley, D.R.4
  • 21
    • 21344461500 scopus 로고    scopus 로고
    • Extracellular electron transfer via microbial nanowires
    • 10.1038/nature03661, 15973408
    • Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, Lovley DR. Extracellular electron transfer via microbial nanowires. Nature 2005, 435(7045):1098-1101. 10.1038/nature03661, 15973408.
    • (2005) Nature , vol.435 , Issue.7045 , pp. 1098-1101
    • Reguera, G.1    McCarthy, K.D.2    Mehta, T.3    Nicoll, J.S.4    Tuominen, M.T.5    Lovley, D.R.6
  • 22
    • 66249098568 scopus 로고    scopus 로고
    • Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells
    • 10.1371/journal.pone.0005628, 2680965, 19461962
    • Nevin KP, Kim BC, Glaven RH, Johnson JP, Woodard TL, Methe BA, Didonato RJ, Covalla SF, Franks AE, Liu A, Lovley DR. Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells. PLoS One 2009, 4(5):e5628. 10.1371/journal.pone.0005628, 2680965, 19461962.
    • (2009) PLoS One , vol.4 , Issue.5
    • Nevin, K.P.1    Kim, B.C.2    Glaven, R.H.3    Johnson, J.P.4    Woodard, T.L.5    Methe, B.A.6    Didonato, R.J.7    Covalla, S.F.8    Franks, A.E.9    Liu, A.10    Lovley, D.R.11
  • 23
    • 79951630056 scopus 로고    scopus 로고
    • Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens
    • 10.1128/JB.01092-10, 3067572, 21169487
    • Rollefson JB, Stephen CS, Tien M, Bond DR. Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens. J Bacteriol 2011, 193(5):1023-1033. 10.1128/JB.01092-10, 3067572, 21169487.
    • (2011) J Bacteriol , vol.193 , Issue.5 , pp. 1023-1033
    • Rollefson, J.B.1    Stephen, C.S.2    Tien, M.3    Bond, D.R.4
  • 24
    • 33747119626 scopus 로고    scopus 로고
    • A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens
    • Mehta T, Childers SE, Glaven R, Lovley DR, Mester T. A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens. Microbiology 2006, 152(Pt 8):2257-2264.
    • (2006) Microbiology , vol.152 , Issue.PART 8 , pp. 2257-2264
    • Mehta, T.1    Childers, S.E.2    Glaven, R.3    Lovley, D.R.4    Mester, T.5
  • 25
    • 46249094501 scopus 로고    scopus 로고
    • Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes
    • Holmes DE, Mester T, O'Neil RA, Perpetua LA, Larrahondo MJ, Glaven R, Sharma ML, Ward JE, Nevin KP, Lovley DR. Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes. Microbiology 2008, 154(Pt 5):1422-1435.
    • (2008) Microbiology , vol.154 , Issue.PART 5 , pp. 1422-1435
    • Holmes, D.E.1    Mester, T.2    O'Neil, R.A.3    Perpetua, L.A.4    Larrahondo, M.J.5    Glaven, R.6    Sharma, M.L.7    Ward, J.E.8    Nevin, K.P.9    Lovley, D.R.10
  • 26
    • 77349123810 scopus 로고    scopus 로고
    • Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes
    • 10.1186/1471-2164-11-40, 2825233, 20078895
    • Butler JE, Young ND, Lovley DR. Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes. BMC Genomics 2010, 11:40. 10.1186/1471-2164-11-40, 2825233, 20078895.
    • (2010) BMC Genomics , vol.11 , pp. 40
    • Butler, J.E.1    Young, N.D.2    Lovley, D.R.3
  • 28
    • 23944477958 scopus 로고    scopus 로고
    • A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens
    • 10.1186/1471-2180-5-41, 1186022, 16000176
    • Afkar E, Reguera G, Schiffer M, Lovley DR. A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens. BMC Microbiol 2005, 5:41. 10.1186/1471-2180-5-41, 1186022, 16000176.
    • (2005) BMC Microbiol , vol.5 , pp. 41
    • Afkar, E.1    Reguera, G.2    Schiffer, M.3    Lovley, D.R.4
  • 29
    • 0030449160 scopus 로고    scopus 로고
    • Polyphasic characterization of the genus Leptothrix: New descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend
    • Spring S, Kampfer P, Ludwig W, Schleifer KH. Polyphasic characterization of the genus Leptothrix: New descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend. Syst Appl Microbiol 1996, 19(4):634-643.
    • (1996) Syst Appl Microbiol , vol.19 , Issue.4 , pp. 634-643
    • Spring, S.1    Kampfer, P.2    Ludwig, W.3    Schleifer, K.H.4
  • 30
    • 0034746567 scopus 로고    scopus 로고
    • CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA
    • 10.1046/j.1365-2958.2001.02264.x, 11136469
    • Stoyanov JV, Hobman JL, Brown NL. CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA. Mol Microbiol 2001, 39(2):502-511. 10.1046/j.1365-2958.2001.02264.x, 11136469.
    • (2001) Mol Microbiol , vol.39 , Issue.2 , pp. 502-511
    • Stoyanov, J.V.1    Hobman, J.L.2    Brown, N.L.3
  • 31
    • 50549104615 scopus 로고    scopus 로고
    • Geobacter sulfurreducens strain engineered for increased rates of respiration
    • 10.1016/j.ymben.2008.06.005, 18644460
    • Izallalen M, Mahadevan R, Burgard A, Postier B, Didonato R, Sun J, Schilling CH, Lovley DR. Geobacter sulfurreducens strain engineered for increased rates of respiration. Metab Eng 2008, 10(5):267-275. 10.1016/j.ymben.2008.06.005, 18644460.
    • (2008) Metab Eng , vol.10 , Issue.5 , pp. 267-275
    • Izallalen, M.1    Mahadevan, R.2    Burgard, A.3    Postier, B.4    Didonato, R.5    Sun, J.6    Schilling, C.H.7    Lovley, D.R.8
  • 34
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: multiple alignment of conserved genomic sequence with rearrangements
    • 10.1101/gr.2289704, 442156, 15231754
    • Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394-1403. 10.1101/gr.2289704, 442156, 15231754.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 35
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 37
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 39
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 10.1126/science.278.5338.631, 9381173
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278(5338):631-637. 10.1126/science.278.5338.631, 9381173.
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 40
    • 0842330093 scopus 로고    scopus 로고
    • The iProClass integrated database for protein functional analysis
    • 10.1016/j.compbiolchem.2003.10.003, 15022647
    • Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC. The iProClass integrated database for protein functional analysis. Comput Biol Chem 2004, 28(1):87-96. 10.1016/j.compbiolchem.2003.10.003, 15022647.
    • (2004) Comput Biol Chem , vol.28 , Issue.1 , pp. 87-96
    • Wu, C.H.1    Huang, H.2    Nikolskaya, A.3    Hu, Z.4    Barker, W.C.5


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