1. PackerL, CadenasE (2011) Lipoic acid: energy metabolism and redox regulation of transcription and cell signaling. J Clin Biochem Nutr 48: 26–32.
2. van HoekMJ, MerksRM (2012) Redox balance is key to explaining full vs. partial switching to low-yield metabolism. BMC Syst Biol 6: 22.
3. KornasA, KuzniakE, SlesakI, MiszalskiZ (2010) The key role of the redox status in regulation of metabolism in photosynthesizing organisms. Acta Biochim Pol 57: 143–151.
4. TrachoothamD, LuW, OgasawaraMA, NilsaRD, HuangP (2008) Redox regulation of cell survival. Antioxid Redox Signal 10: 1343–1374.
5. BergerF, Ramirez-HernandezMH, ZieglerM (2004) The new life of a centenarian: signalling functions of NAD(P). Trends Biochem Sci 29: 111–118.
6. BrekasisD, PagetMS (2003) A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2). EMBO J 22: 4856–4865.
7. AbateC, PatelL, RauscherFJ (1990) Redox regulation of fos and jun DNA-binding activity in vitro. Science 249: 1157–1161.
8. DanonA, MayfieldSP (1994) Light-regulated translation of chloroplast messenger RNAs through redox potential. Science 266: 1717–1719.
9. HaddadJJ (2004) Oxygen sensing and oxidant/redox-related pathways. Biochem Biophys Res Commun 316: 969–977.
10. SchaferFQ, BuettnerGR (2001) Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple. Free Radic Biol Med 30: 1191–1212.
11. ZhangQ, PistonDW, GoodmanRH (2002) Regulation of corepressor function by nuclear NADH. Science 295: 1895–1897.
12. RutterJ, ReickM, WuLC, McKnightSL (2001) Regulation of clock and NPAS2 DNA binding by the redox state of NAD cofactors. Science 293: 510–514.
13. SnoepJL, de GraefMR, WestphalAH, de KokA, Teixeira de MattosMJ, et al. (1993) Differences in sensitivity to NADH of purified pyruvate dehydrogenase complexes of Enterococcus faecalis, Lactococcus lactis, Azotobacter vinelandii and Escherichia coli: implications for their activity in vivo. FEMS Microbiol Lett 114: 279–283.
14. LeonardoMR, DaillyY, ClarkDP (1996) Role of NAD in regulating the adhE gene of Escherichia coli. J Bacteriol 178: 6013–6018.
15. AlvarezAF, GeorgellisD (2010) In vitro and in vivo analysis of the ArcB/A redox signaling pathway. Methods Enzymol 471: 205–228.
16. RolfeMD, Ter BeekA, GrahamAI, TrotterEW, AsifHM, et al. (2011) Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations. J Biol Chem 286: 10147–10154.
17. IuchiS, LinEC (1992) Purification and phosphorylation of the Arc regulatory components of Escherichia coli. J Bacteriol 174: 5617–5623.
18. GeorgellisD, KwonO, LinEC (2001) Quinones as the redox signal for the Arc two-component system of bacteria. Science 292: 2314–2316.
19. MalpicaR, FrancoB, RodriguezC, KwonO, GeorgellisD (2004) Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. Proc Natl Acad Sci U S A 101: 13318–13323.
20. BekkerM, AlexeevaS, LaanW, SawersG, Teixeira de MattosJ, et al. (2010) The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool. J Bacteriol 192: 746–754.
21. GeorgellisD, KwonO, LinEC (1999) Amplification of signaling activity of the Arc two-component system of Escherichia coli by anaerobic metabolites. An in vitro study with different protein modules. J Biol Chem 274: 35950–35954.
22. HolmAK, BlankLM, OldigesM, SchmidA, SolemC, et al. (2010) Metabolic and transcriptional response to cofactor perturbations in Escherichia coli. J Biol Chem 285: 17498–17506.
23. ChaoG, ShenJ, TsengCP, ParkSJ, GunsalusRP (1997) Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products. J Bacteriol 179: 4299–4304.
24. LynchAS, LinEC (1996) Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters. J Bacteriol 178: 6238–6249.
25. ChoBK, KnightEM, PalssonBO (2006) Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152: 2207–2219.
26. CunninghamL, GeorgellisD, GreenJ, GuestJR (1998) Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterization of an ArcA binding site in the lpd promoter. FEMS Microbiol Lett 169: 403–408.
27. ShenJ, GunsalusRP (1997) Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Mol Microbiol 26: 223–236.
28. PellicerMT, LynchAS, De WulfP, BoydD, AguilarJ, et al. (1999) A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli. Mol Gen Genet 261: 170–176.
29. PellicerMT, FernandezC, BadiaJ, AguilarJ, LinEC, et al. (1999) Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter. J Biol Chem 274: 1745–1752.
30. DrapalN, SawersG (1995) Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region. Mol Microbiol 16: 597–607.
31. NesbitAD, FleischhackerAS, TeterSJ, KileyPJ (2012) ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli. J Bacteriol 194: 6892–6899.
32. LiuX, De WulfP (2004) Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling. J Biol Chem 279: 12588–12597.
33. SalmonKA, HungSP, SteffenNR, KruppR, BaldiP, et al. (2005) Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem 280: 15084–15096.
34. GerasimovaAVGM, MakeevVY, MironovAAaFA (2003) ArcA regulator of Gamma-Proteobacteria- Identification of the Binding Signal and Description of the Regulon. Biophysics 48: S21–S25.
35. WangX, GaoH, ShenY, WeinstockGM, ZhouJ, et al. (2008) A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic Acids Res 36: 4863–4871.
36. OgasawaraH, TeramotoJ, YamamotoS, HiraoK, YamamotoK, et al. (2005) Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli. FEMS Microbiol Lett 251: 243–249.
37. LeeYS, HanJS, JeonY, HwangDS (2001) The Arc two-component signal transduction system inhibits in vitro Escherichia coli chromosomal initiation. J Biol Chem 276: 9917–9923.
38. JeongJY, KimYJ, ChoN, ShinD, NamTW, et al. (2004) Expression of ptsG encoding the major glucose transporter is regulated by ArcA in Escherichia coli. J Biol Chem 279: 38513–38518.
39. MikaF, HenggeR (2005) A two-component phosphotransfer network involving ArcB, ArcA, and RssB coordinates synthesis and proteolysis of sigmaS (RpoS) in E. coli. Genes Dev 19: 2770–2781.
40. TardatB, TouatiD (1993) Iron and oxygen regulation of Escherichia coli MnSOD expression: competition between the global regulators Fur and ArcA for binding to DNA. Mol Microbiol 9: 53–63.
41. LunDS, SherridA, WeinerB, ShermanDR, GalaganJE (2009) A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol 10: R142.
42. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36.
43. GaoR, StockAM (2009) Biological insights from structures of two-component proteins. Annu Rev Microbiol 63: 133–154.
44. GrimaudR, EzratyB, MitchellJK, LafitteD, BriandC, et al. (2001) Repair of oxidized proteins. Identification of a new methionine sulfoxide reductase. J Biol Chem 276: 48915–48920.
45. RitzD, PatelH, DoanB, ZhengM, AslundF, et al. (2000) Thioredoxin 2 is involved in the oxidative stress response in Escherichia coli. J Biol Chem 275: 2505–2512.
46. O'HandleySF, FrickDN, DunnCA, BessmanMJ (1998) Orf186 represents a new member of the Nudix hydrolases, active on adenosine(5′)triphospho(5′)adenosine, ADP-ribose, and NADH. J Biol Chem 273: 3192–3197.
47. KeselerIM, Collado-VidesJ, Santos-ZavaletaA, Peralta-GilM, Gama-CastroS, et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39: D583–590.
48. MuirM, WilliamsL, FerenciT (1985) Influence of transport energization on the growth yield of Escherichia coli. J Bacteriol 163: 1237–1242.
49. MyersKS, YanH, OngIM, ChungD, LiangK, et al. (2013) Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding. PLoS Genet 9: e1003565.
50. KimD, HongJS, QiuY, NagarajanH, SeoJH, et al. (2012) Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 8: e1002867.
51. VolbedaA, DarnaultC, ParkinA, SargentF, ArmstrongFA, et al. (2013) Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b. Structure 21: 184–190.
52. AtlungT, BrondstedL (1994) Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase. J Bacteriol 176: 5414–5422.
53. MaZ, GongS, RichardH, TuckerDL, ConwayT, et al. (2003) GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Mol Microbiol 49: 1309–1320.
54. TramontiA, ViscaP, De CanioM, FalconiM, De BiaseD (2002) Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol 184: 2603–2613.
55. GongS, RichardH, FosterJW (2003) YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli. J Bacteriol 185: 4402–4409.
56. MatesAK, SayedAK, FosterJW (2007) Products of the Escherichia coli acid fitness island attenuate metabolite stress at extremely low pH and mediate a cell density-dependent acid resistance. J Bacteriol 189: 2759–2768.
57. DurandS, StorzG (2010) Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol 75: 1215–1231.
58. BoysenA, Moller-JensenJ, KallipolitisB, Valentin-HansenP, OvergaardM (2010) Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli. J Biol Chem 285: 10690–10702.
59. MakinoK, AmemuraM, KawamotoT, KimuraS, ShinagawaH, et al. (1996) DNA binding of PhoB and its interaction with RNA polymerase. J Mol Biol 259: 15–26.
60. PrattLA, SilhavyTJ (1994) OmpR mutants specifically defective for transcriptional activation. J Mol Biol 243: 579–594.
61. SlauchJM, RussoFD, SilhavyTJ (1991) Suppressor mutations in rpoA suggest that OmpR controls transcription by direct interaction with the alpha subunit of RNA polymerase. J Bacteriol 173: 7501–7510.
62. CotterPA, MelvilleSB, AlbrechtJA, GunsalusRP (1997) Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol Microbiol 25: 605–615.
63. FerrandezA, GarciaJL, DiazE (2000) Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli. J Biol Chem 275: 12214–12222.
64. PapenfortK, SaidN, WelsinkT, LucchiniS, HintonJC, et al. (2009) Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 74: 139–158.
65. MandinP, GottesmanS (2010) Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J 29: 3094–3107.
66. AlexeevaS, HellingwerfKJ, Teixeira de MattosMJ (2003) Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J Bacteriol 185: 204–209.
67. LevanonSS, SanKY, BennettGN (2005) Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol Bioeng 89: 556–564.
68. EvansMR, FinkRC, Vazquez-TorresA, PorwollikS, Jones-CarsonJ, et al. (2011) Analysis of the ArcA regulon in anaerobically grown Salmonella entericasv. Typhimurium. BMC Microbiol 11: 58.
69. IuchiS, AristarkhovA, DongJM, TaylorJS, LinEC (1994) Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase. J Bacteriol 176: 1695–1701.
70. BidartGN, RuizJA, de AlmeidaA, MendezBS, NikelPI (2012) Manipulation of the anoxic metabolism in Escherichia coli by ArcB deletion variants in the ArcBA two-component system. Appl Environ Microbiol 78: 8784–8794.
71. MatsubaraM, KitaokaSI, TakedaSI, MizunoT (2000) Tuning of the porin expression under anaerobic growth conditions by his-to-Asp cross-phosphorelay through both the EnvZ-osmosensor and ArcB-anaerosensor in Escherichia coli. Genes Cells 5: 555–569.
72. NystromT, LarssonC, GustafssonL (1996) Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis. EMBO J 15: 3219–3228.
73. JonesSA, ChowdhuryFZ, FabichAJ, AndersonA, SchreinerDM, et al. (2007) Respiration of Escherichia coli in the mouse intestine. Infect Immun 75: 4891–4899.
74. GovantesF, OrjaloAV, GunsalusRP (2000) Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon. Mol Microbiol 38: 1061–1073.
75. AtlungT, SundS, OlesenK, BrondstedL (1996) The histone-like protein H-NS acts as a transcriptional repressor for expression of the anaerobic and growth phase activator AppY of Escherichia coli. J Bacteriol 178: 3418–3425.
76. WybornNR, MessengerSL, HendersonRA, SawersG, RobertsRE, et al. (2002) Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products. Microbiology 148: 1015–1026.
77. SirkoA, ZeheleinE, FreundlichM, SawersG (1993) Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli. J Bacteriol 175: 5769–5777.
78. StrohmaierH, NoigesR, KotschanS, SawersG, HogenauerG, et al. (1998) Signal transduction and bacterial conjugation: characterization of the role of ArcA in regulating conjugative transfer of the resistance plasmid R1. J Mol Biol 277: 309–316.
79. RolfeMD, OconeA, StapletonMR, HallS, TrotterEW, et al. (2012) Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations. Open Biol 2: 120091.
80. YoshidaT, QinL, EggerLA, InouyeM (2006) Transcription regulation of ompF and ompC by a single transcription factor, OmpR. J Biol Chem 281: 17114–17123.
81. KimSK, KimuraS, ShinagawaH, NakataA, LeeKS, et al. (2000) Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex. J Bacteriol 182: 5596–5599.
82. KasaharaM, MakinoK, AmemuraM, NakataA, ShinagawaH (1991) Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters. J Bacteriol 173: 549–558.
83. YangC, HuangTW, WenSY, ChangCY, TsaiSF, et al. (2012) Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli. PLoS One 7: e47314.
84. PerkinsTT, DaviesMR, KlemmEJ, RowleyG, WilemanT, et al. (2013) ChIP-seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization. Mol Microbiol 87: 526–538.
85. GriffithKL, GrossmanAD (2008) A degenerate tripartite DNA-binding site required for activation of ComA-dependent quorum response gene expression in Bacillus subtilis. J Mol Biol 381: 261–275.
86. KimSK, MakinoK, AmemuraM, ShinagawaH, NakataA (1993) Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli. J Bacteriol 175: 1316–1324.
87. NeidhardtFC, BlochPL, SmithDF (1974) Culture medium for enterobacteria. J Bacteriol 119: 736–747.
88. KangY, WeberKD, QiuY, KileyPJ, BlattnerFR (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187: 1135–1160.
89. Miller JH (1972) Experiments in molecular genetics. [Cold Spring Harbor, N.Y.]: Cold Spring Harbor Laboratory.
90. DavisSE, MooneyRA, KaninEI, GrassJ, LandickR, et al. (2011) Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide. Methods Enzymol 498: 449–471.
91. HuberW, von HeydebreckA, SultmannH, PoustkaA, VingronM (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl 1: S96–104.
92. DufourYS, LandickR, DonohueTJ (2008) Organization and evolution of the biological response to singlet oxygen stress. J Mol Biol 383: 713–730.
93. BiedaM, XuX, SingerMA, GreenR, FarnhamPJ (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 16: 595–605.
94. HomannOR, JohnsonAD (2010) MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol 8: 49.
95. LiR, YuC, LiY, LamTW, YiuSM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967.
96. ValouevA, JohnsonDS, SundquistA, MedinaC, AntonE, et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829–834.
97. SchneiderTD (1997) Information content of individual genetic sequences. J Theor Biol 189: 427–441.
98. BlattnerFR, PlunkettG (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453–1462.
99. BlancoAG, SolaM, Gomis-RuthFX, CollM (2002) Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 10: 701–713.
100. SchneiderTD (1997) Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res 25: 4408–4415.
101. DatsenkoKA, WannerBL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97: 6640–6645.
102. KhodurskyAB, BernsteinJA, PeterBJ, RhodiusV, WendischVF, et al. (2003) Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods Mol Biol 224: 61–78.
103. BolstadBM, IrizarryRA, AstrandM, SpeedTP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193.
104. SchwalbachMS, KeatingDH, TremaineM, MarnerWD, ZhangY, et al. (2012) Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol 78: 3442–3457.
105. BeattyCM, BrowningDF, BusbySJ, WolfeAJ (2003) Cyclic AMP receptor protein-dependent activation of the Escherichia coli acs P2 promoter by a synergistic class III mechanism. J Bacteriol 185: 5148–5157.
106. FerrandezA, MinambresB, GarciaB, OliveraER, LuengoJM, et al. (1998) Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J Biol Chem 273: 25974–25986.
107. FraleyCD, KimJH, McCannMP, MatinA (1998) The Escherichia coli starvation gene cstC is involved in amino acid catabolism. J Bacteriol 180: 4287–4290.
108. NakaoT, YamatoI, AnrakuY (1987) Nucleotide sequence of putC, the regulatory region for the put regulon of Escherichia coli K12. Mol Gen Genet 210: 364–368.
109. DaviesSJ, GolbyP, OmraniD, BroadSA, HarringtonVL, et al. (1999) Inactivation and regulation of the aerobic C(4)-dicarboxylate transport (dctA) gene of Escherichia coli. J Bacteriol 181: 5624–5635.
110. ProstJF, NegreD, OudotC, MurakamiK, IshihamaA, et al. (1999) Cra-dependent transcriptional activation of the icd gene of Escherichia coli. J Bacteriol 181: 893–898.
111. NesbitAD, GielJL, RoseJC, KileyPJ (2009) Sequence-specific binding to a subset of IscR-regulated promoters does not require IscR Fe-S cluster ligation. J Mol Biol 387: 28–41.
112. MaxamAM, GilbertW (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol 65: 499–560.
113. SchneiderTD, StephensRM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097–6100.
114. NeuwegerH, PersickeM, AlbaumSP, BekelT, DondrupM, et al. (2009) Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Syst Biol 3: 82.