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• W1987005877 abstract "The ArcAB two-component system of Escherichia coli regulates the aerobic/anaerobic expression of genes that encode respiratory proteins whose synthesis is coordinated during aerobic/anaerobic cell growth. A genomic study of E. coli was undertaken to identify other potential targets of oxygen and ArcA regulation. A group of 175 genes generated from this study and our previous study on oxygen regulation (Salmon, K., Hung, S. P., Mekjian, K., Baldi, P., Hatfield, G. W., and Gunsalus, R. P. (2003) J. Biol. Chem. 278, 29837–29855), called our gold standard gene set, have p values <0.00013 and a posterior probability of differential expression value of 0.99. These 175 genes clustered into eight expression patterns and represent genes involved in a large number of cell processes, including small molecule biosynthesis, macromolecular synthesis, and aerobic/anaerobic respiration and fermentation. In addition, 119 of these 175 genes were also identified in our previous study of the fnr allele. A MEME/weight matrix method was used to identify a new putative ArcA-binding site for all genes of the E. coli genome. 16 new sites were identified upstream of genes in our gold standard set. The strict statistical analyses that we have performed on our data allow us to predict that 1139 genes in the E. coli genome are regulated either directly or indirectly by the ArcA protein with a 99% confidence level. The ArcAB two-component system of Escherichia coli regulates the aerobic/anaerobic expression of genes that encode respiratory proteins whose synthesis is coordinated during aerobic/anaerobic cell growth. A genomic study of E. coli was undertaken to identify other potential targets of oxygen and ArcA regulation. A group of 175 genes generated from this study and our previous study on oxygen regulation (Salmon, K., Hung, S. P., Mekjian, K., Baldi, P., Hatfield, G. W., and Gunsalus, R. P. (2003) J. Biol. Chem. 278, 29837–29855), called our gold standard gene set, have p values <0.00013 and a posterior probability of differential expression value of 0.99. These 175 genes clustered into eight expression patterns and represent genes involved in a large number of cell processes, including small molecule biosynthesis, macromolecular synthesis, and aerobic/anaerobic respiration and fermentation. In addition, 119 of these 175 genes were also identified in our previous study of the fnr allele. A MEME/weight matrix method was used to identify a new putative ArcA-binding site for all genes of the E. coli genome. 16 new sites were identified upstream of genes in our gold standard set. The strict statistical analyses that we have performed on our data allow us to predict that 1139 genes in the E. coli genome are regulated either directly or indirectly by the ArcA protein with a 99% confidence level. Escherichia coli thrives in the gastrointestinal tract of many warm-blooded animals as a commensal or as a pathogen depending on a strain-dependent complement of genes (2Blattner F.R. Plunkett G. II I Bloch C.A. Perna N.T. Burland V. Riley M. Collado-Vides J. Glasner J.D. Rode C.K. Mayhew G.F. Gregor J. Davis N.W. Kirkpatrick H.A. Goeden M.A. Rose D.J. Mau B. Shao Y. Science. 1997; 277: 1453-1474Crossref PubMed Scopus (6056) Google Scholar). These enteric bacteria have the ability to switch between aerobic and anaerobic growth if oxygen is limiting. In response to microenvironments in the host, each individual cell adjusts its metabolic pathways to optimize energy generation via aerobic and/or anaerobic respiration or by fermentation of simple sugars (3Gunsalus R.P. Park S.J. Res. Microbiol. 1994; 145: 437-450Crossref PubMed Scopus (168) Google Scholar). Many other cellular functions also are adjusted in response to oxygen availability, such as alterations in gene expression levels of membrane-associated nutrient uptake and/or excretion systems, biosynthetic pathways, and macromolecular synthesis (3Gunsalus R.P. Park S.J. Res. Microbiol. 1994; 145: 437-450Crossref PubMed Scopus (168) Google Scholar). Expression of E. coli genes involved in oxygen utilization is down-regulated as oxygen is depleted, and in a reciprocal fashion, expression of genes encoding alternative anaerobic electron transport pathways or genes needed for fermentation is switched on. Many of these metabolic transitions are controlled at the transcriptional level by the activities of the ferric nitrate reductase global regulatory protein FNR and/or the two-component ArcAB regulatory system (4Guest J.R. Attwood M.M. Machado R.S. Matqi K.Y. Shaw J.E. Turner S.L. Microbiology. 1997; 143: 457-466Crossref PubMed Scopus (19) Google Scholar, 5Lynch A.S. Lin E.C.C. Lin E.C.C. Lynch A.S. Regulation of Gene Expression in E. coli. R. G. Landes Co., Austin, TX1996: 362-381Google Scholar). The role of the FNR protein in the global control of E. coli gene expression has been profiled in response to anaerobiosis (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar). Based on this analysis of whole genome transcription data, it was estimated that the expression of over one-third of the genes expressed during growth under aerobic conditions are altered when E. coli cells transition to an anaerobic growth state and that the expression of half of these genes is modulated either directly or indirectly by FNR. Thus, the fnr gene family was estimated to be ∼10-fold larger than the 70 members previously recognized as members of the fnr gene regulatory network (6Lynch A.S. Lin E.C.C. Neidhart F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. 1. ASM Press, Washington, D. C.1996: 1526-1549Google Scholar, 7Guest J.R. Green J. Irvine A. Spiro S. Lin E.C.C. Lynch A.S. Regulation of Gene Expression in Escherichia coli. R. G. Landes Co., Austin, TX1996: 317-342Crossref Google Scholar). The ArcAB (aerobic respiratory control) two-component regulatory system is recognized as a second global regulator of anaerobic gene regulation (3Gunsalus R.P. Park S.J. Res. Microbiol. 1994; 145: 437-450Crossref PubMed Scopus (168) Google Scholar, 6Lynch A.S. Lin E.C.C. Neidhart F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. 1. ASM Press, Washington, D. C.1996: 1526-1549Google Scholar, 8Bauer C.E. Elsen S. Bird T.H. Annu. Rev. Microbiol. 1999; 53: 495-523Crossref PubMed Scopus (201) Google Scholar). The ArcAB system is composed of a classical OmpR-like receiver regulator, ArcA, and a membrane-associated sensor transmitter protein, ArcB (6Lynch A.S. Lin E.C.C. Neidhart F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. 1. ASM Press, Washington, D. C.1996: 1526-1549Google Scholar). Together, these components have been shown to regulate expression of oxygen-requiring pathways, including the tricarboxylic acid cycle (e.g. sdhCDAB, icd, fumA, mdh, gltA, acnA, and acnB), and the aerobic cytochrome oxidase complexes (9Park S.J. Chao G. Gunsalus R.P. J. Bacteriol. 1997; 179: 4138-4142Crossref PubMed Google Scholar, 10Park S.J. Cotter P.A. Gunsalus R.P. J. Bacteriol. 1995; 177: 6652-6656Crossref PubMed Google Scholar, 11Park S.J. Gunsalus R.P. J. Bacteriol. 1995; 177: 6255-6262Crossref PubMed Scopus (129) Google Scholar, 12Park S.J. McCabe J. Turna J. Gunsalus R.P. J. Bacteriol. 1994; 176: 5086-5092Crossref PubMed Google Scholar, 13Park S.J. Tseng C.P. Gunsalus R.P. Mol. Microbiol. 1995; 15: 473-482Crossref PubMed Scopus (114) Google Scholar, 14Cotter P.A. Chepuri V. Gennis R.B. Gunsalus R.P. J. Bacteriol. 1990; 172: 6333-6338Crossref PubMed Scopus (208) Google Scholar, 15Cotter P.A. Gunsalus R.P. J. Bacteriol. 1989; 171: 3817-3823Crossref PubMed Google Scholar, 16Cotter P.A. Gunsalus R.P. FEMS Microbiol. Lett. 1992; 70: 31-36Crossref PubMed Google Scholar, 17Cotter P.A. Melville S.B. Albrecht J.A. Gunsalus R.P. Mol. Microbiol. 1997; 25: 605-615Crossref PubMed Scopus (107) Google Scholar, 18Govantes F. Albrecht J.A. Gunsalus R.P. Mol. Microbiol. 2000; 37: 1456-1469Crossref PubMed Scopus (50) Google Scholar). ArcAB is also known to be required for proper expression of certain catabolic genes for pyruvate utilization and sugar fermentation (19Drapal N. Sawers G. Mol. Microbiol. 1995; 16: 597-607Crossref PubMed Scopus (55) Google Scholar, 20Jeong J.Y. Kim Y.J. Cho N. Shin D. Nam T.W. Ryu S. Seok Y.J. J. Biol. Chem. 2004; 279: 38513-38518Abstract Full Text Full Text PDF PubMed Scopus (49) Google Scholar, 21Sawers G. Suppmann B. J. Bacteriol. 1992; 174: 3474-3478Crossref PubMed Google Scholar). In this genome-based study, we have identified additional E. coli genes under oxygen control that are differentially expressed in response to the ArcA global regulatory protein. This was accomplished by the use of DNA microarrays to analyze gene expression profiles in E. coli cells cultured at steady-state growth rates under aerobic (+O2) or anaerobic (-O2) growth conditions and in cells cultured under anaerobic growth conditions in the presence (-O2, +ArcA) or absence (-O2, -ArcA) of the ArcA protein or in otherwise arcA+ and arcA- isogenic strains. These experiments show that about one-half of the genes whose expression levels are affected by aerobic to anaerobic transitions are also affected by the ArcA protein. Thus, the number of E. coli genes differentially regulated by the ArcA protein is much larger than the 30 (5Lynch A.S. Lin E.C.C. Lin E.C.C. Lynch A.S. Regulation of Gene Expression in E. coli. R. G. Landes Co., Austin, TX1996: 362-381Google Scholar) or 100 (22Liu X. De Wulf P. J. Biol. Chem. 2004; 279: 12588-12597Abstract Full Text Full Text PDF PubMed Scopus (157) Google Scholar) genes/operons previously recognized. The results of the gene expression profiling experiments further show that as many as two-thirds of the genes whose expression levels are affected by the ArcA protein are also affected by the FNR protein (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar). Chemicals and Reagents—Avian myeloblastosis virus reverse transcriptase and Sephadex G-25 Quickspin columns were obtained from Roche Applied Science. Phenol and the DNA-free kit were purchased from Ambion Inc. Ribonuclease inhibitor III was purchased from Pan-Vera/Takara. Ultrapure deoxynucleoside triphosphates were purchased from Amersham Biosciences. Random hexamer oligonucleotides and T4 polynucleotide kinase were obtained from New England Biolabs Inc., and [α-33P]dCTP (2–3000 Ci/mmol) was obtained from PerkinElmer Life Sciences. DNA filter arrays (Panorama E. coli gene arrays) were obtained from Sigma. SYBR Gold was purchased from Molecular Probes, Inc.. All other chemicals were obtained from Sigma. All reagents and baked glassware used in RNA manipulations were treated with diethyl pyrocarbonate prior to their use. Bacterial Strains and Growth Conditions—E. coli strains MC4100 (F-araD139 Δ(argF-lac)U169 rpsL150 relA1 flb-5301 deoC1 ptsF25 rbsR) (23Silhavy T.J. Berman M.L. Enquist L.W. Experiments with Gene Fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY1984Google Scholar) and PC35 (MC4100 ΔarcA::kan) (15Cotter P.A. Gunsalus R.P. J. Bacteriol. 1989; 171: 3817-3823Crossref PubMed Google Scholar) were used in this study. Cells were grown in MOPS 1The abbreviations used are: MOPS, 4-morpholinepropanesulfonic acid; ORF, open reading frame; PPDE, posterior probability of differential expression. medium (24Neidhardt F.C. Bloch P.L. Smith D.F. J. Bacteriol. 1974; 119: 736-747Crossref PubMed Google Scholar) containing 40 mm glucose. Aerobic cultures were grown as described previously (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar) in 125-ml Erlenmeyer flasks with constant aeration. Anaerobic cultures were grown in 15-ml anaerobic tubes fitted with butyl rubber stoppers (15Cotter P.A. Gunsalus R.P. J. Bacteriol. 1989; 171: 3817-3823Crossref PubMed Google Scholar). The same medium was made anaerobic by flushing with O2-free N2 gas for 20 min and then dispensed anaerobically into N2-flushed tubes. Cultures of the indicated strain were inoculated from overnight cultures grown under identical conditions (15Cotter P.A. Gunsalus R.P. J. Bacteriol. 1989; 171: 3817-3823Crossref PubMed Google Scholar). Cells were grown to A600 = 0.5–0.6 (mid-exponential growth phase) and harvested as described previously (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar, 25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar). Total RNA Isolation, cDNA Synthesis, and Target Labeling Conditions—Total RNA was isolated from 10-ml cultures; cDNA was synthesized and labeled with [α-33P]dCTP; and filters were hybridized exactly as described by Hung et al. (25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar). Stripping and reusing filters four times as described here results in a <3% increase in variance (26Baldi P. Hatfield G.W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press, Cambridge, UK2002Crossref Google Scholar). Data Acquisition—The commercial software package DNA Array-Vision obtained from Research Imaging Inc. was used to grid the 16-bit image file obtained from a PhosphorImager, to record the pixel density of each of the 18,432 addresses on each filter, and to perform the background subtractions. 8580 of the addresses on each filter were spotted with duplicate copies of each of the 4290 E. coli open reading frames (ORFs). The remaining 9852 empty addresses were used for background measurements. Because the backgrounds were constant, a global average background measurement was subtracted from each experimental measurement, although local background calculations are possible. Experimental Design—The experiments described here (Fig. 1) were performed at the same time as our previously reported experiments profiling gene expression levels in the presence or absence of oxygen and FNR (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar). The data for strain MC4100 (ArcA+) grown aerobically (Experiment 1, Filters 1 and 2) and anaerobically (Experiment 2, Filters 3 and 4) have been reported by Salmon et al. (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar). For Experiment 3, Filters 5 and 6 were hybridized with random hexamer-generated 33P-labeled cDNA fragments complementary to each of three independently prepared RNA preparations (RNA 25–27) obtained from three individual cultures of strain PC35 (arcA-) grown under anaerobic conditions. These three 33P-labeled cDNA target preparations were pooled prior to hybridization to the full-length ORF probes on the filters (Experiment 3, Replicate 1, Filters 5 and 6). Following PhosphorImager analysis, these filters were stripped and again hybridized with pooled 33P-labeled cDNA target fragments complementary to each of another three independently prepared RNA preparations (RNA 28–30) from the same strain (PC35; Experiment 3, Replicate 2). This procedure was repeated one more time with Filters 5 and 6 with yet another independently prepared pool of cDNA targets (Experiment 3, Replicates 3; RNA 31–33). The data for the fourth replicate of this experiment were lost. This experimental design produced duplicate filter data for four replicates performed with cDNA targets complementary to four independent sets of pooled RNA preparations for Experiments 1 and 2. Thus, because each filter contained duplicate spots for each ORF and duplicate filters were used for each experiment, a total of 16 measurements were obtained, four measurements for each ORF from each of four replicates. Duplicate filter data were obtained for three replicates performed with cDNA targets complementary to three independent sets of pooled RNA preparations for Experiment 3. Thus, because each filter contained duplicate spots for each ORF and duplicate filters were used for each experiment, a total of 12 measurements were obtained, four measurements for each ORF from each of three replicates. Statistical Analyses—Data processing and statistical methods implemented in the Cyber-T software used for the analysis and interpretation of the data obtained from the DNA microarray experiments described in this study were the same as those described previously by Salmon et al. (1Salmon K. Hung S.P. Mekjian K. Baldi P. Hatfield G.W. Gunsalus R.P. J. Biol. Chem. 2003; 278: 29837-29855Abstract Full Text Full Text PDF PubMed Scopus (240) Google Scholar). For each target signal, a background subtracted estimate of the expression level was obtained and scaled to total counts on the membrane by dividing each individual gene expression value by the total of all target signals on the membrane. Thus, each normalized gene level is expressed as a fraction of the total mRNA hybridized to each DNA array. For any given measurement, a value greater than zero (indicating an expression level) or a zero (indicating an expression level lower than background) was obtained. Only those genes exhibiting an expression level greater than zero in all replicates were used for statistical analysis. These gene expression level measurements were analyzed by a regularized t test based on a Bayesian statistical framework (25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar, 26Baldi P. Hatfield G.W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press, Cambridge, UK2002Crossref Google Scholar, 27Hatfield G.W. Hung S.P. Baldi P. Mol. Microbiol. 2003; 47: 871-877Crossref PubMed Scopus (101) Google Scholar, 28Long A.D. Mangalam H.J. Chan B.Y. Tolleri L. Hatfield G.W. Baldi P. J. Biol. Chem. 2001; 276: 19937-19944Abstract Full Text Full Text PDF PubMed Scopus (308) Google Scholar, 29Baldi P. Long A.D. Bioinformatics. 2001; 17: 509-519Crossref PubMed Scopus (1317) Google Scholar). For analysis of the data reported here, we ranked the mean gene expression levels of the replicate experiments in ascending order, used a sliding window of 101 genes, and assigned the average S.D. of the 50 genes ranked below and above each gene as the Bayesian S.D. for that gene. The p values for each gene measurement based on a regularized t test with a confidence value of 10 are reported in the Supplemental Material. A comprehensive discussion of the use of a regularized t test and the modifications applicable to the analysis of DNA microarray data of the type presented here is described in detail elsewhere (26Baldi P. Hatfield G.W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press, Cambridge, UK2002Crossref Google Scholar). Gene measurements containing zero expression values in one or more replicates were set aside. Among this set of genes, those with zero expression values for all replicates in one experiment and all values greater than zero for all measurements of another experiment were identified. Because these gene measurements could not be analyzed with a t test, the significance of these results was evaluated by ranking these genes in ascending order according to their coefficients of variance of the four greater than zero measurements of each experiment. Cyber-T employs a mixture model-based method described by Allison et al. (30Allison D.B. Gadbury G.L. Heo M. Fernndez J.R. Lee C.K. Prolla T.A. Weindruch R. Comput. Stat. Data Anal. 2002; 39: 1-20Crossref Google Scholar) for the computation of the global false positive and false negative levels inherent in a DNA microarray experiment (25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar, 26Baldi P. Hatfield G.W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press, Cambridge, UK2002Crossref Google Scholar). With this method, described by Hung et al. (25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar), we estimated the rates of false positives and false negatives as well as true positives and true negatives at any given p value threshold. In other words, we obtained a posterior probability of differential expression PPDE(p) value for each gene measurement and a PPDE(<p) value at any given p value threshold based on the experiment-wide global false positive level and the p value exhibited by that gene (25Hung S.P. Baldi P. Hatfield G.W. J. Biol. Chem. 2002; 277: 40309-40323Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar, 26Baldi P. Hatfield G.W. DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press, Cambridge, UK2002Crossref Google Scholar). In most instances, PPDE(<p) values are reported below and Tables I, II, III, IV, V, VI, VII, VIII. However, both PPDE(p) and PPDE(<p) values are given for each gene in the Supplemental Material.Table IRegulatory pattern I: genes that exhibit decreased levels during anaerobic growth and increased levels in an ArcA-deficient strainGene name (NIH) and b no.p value (+O2, +arcA vs. -O2, +arcA)PPDE(<p) (-O2, +arcA vs. -O2, +arcA)p value (-O2, +arcA vs. -O2, -arcA)PPDE(<p) (-O2, +arcA vs. -O2, +arcA)-Fold (+O2, +arcA vs. -O2, +arcA)-Fold (-O2, +arcA vs. -O2, -arcA)Predicted ArcA siteaDistance is upstream from the start codon of the gene or the first gene of the operon (if internal). Sites are predicted from the gene promoter. Other putative ArcA-binding sites may also be predicted upstream of a secondary promoter, but are not mentioned hereycdC (b1013)1.58E-050.99990392.90E-040.9994196-1.762.53rpsA (b0911)7.17E-050.99970692.52E-040.9994788-1.912.90rplX (b3309)4.68E-101.00000001.26E-040.9996910-3.352.98rpsT (b0023)1.90E-050.99988982.65E-040.9994589-2.263.20talA (b2464)2.21E-040.99932792.16E-040.9995354-1.643.46prlA (b3300)2.35E-070.99999577.76E-070.9999935-2.123.49crr (b2417)2.14E-090.99999995.06E-050.9998458-3.233.63rbsC (b3750)2.89E-070.99999497.32E-050.9997959-2.073.76oppA (b1243)8.78E-050.99965973.03E-101.0000000-1.663.79113, 324, 472rpsJ (b3321)6.28E-060.99995121.09E-040.9997244-2.103.80pal (b0741)3.90E-080.99999881.45E-050.9999403-2.643.91301tufA (b3339)1.59E-070.99999676.16E-141.0000000-1.664.01ompA (b0957)1.48E-060.99998313.86E-060.9999781-2.274.02yajG (b0434)7.73E-050.99969022.24E-050.9999169-1.954.17rbsD (b3748)3.85E-080.99999897.40E-050.9997942-2.814.83speD (b0120)6.41E-060.99995045.07E-050.9998454-2.305.11yjcU (b4085)1.81E-070.99999642.81E-040.9994337-1.835.20yceD (b1088)2.00E-101.00000003.45E-050.9998847-2.905.27rplS (b2606)3.02E-050.99984504.23E-080.9999993-2.235.81atpG (b3733)2.56E-070.99999541.04E-040.9997345-1.946.07124, 385speE (b0121)7.18E-060.99994615.70E-060.9999705-2.106.32yfiA (b2597)7.16E-111.00000004.68E-060.9999746-10.417.49nuoE (b2285)2.34E-090.99999992.61E-060.9999837-2.798.83149, 190rplT (b1716)4.41E-060.99996243.48E-050.9998838-2.789.01gatY (b2096)3.49E-070.99999427.81E-060.9999626-2.7410.72515, 520icdA (b1136)1.03E-111.00000001.38E-050.9999423-2.7414.04111sdhA (b0723)2.06E-070.99999613.90E-050.9998733-4.0314.5469, 267, 330lpdA (b0116)1.29E-111.00000002.29E-060.9999852-4.7515.29219, 230, 232gpmA (b0755)1.27E-090.99999993.85E-060.9999781-7.1816.95rplM (b3231)3.40E-070.99999433.07E-060.9999816-2.5717.05mdh (b3236)4.00E-040.99896052.89E-040.9994210-1.8417.95229nuoB (b2287)1.32E-040.99954142.12E-040.9995422-6.4819.34149, 190trpB (b1261)3.12E-101.00000004.43E-050.9998606-2.8519.9746cyoA (b0432)9.70E-100.99999995.06E-050.9998457-9.9823.3062, 82, 235, 246sdhB (b0724)1.25E-050.99991882.09E-040.9995476-2.5227.8769, 267, 330sucD (b0729)2.42E-050.99986847.28E-050.9997967-5.0486.1469, 267, 330gltA (b0720)3.09E-050.99984213.80E-060.9999783-2.60107.01348a Distance is upstream from the start codon of the gene or the first gene of the operon (if internal). Sites are predicted from the gene promoter. Other putative ArcA-binding sites may also be predicted upstream of a secondary promoter, but are not mentioned here Open table in a new tab Table IIRegulatory pattern II: genes that exhibit increased levels during anaerobic growth and further decreased levels in an ArcA-deficient strainGene name (NIH) and b no.p value (+O2, +arcA vs. -O2, +arcA)PPDE(<p) (-O2, +arcA vs. -O2, -arcA)p value (-O2, +arcA vs. -O2, -arcA)PPDE(<p) (-O2, +arcA vs. -O2, -arcA)-Fold (+O2, +arcA vs. -O2, +arcA)-Fold (-O2, +arcA vs. -O2, -arcA)Predicted ArcA siteaDistance is upstream from the start codon of the gene or the first gene of the operon (if internal). Sites are predicted from the gene promoter. Other putative ArcA-binding sites may also be predicted upstream of a secondary promoter, but are not mentioned hereyhjE (b3523)1.29E-040.99954851.79E-070.99999792.20-50.94202yabM (b0070)3.01E-040.99915777.13E-070.99999392.30-29.69pyrD (b0945)5.36E-060.99995654.37E-060.99997594.95-18.91nfrA (b0568)1.87E-050.99989094.71E-060.99997454.71-16.63yadQ (b0155)2.80E-040.99920133.23E-070.99999671.99-16.01dinG (b0799)3.20E-040.99911821.60E-070.9999981.83-11.79yhhT (b3474)3.06E-040.99914715.24E-070.99999522.14-11.26gadB (b1493)1.87E-080.99999931.47E-060.999989523.98-11.23gadA (b3517)5.14E-070.99999232.50E-050.999909622.98-9.44567glnD (b0167)8.77E-050.99966012.46E-060.99998442.55-8.58560mobB (b3856)5.57E-060.99995538.68E-070.99999293.26-7.83yadR (b0156)2.03E-050.99988432.00E-060.99998673.60-7.47yafZ (b0252)2.57E-040.99925051.64E-060.99998862.04-7.38aroM (b0390)1.81E-040.99942071.72E-060.99998812.19-7.13wecE (b3791)1.34E-040.99953593.41E-060.999982.29-6.48yghQ (b2983)4.25E-040.99891432.41E-060.99998471.98-6.38tra5_2 (b0541)1.38E-040.99952455.22E-070.99999521.90-6.31pnuC (b0751)1.71E-050.99989789.66E-060.99995613.38-6.22B1172 (b1172)1.20E-070.99999741.71E-050.999932216.47-6.14gadX (b3516)2.32E-060.99997661.31E-040.999681816.09-6.111,227,238,249mrcA (b3396)2.50E-040.99926551.86E-060.99998742.00-6.09yhjJ (b3527)2.90E-040.99917917.03E-060.99996552.08-5.77sbcC (b0397)3.89E-040.99898271.59E-050.99993572.17-5.59yhjW (b3546)1.57E-050.9999042.46E-070.99999732.15-5.58yhjD (b3522)8.40E-050.99967064.68E-050.99985453.01-5.18xylR (b3569)3.55E-040.99904944.52E-060.99997531.92-5.11112gadW (b3515)2.41E-050.99986871.06E-040.999733.71-4.63131recC (b2822)2.98E-050.99984621.08E-070.99999851.78-4.62yidE (b3685)1.72E-040.9994422.31E-060.99998511.82-4.36yheF (b3325)2.72E-040.9992171.57E-050.99993662.01-4.36B2866 (b2866)5.29E-060.9999579.06E-070.99999272.10-4.03appC (b0978)4.83E-090.99999987.60E-070.99999363.50-4.01speC (b2965)2.86E-040.99918852.02E-060.99998661.68-2.97glgA (b3429)1.74E-040.99943715.85E-060.999971.85-2.90yhhJ (b3485)3.34E-040.999098.61E-050.99976922.26-2.79narY (b1467)3.93E-050.99981181.23E-050.99994722.39-2.72recB (b2820)9.51E-060.99993371.79E-060.99998781.97-2.68yjiE (b4327)1.32E-040.99954181.13E-070.99999851.53-2.65glnE (b3053)5.30E-050.99976542.60E-060.99998381.80-2.55degQ (b3234)4.54E-040.99885981.20E-040.99970382.10-2.47nanT (b3224)7.22E-050.99970531.01E-050.99995461.87-2.46appB (b0979)3.31E-090.99999982.48E-050.99991019.26-2.43rhaA (b3903)1.48E-040.99949993.29E-060.99998061.67-2.41cdh (b3918)4.00E-040.99896083.09E-040.99939152.42-2.28hycD (b2722)1.50E-050.99990732.65E-050.99990552.40-2.2155rarD (b3819)3.61E-040.9990367.45E-050.99979321.99-2.19395ydbA_2 (b1405)9.98E-080.99999771.83E-060.99998762.33-2.9495hdeA (b3510)4.82E-090.99999981.76E-040.999602540.69-2.83hyaB (b0973)7.30E-080.99999822.57E-040.99947094.50-2.83tdh (b3616)3.20E-050.99983816.46E-050.99981441.92-2.62uraA (b2497)7.91E-050.99968481.14E-040.9997151.97-2.60yjcS (b4083)9.51E-050.99963913.36E-050.9998871.72-2.58tynA (b1386)1.73E-040.99943872.02E-040.99955851.82-2.52yhdR (b3246)2.96E-040.99916741.30E-040.99968461.69-2.42yphB (b2544)2.71E-040.999222.88E-040.99942241.86-2.38glgC (b3430)4.69E-040.99883275.35E-050.99983911.45-2.15yhgF (b3407)3.41E-040.99907621.65E-040.99962111.50-2.10a Distance is upstream from the start codon of the gene or the first gene of the operon (if internal). Sites are predicted from the gene promoter. Other putative ArcA-binding sites may also be predicted upstream of a secondary promoter, but are not mentioned here Open table in a new tab Table IIIRegulatory pattern III: genes that exhibit decreased levels during anaerobic growth that are unaffected in an ArcA-deficient strainGene name (NIH) and b no.p value (+O2, +arcA vs. -O2, +arcA)PPDE(<p) (-O2, +arcA vs. -O2, -arcA)p value (-O2, +arcA vs. -O2, -arcA)PPDE(<p) (-O2, +arcA vs. -O2, -arcA)-Fold (+O2, +arcA vs. -O2, +arcA)-Fold (-O2, +arcA vs. -O2, -arcA)Predicted ArcA siteaDistance is upstream from the start codon of the gene or the first gene of the operon (if internal). Sites are predicted from the gene promoter. Other putative ArcA-binding sites may also be predicted upstream of a secondary promoter, but are not mentioned hereylcB (b0572)4.14E-1016.21E-010.7667727-8.171.15eaeH (b0297)4.12E-040.99893774.30E-010.8257776-2.33-1." @default.
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• W1987005877 date "2005-04-01" @default.
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• W1987005877 title "Global Gene Expression Profiling in Escherichia coli K12" @default.
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• W1987005877 doi "https://doi.org/10.1074/jbc.m414030200" @default.
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