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Volumn 11, Issue 2, 2015, Pages

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; ESCHERICHIA COLI; METABOLISM; PHYSIOLOGY; TRANSCRIPTION;

EID: 84924390031     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004103     Document Type: Article
Times cited : (24)

References (87)
  • 1
    • 0028212112 scopus 로고
    • Multiple molecular levels of cell cycle regulation
    • Pardee AB, (1994) Multiple molecular levels of cell cycle regulation. J Cell Biochem 54: 375–378. 8014185
    • (1994) J Cell Biochem , vol.54 , pp. 375-378
    • Pardee, A.B.1
  • 2
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • Herrgard MJ, Covert MW, Palsson BO, (2004) Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 15: 70–77. 15102470
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 70-77
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 3
    • 84870305264 scopus 로고    scopus 로고
    • Wisdom of crowds for robust gene network inference
    • Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, et al. (2012) Wisdom of crowds for robust gene network inference. Nat Methods 9: 796–804. doi: 10.1038/nmeth.2016 22796662
    • (2012) Nat Methods , vol.9 , pp. 796-804
    • Marbach, D.1    Costello, J.C.2    Kuffner, R.3    Vega, N.M.4    Prill, R.J.5
  • 4
    • 36249019789 scopus 로고    scopus 로고
    • Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference
    • Stolovitzky G, Monroe D, Califano A, (2007) Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci 1115: 1–22. 17925349
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 1-22
    • Stolovitzky, G.1    Monroe, D.2    Califano, A.3
  • 5
    • 33747813561 scopus 로고    scopus 로고
    • The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, et al. (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7: R36. 16686963
    • (2006) Genome Biol , vol.7 , pp. 36
    • Bonneau, R.1    Reiss, D.J.2    Shannon, P.3    Facciotti, M.4    Hood, L.5
  • 6
    • 77957110013 scopus 로고    scopus 로고
    • Advantages and limitations of current network inference methods
    • De Smet R, Marchal K, (2010) Advantages and limitations of current network inference methods. Nat Rev Microbiol 8: 717–729. doi: 10.1038/nrmicro2419 20805835
    • (2010) Nat Rev Microbiol , vol.8 , pp. 717-729
    • De Smet, R.1    Marchal, K.2
  • 7
    • 60149110901 scopus 로고    scopus 로고
    • Module networks revisited: computational assessment and prioritization of model predictions
    • Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T, (2009) Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 25: 490–496. doi: 10.1093/bioinformatics/btn658 19136553
    • (2009) Bioinformatics , vol.25 , pp. 490-496
    • Joshi, A.1    De Smet, R.2    Marchal, K.3    Van de Peer, Y.4    Michoel, T.5
  • 8
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal E, Shapira M, Regev A, Pe’er D, Botstein D, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166–176. 12740579
    • (2003) Nat Genet , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe’er, D.4    Botstein, D.5
  • 9
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8. 17214507
    • (2007) PLoS Biol , vol.5 , pp. 8
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5
  • 10
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using tree-based methods
    • Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P, (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS One 5. doi: 10.1371/journal.pone.0014462 21283510
    • (2010) PLoS One , vol.5
    • Huynh-Thu, V.A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 12
    • 73149094538 scopus 로고    scopus 로고
    • Inferring the transcriptional network of Bacillus subtilis
    • Fadda A, Fierro AC, Lemmens K, Monsieurs P, Engelen K, et al. (2009) Inferring the transcriptional network of Bacillus subtilis. Mol Biosyst 5: 1840–1852. doi: 10.1039/b907310h 20023724
    • (2009) Mol Biosyst , vol.5 , pp. 1840-1852
    • Fadda, A.1    Fierro, A.C.2    Lemmens, K.3    Monsieurs, P.4    Engelen, K.5
  • 13
    • 77954254495 scopus 로고    scopus 로고
    • RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
    • Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, et al. (2010) RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res 38: W299–307. doi: 10.1093/nar/gkq531 20542910
    • (2010) Nucleic Acids Res , vol.38 , pp. 299-307
    • Novichkov, P.S.1    Rodionov, D.A.2    Stavrovskaya, E.D.3    Novichkova, E.S.4    Kazakov, A.E.5
  • 14
    • 34548219522 scopus 로고    scopus 로고
    • Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    • Rodionov DA, (2007) Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 107: 3467–3497. 17636889
    • (2007) Chem Rev , vol.107 , pp. 3467-3497
    • Rodionov, D.A.1
  • 15
    • 28444484981 scopus 로고    scopus 로고
    • Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
    • Wang T, Stormo GD, (2005) Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci U S A 102: 17400–17405. 16301543
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 17400-17405
    • Wang, T.1    Stormo, G.D.2
  • 16
    • 0036220597 scopus 로고    scopus 로고
    • Mining genome databases to identify and understand new gene regulatory systems
    • Stormo GD, Tan K, (2002) Mining genome databases to identify and understand new gene regulatory systems. Curr Opin Microbiol 5: 149–153. 11934610
    • (2002) Curr Opin Microbiol , vol.5 , pp. 149-153
    • Stormo, G.D.1    Tan, K.2
  • 17
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa M, Li N, Bailey TL, Church GM, De Moor B, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23: 137–144. 15637633
    • (2005) Nat Biotechnol , vol.23 , pp. 137-144
    • Tompa, M.1    Li, N.2    Bailey, T.L.3    Church, G.M.4    De Moor, B.5
  • 18
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio A, Collado-Vides J, (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6: 482–489. 14572541
    • (2003) Curr Opin Microbiol , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 19
    • 14644388890 scopus 로고    scopus 로고
    • Making connections between novel transcription factors and their DNA motifs
    • Tan K, McCue LA, Stormo GD, (2005) Making connections between novel transcription factors and their DNA motifs. Genome Res 15: 312–320. 15653829
    • (2005) Genome Res , vol.15 , pp. 312-320
    • Tan, K.1    McCue, L.A.2    Stormo, G.D.3
  • 20
    • 1842505125 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • Sandelin A, Wasserman WW, (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol Biol 338: 207–215. 15066426
    • (2004) J Mol Biol , vol.338 , pp. 207-215
    • Sandelin, A.1    Wasserman, W.W.2
  • 21
    • 79960558167 scopus 로고    scopus 로고
    • iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
    • Imam S, Yilmaz S, Sohmen U, Gorzalski AS, Reed JL, et al. (2011) iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC Syst Biol 5: 116. doi: 10.1186/1752-0509-5-116 21777427
    • (2011) BMC Syst Biol , vol.5 , pp. 116
    • Imam, S.1    Yilmaz, S.2    Sohmen, U.3    Gorzalski, A.S.4    Reed, J.L.5
  • 23
    • 71849086611 scopus 로고    scopus 로고
    • Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde
    • Atsumi S, Higashide W, Liao JC, (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 27: 1177–1180. doi: 10.1038/nbt.1586 19915552
    • (2009) Nat Biotechnol , vol.27 , pp. 1177-1180
    • Atsumi, S.1    Higashide, W.2    Liao, J.C.3
  • 24
    • 84883727891 scopus 로고    scopus 로고
    • Global insights into energetic and metabolic networks in Rhodobacter sphaeroides
    • Imam S, Noguera DR, Donohue TJ, (2013) Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. BMC Syst Biol 7: 89. doi: 10.1186/1752-0509-7-89 24034347
    • (2013) BMC Syst Biol , vol.7 , pp. 89
    • Imam, S.1    Noguera, D.R.2    Donohue, T.J.3
  • 25
    • 0002061480 scopus 로고    scopus 로고
    • Polyhydroxybutyrate accumulation and hydrogen evolution by Rhodobacter sphaeroides as a function of nitrogen availability
    • Khatipov E, Miyake M., Miyake J., Asada Y., (1999) Polyhydroxybutyrate accumulation and hydrogen evolution by Rhodobacter sphaeroides as a function of nitrogen availability. Biohydrogen III: 157–161.
    • (1999) Biohydrogen , vol.III , pp. 157-161
    • Khatipov, E.1    Miyake, M.2    Miyake, J.3    Asada, Y.4
  • 26
    • 77952242863 scopus 로고    scopus 로고
    • Coenzyme Q10 production in a 150-l reactor by a mutant strain of Rhodobacter sphaeroides
    • Kien NB, Kong IS, Lee MG, Kim JK, (2010) Coenzyme Q10 production in a 150-l reactor by a mutant strain of Rhodobacter sphaeroides. J Ind Microbiol Biotechnol 37: 521–529. doi: 10.1007/s10295-010-0699-4 20195885
    • (2010) J Ind Microbiol Biotechnol , vol.37 , pp. 521-529
    • Kien, N.B.1    Kong, I.S.2    Lee, M.G.3    Kim, J.K.4
  • 27
    • 82955205919 scopus 로고    scopus 로고
    • 2 production by Rhodobacter sphaeroides
    • Kontur WS, Ziegelhoffer EC, Spero MA, Imam S, Noguera DR, et al. (2011) Pathways involved in reductant distribution during photobiological H2 production by Rhodobacter sphaeroides. Appl Environ Microbiol 77: 7425–7429. doi: 10.1128/AEM.05273-11 21856820
    • (2011) Appl Environ Microbiol , vol.77 , pp. 7425-7429
    • Kontur, W.S.1    Ziegelhoffer, E.C.2    Spero, M.A.3    Imam, S.4    Noguera, D.R.5
  • 30
    • 76649103695 scopus 로고    scopus 로고
    • Electron partitioning during light- and nutrient-powered hydrogen production by Rhodobacter sphaeroides
    • Yilmaz LS, Kontur WS, Sanders AP, Sohmen U, Donohue TJ, et al. (2010) Electron partitioning during light- and nutrient-powered hydrogen production by Rhodobacter sphaeroides. Bioenerg Res Volume: 55–66.
    • (2010) Bioenerg Res Volume , pp. 55-66
    • Yilmaz, L.S.1    Kontur, W.S.2    Sanders, A.P.3    Sohmen, U.4    Donohue, T.J.5
  • 31
    • 84876546158 scopus 로고    scopus 로고
    • A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes
    • Wolf YI, Koonin EV, (2012) A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes. Genome Biol Evol 4: 1286–1294. doi: 10.1093/gbe/evs100 23160176
    • (2012) Genome Biol Evol , vol.4 , pp. 1286-1294
    • Wolf, Y.I.1    Koonin, E.V.2
  • 32
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ, Jr.Roos DS, (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178–2189. 12952885
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 33
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575–1584. 11917018
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 34
    • 33747823564 scopus 로고    scopus 로고
    • MEME: discovering and analyzing DNA and protein sequence motifs
    • Bailey TL, Williams N, Misleh C, Li WW, (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369–373. 16845028
    • (2006) Nucleic Acids Res , vol.34 , pp. 369-373
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 36
    • 0036108622 scopus 로고    scopus 로고
    • A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    • Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, et al. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 9: 447–464. 12015892
    • (2002) J Comput Biol , vol.9 , pp. 447-464
    • Thijs, G.1    Marchal, K.2    Lescot, M.3    Rombauts, S.4    De Moor, B.5
  • 37
    • 63449134229 scopus 로고    scopus 로고
    • DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
    • Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, et al. (2009) DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol 10: R27. doi: 10.1186/gb-2009-10-3-r27 19265557
    • (2009) Genome Biol , vol.10 , pp. 27
    • Lemmens, K.1    De Bie, T.2    Dhollander, T.3    De Keersmaecker, S.C.4    Thijs, I.M.5
  • 38
    • 77950910419 scopus 로고    scopus 로고
    • Revealing strengths and weaknesses of methods for gene network inference
    • Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A 107: 6286–6291. doi: 10.1073/pnas.0913357107 20308593
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 6286-6291
    • Marbach, D.1    Prill, R.J.2    Schaffter, T.3    Mattiussi, C.4    Floreano, D.5
  • 40
    • 78651299341 scopus 로고    scopus 로고
    • RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
    • Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res 39: D98–105. doi: 10.1093/nar/gkq1110 21051347
    • (2011) Nucleic Acids Res , vol.39 , pp. 98-105
    • Gama-Castro, S.1    Salgado, H.2    Peralta-Gil, M.3    Santos-Zavaleta, A.4    Muniz-Rascado, L.5
  • 41
    • 67849122320 scopus 로고    scopus 로고
    • MEME SUITE: tools for motif discovery and searching
    • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208. doi: 10.1093/nar/gkp335 19458158
    • (2009) Nucleic Acids Res , vol.37 , pp. 202-208
    • Bailey, T.L.1    Boden, M.2    Buske, F.A.3    Frith, M.4    Grant, C.E.5
  • 43
    • 77949644952 scopus 로고    scopus 로고
    • Towards a rigorous assessment of systems biology models: the DREAM3 challenges
    • Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, et al. (2010) Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One 5: e9202. doi: 10.1371/journal.pone.0009202 20186320
    • (2010) PLoS One , vol.5 , pp. 9202
    • Prill, R.J.1    Marbach, D.2    Saez-Rodriguez, J.3    Sorger, P.K.4    Alexopoulos, L.G.5
  • 44
    • 0030756106 scopus 로고    scopus 로고
    • The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions
    • Unden G, Schirawski J, (1997) The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions. Molecular microbiology 25: 205–210. 9282732
    • (1997) Molecular microbiology , vol.25 , pp. 205-210
    • Unden, G.1    Schirawski, J.2
  • 45
    • 0023664923 scopus 로고
    • Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli
    • Bagg A, Neilands JB, (1987) Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli. Biochemistry 26: 5471–5477. 2823881
    • (1987) Biochemistry , vol.26 , pp. 5471-5477
    • Bagg, A.1    Neilands, J.B.2
  • 46
    • 33750938822 scopus 로고    scopus 로고
    • The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation
    • Caldara M, Charlier D, Cunin R, (2006) The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. Microbiology 152: 3343–3354. 17074904
    • (2006) Microbiology , vol.152 , pp. 3343-3354
    • Caldara, M.1    Charlier, D.2    Cunin, R.3
  • 47
    • 0029941168 scopus 로고    scopus 로고
    • The catabolite repressor/activator (Cra) protein of enteric bacteria
    • Saier MH, Jr.Ramseier TM, (1996) The catabolite repressor/activator (Cra) protein of enteric bacteria. J Bacteriol 178: 3411–3417. 8655535
    • (1996) J Bacteriol , vol.178 , pp. 3411-3417
    • Saier, M.H.1    Ramseier, T.M.2
  • 48
    • 84870694724 scopus 로고    scopus 로고
    • Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome
    • Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, et al. (2012) Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. J Bacteriol 194: 7016–7017. doi: 10.1128/JB.01214-12 23209255
    • (2012) J Bacteriol , vol.194 , pp. 7016-7017
    • Kontur, W.S.1    Schackwitz, W.S.2    Ivanova, N.3    Martin, J.4    Labutti, K.5
  • 49
    • 18244372493 scopus 로고    scopus 로고
    • The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1
    • Mackenzie C, Choudhary M, Larimer FW, Predki PF, Stilwagen S, et al. (2001) The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1. Photosynth Res 70: 19–41. 16228360
    • (2001) Photosynth Res , vol.70 , pp. 19-41
    • Mackenzie, C.1    Choudhary, M.2    Larimer, F.W.3    Predki, P.F.4    Stilwagen, S.5
  • 50
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The gene ontology consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25: 25–29. 10802651
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 51
    • 53849095651 scopus 로고    scopus 로고
    • The use of chromatin immunoprecipitation to define PpsR binding activity in Rhodobacter sphaeroides 2.4.1
    • Bruscella P, Eraso JM, Roh JH, Kaplan S, (2008) The use of chromatin immunoprecipitation to define PpsR binding activity in Rhodobacter sphaeroides 2.4.1. J Bacteriol 190: 6817–6828. doi: 10.1128/JB.00719-08 18689484
    • (2008) J Bacteriol , vol.190 , pp. 6817-6828
    • Bruscella, P.1    Eraso, J.M.2    Roh, J.H.3    Kaplan, S.4
  • 52
    • 0028904224 scopus 로고
    • Genetic evidence that PpsR from Rhodobacter sphaeroides 2.4.1 functions as a repressor of puc and bchF expression
    • Gomelsky M, Kaplan S, (1995) Genetic evidence that PpsR from Rhodobacter sphaeroides 2.4.1 functions as a repressor of puc and bchF expression. J Bacteriol 177: 1634–1637. 7883723
    • (1995) J Bacteriol , vol.177 , pp. 1634-1637
    • Gomelsky, M.1    Kaplan, S.2
  • 53
    • 77957325735 scopus 로고    scopus 로고
    • Reconstruction of the core and extended regulons of global transcription factors
    • Dufour YS, Kiley PJ, Donohue TJ, (2010) Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet 6: e1001027. doi: 10.1371/journal.pgen.1001027 20661434
    • (2010) PLoS Genet , vol.6 , pp. 1001027
    • Dufour, Y.S.1    Kiley, P.J.2    Donohue, T.J.3
  • 54
    • 0031941632 scopus 로고    scopus 로고
    • Role of the fnrL gene in photosystem gene expression and photosynthetic growth of Rhodobacter sphaeroides 2.4.1
    • Zeilstra-Ryalls JH, Kaplan S, (1998) Role of the fnrL gene in photosystem gene expression and photosynthetic growth of Rhodobacter sphaeroides 2.4.1. J Bacteriol 180: 1496–1503. 9515919
    • (1998) J Bacteriol , vol.180 , pp. 1496-1503
    • Zeilstra-Ryalls, J.H.1    Kaplan, S.2
  • 55
    • 0028889264 scopus 로고
    • Aerobic and anaerobic regulation in Rhodobacter sphaeroides 2.4.1: the role of the fnrL gene
    • Zeilstra-Ryalls JH, Kaplan S, (1995) Aerobic and anaerobic regulation in Rhodobacter sphaeroides 2.4.1: the role of the fnrL gene. J Bacteriol 177: 6422–6431. 7592416
    • (1995) J Bacteriol , vol.177 , pp. 6422-6431
    • Zeilstra-Ryalls, J.H.1    Kaplan, S.2
  • 56
    • 0027976503 scopus 로고
    • prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacter sphaeroides
    • Eraso JM, Kaplan S, (1994) prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacter sphaeroides. J Bacteriol 176: 32–43. 8282708
    • (1994) J Bacteriol , vol.176 , pp. 32-43
    • Eraso, J.M.1    Kaplan, S.2
  • 57
    • 47249107417 scopus 로고    scopus 로고
    • Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis
    • Eraso JM, Roh JH, Zeng X, Callister SJ, Lipton MS, et al. (2008) Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis. J Bacteriol 190: 4831–4848. doi: 10.1128/JB.00301-08 18487335
    • (2008) J Bacteriol , vol.190 , pp. 4831-4848
    • Eraso, J.M.1    Roh, J.H.2    Zeng, X.3    Callister, S.J.4    Lipton, M.S.5
  • 58
    • 0029016713 scopus 로고
    • Oxygen-insensitive synthesis of the photosynthetic membranes of Rhodobacter sphaeroides: a mutant histidine kinase
    • Eraso JM, Kaplan S, (1995) Oxygen-insensitive synthesis of the photosynthetic membranes of Rhodobacter sphaeroides: a mutant histidine kinase. J Bacteriol 177: 2695–2706. 7751278
    • (1995) J Bacteriol , vol.177 , pp. 2695-2706
    • Eraso, J.M.1    Kaplan, S.2
  • 59
    • 58449114492 scopus 로고    scopus 로고
    • Protein-protein interactions between CbbR and RegA (PrrA), transcriptional regulators of the cbb operons of Rhodobacter sphaeroides
    • Dangel AW, Tabita FR, (2009) Protein-protein interactions between CbbR and RegA (PrrA), transcriptional regulators of the cbb operons of Rhodobacter sphaeroides. Molecular microbiology 71: 717–729. doi: 10.1111/j.1365-2958.2008.06558.x 19077171
    • (2009) Molecular microbiology , vol.71 , pp. 717-729
    • Dangel, A.W.1    Tabita, F.R.2
  • 60
    • 0344237366 scopus 로고    scopus 로고
    • Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity
    • Laguri C, Phillips-Jones MK, Williamson MP, (2003) Solution structure and DNA binding of the effector domain from the global regulator PrrA (RegA) from Rhodobacter sphaeroides: insights into DNA binding specificity. Nucleic Acids Res 31: 6778–6787. 14627811
    • (2003) Nucleic Acids Res , vol.31 , pp. 6778-6787
    • Laguri, C.1    Phillips-Jones, M.K.2    Williamson, M.P.3
  • 61
    • 84867095346 scopus 로고    scopus 로고
    • Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ
    • Mank NN, Berghoff BA, Hermanns YN, Klug G, (2012) Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ. Proc Natl Acad Sci U S A 109: 16306–16311. doi: 10.1073/pnas.1207067109 22988125
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 16306-16311
    • Mank, N.N.1    Berghoff, B.A.2    Hermanns, Y.N.3    Klug, G.4
  • 62
    • 64549161094 scopus 로고    scopus 로고
    • Visualization, documentation, analysis, and communication of large-scale gene regulatory networks
    • Longabaugh WJ, Davidson EH, Bolouri H, (2009) Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim Biophys Acta 1789: 363–374. doi: 10.1016/j.bbagrm.2008.07.014 18757046
    • (2009) Biochim Biophys Acta , vol.1789 , pp. 363-374
    • Longabaugh, W.J.1    Davidson, E.H.2    Bolouri, H.3
  • 64
    • 0028227705 scopus 로고
    • Sequencing, chromosomal inactivation, and functional expression in Escherichia coli of ppsR, a gene which represses carotenoid and bacteriochlorophyll synthesis in Rhodobacter sphaeroides
    • Penfold RJ, Pemberton JM, (1994) Sequencing, chromosomal inactivation, and functional expression in Escherichia coli of ppsR, a gene which represses carotenoid and bacteriochlorophyll synthesis in Rhodobacter sphaeroides. J Bacteriol 176: 2869–2876. 8188588
    • (1994) J Bacteriol , vol.176 , pp. 2869-2876
    • Penfold, R.J.1    Pemberton, J.M.2
  • 65
    • 0029093864 scopus 로고
    • appA, a novel gene encoding a trans-acting factor involved in the regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1
    • Gomelsky M, Kaplan S, (1995) appA, a novel gene encoding a trans-acting factor involved in the regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 177: 4609–4618. 7642486
    • (1995) J Bacteriol , vol.177 , pp. 4609-4618
    • Gomelsky, M.1    Kaplan, S.2
  • 66
    • 0032567446 scopus 로고    scopus 로고
    • AppA, a redox regulator of photosystem formation in Rhodobacter sphaeroides 2.4.1, is a flavoprotein. Identification of a novel fad binding domain
    • Gomelsky M, Kaplan S, (1998) AppA, a redox regulator of photosystem formation in Rhodobacter sphaeroides 2.4.1, is a flavoprotein. Identification of a novel fad binding domain. J Biol Chem 273: 35319–35325. 9857073
    • (1998) J Biol Chem , vol.273 , pp. 35319-35325
    • Gomelsky, M.1    Kaplan, S.2
  • 67
    • 0031026315 scopus 로고    scopus 로고
    • Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1
    • Gomelsky M, Kaplan S, (1997) Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 179: 128–134. 8981989
    • (1997) J Bacteriol , vol.179 , pp. 128-134
    • Gomelsky, M.1    Kaplan, S.2
  • 68
    • 0037031561 scopus 로고    scopus 로고
    • AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides
    • Masuda S, Bauer CE, (2002) AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell 110: 613–623. 12230978
    • (2002) Cell , vol.110 , pp. 613-623
    • Masuda, S.1    Bauer, C.E.2
  • 69
    • 77951042893 scopus 로고    scopus 로고
    • MochiView: versatile software for genome browsing and DNA motif analysis
    • Homann OR, Johnson AD, (2010) MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol 8: 49. doi: 10.1186/1741-7007-8-49 20409324
    • (2010) BMC Biol , vol.8 , pp. 49
    • Homann, O.R.1    Johnson, A.D.2
  • 70
    • 33646231984 scopus 로고    scopus 로고
    • In vitro and in vivo analysis of the role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA gene expression
    • Ranson-Olson B, Jones DF, Donohue TJ, Zeilstra-Ryalls JH, (2006) In vitro and in vivo analysis of the role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA gene expression. J Bacteriol 188: 3208–3218. 16621813
    • (2006) J Bacteriol , vol.188 , pp. 3208-3218
    • Ranson-Olson, B.1    Jones, D.F.2    Donohue, T.J.3    Zeilstra-Ryalls, J.H.4
  • 71
    • 84919608419 scopus 로고    scopus 로고
    • Global analysis of photosynthesis transcriptional regulatory networks
    • Imam S, Noguera DR, Donohue TJ, (2014) Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 10: e1004837. doi: 10.1371/journal.pgen.1004837 25503406
    • (2014) PLoS Genet , vol.10 , pp. 1004837
    • Imam, S.1    Noguera, D.R.2    Donohue, T.J.3
  • 72
    • 0026509084 scopus 로고
    • Cyclic AMP in prokaryotes
    • Botsford JL, Harman JG, (1992) Cyclic AMP in prokaryotes. Microbiol Rev 56: 100–122. 1315922
    • (1992) Microbiol Rev , vol.56 , pp. 100-122
    • Botsford, J.L.1    Harman, J.G.2
  • 73
    • 84887308033 scopus 로고    scopus 로고
    • The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally
    • Park DM, Akhtar MS, Ansari AZ, Landick R, Kiley PJ, (2013) The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PLoS Genet 9: e1003839. doi: 10.1371/journal.pgen.1003839 24146625
    • (2013) PLoS Genet , vol.9 , pp. 1003839
    • Park, D.M.1    Akhtar, M.S.2    Ansari, A.Z.3    Landick, R.4    Kiley, P.J.5
  • 74
    • 0032450017 scopus 로고    scopus 로고
    • Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter
    • Cunningham L, Georgellis D, Green J, Guest JR, (1998) Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter. FEMS Microbiol Lett 169: 403–408. 9868788
    • (1998) FEMS Microbiol Lett , vol.169 , pp. 403-408
    • Cunningham, L.1    Georgellis, D.2    Green, J.3    Guest, J.R.4
  • 75
    • 80053915498 scopus 로고    scopus 로고
    • Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis
    • Leyn SA, Li X, Zheng Q, Novichkov PS, Reed S, et al. (2011) Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem 286: 35782–35794. doi: 10.1074/jbc.M111.267963 21849503
    • (2011) J Biol Chem , vol.286 , pp. 35782-35794
    • Leyn, S.A.1    Li, X.2    Zheng, Q.3    Novichkov, P.S.4    Reed, S.5
  • 76
    • 84868000088 scopus 로고    scopus 로고
    • Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima
    • Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA, (2012) Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol 14: 2920–2934. doi: 10.1111/j.1462-2920.2012.02856.x 22925190
    • (2012) Environ Microbiol , vol.14 , pp. 2920-2934
    • Rodionova, I.A.1    Scott, D.A.2    Grishin, N.V.3    Osterman, A.L.4    Rodionov, D.A.5
  • 77
    • 0035909963 scopus 로고    scopus 로고
    • IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins
    • Schwartz CJ, Giel JL, Patschkowski T, Luther C, Ruzicka FJ, et al. (2001) IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins. Proc Natl Acad Sci U S A 98: 14895–14900. 11742080
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 14895-14900
    • Schwartz, C.J.1    Giel, J.L.2    Patschkowski, T.3    Luther, C.4    Ruzicka, F.J.5
  • 78
    • 84878896186 scopus 로고    scopus 로고
    • Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity
    • Rajagopalan S, Teter SJ, Zwart PH, Brennan RG, Phillips KJ, et al. (2013) Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity. Nat Struct Mol Biol 20: 740–747. doi: 10.1038/nsmb.2568 23644595
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 740-747
    • Rajagopalan, S.1    Teter, S.J.2    Zwart, P.H.3    Brennan, R.G.4    Phillips, K.J.5
  • 79
    • 33745187803 scopus 로고    scopus 로고
    • IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins
    • Yeo WS, Lee JH, Lee KC, Roe JH, (2006) IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins. Molecular microbiology 61: 206–218. 16824106
    • (2006) Molecular microbiology , vol.61 , pp. 206-218
    • Yeo, W.S.1    Lee, J.H.2    Lee, K.C.3    Roe, J.H.4
  • 80
    • 0036947502 scopus 로고    scopus 로고
    • RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum
    • Todd JD, Wexler M, Sawers G, Yeoman KH, Poole PS, et al. (2002) RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum. Microbiology 148: 4059–4071. 12480909
    • (2002) Microbiology , vol.148 , pp. 4059-4071
    • Todd, J.D.1    Wexler, M.2    Sawers, G.3    Yeoman, K.H.4    Poole, P.S.5
  • 81
    • 0142106372 scopus 로고    scopus 로고
    • The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA
    • Wacker I, Ludwig H, Reif I, Blencke HM, Detsch C, et al. (2003) The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA. Microbiology 149: 3001–3009. 14523131
    • (2003) Microbiology , vol.149 , pp. 3001-3009
    • Wacker, I.1    Ludwig, H.2    Reif, I.3    Blencke, H.M.4    Detsch, C.5
  • 82
    • 34249845809 scopus 로고    scopus 로고
    • Validating module network learning algorithms using simulated data
    • Michoel T, Maere S, Bonnet E, Joshi A, Saeys Y, et al. (2007) Validating module network learning algorithms using simulated data. BMC Bioinformatics 8 Suppl 2: S5. doi: 10.1186/1471-2105-8-S10-S5 18269699
    • (2007) BMC Bioinformatics , vol.8 , Issue.Suppl 2 , pp. 5
    • Michoel, T.1    Maere, S.2    Bonnet, E.3    Joshi, A.4    Saeys, Y.5
  • 83
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover
    • Dermitzakis ET, Clark AG, (2002) Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19: 1114–1121. 12082130
    • (2002) Mol Biol Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 84
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193. 12538238
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 85
    • 13944268797 scopus 로고    scopus 로고
    • A novel method for accurate operon predictions in all sequenced prokaryotes
    • Price MN, Huang KH, Alm EJ, Arkin AP, (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33: 880–892. 15701760
    • (2005) Nucleic Acids Res , vol.33 , pp. 880-892
    • Price, M.N.1    Huang, K.H.2    Alm, E.J.3    Arkin, A.P.4
  • 86
    • 52949112607 scopus 로고    scopus 로고
    • Organization and evolution of the biological response to singlet oxygen stress
    • Dufour YS, Landick R, Donohue TJ, (2008) Organization and evolution of the biological response to singlet oxygen stress. J Mol Biol 383: 713–730. doi: 10.1016/j.jmb.2008.08.017 18723027
    • (2008) J Mol Biol , vol.383 , pp. 713-730
    • Dufour, Y.S.1    Landick, R.2    Donohue, T.J.3
  • 87
    • 84866951830 scopus 로고    scopus 로고
    • Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
    • Dufour YS, Imam S, Koo BM, Green HA, Donohue TJ, (2012) Convergence of the transcriptional responses to heat shock and singlet oxygen stresses. PLoS Genet 8: e1002929. doi: 10.1371/journal.pgen.1002929 23028346
    • (2012) PLoS Genet , vol.8 , pp. 1002929
    • Dufour, Y.S.1    Imam, S.2    Koo, B.M.3    Green, H.A.4    Donohue, T.J.5


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