A Reassessment of the FNR Regulon and Transcriptomic Analysis of the Effects of Nitrate, Nitrite, NarXL, and NarQP as Escherichia coli K12 Adapts from Aerobic to Anaerobic Growth

Molecular Cloning: A Laboratory Manual

Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589

Molecular cloning: A laboratory manual

Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902

The complete genome sequence of Escherichia coli K-12.

Blattner, F., Plunkett, G., Bloch, C., Perna, N., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C., Mayhew, G., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,996

Current Protocols in Molecular Biology

(2018) · Current Protocols in Molecular Biology · doi:10.1002/(issn)1934-3647 · Cited by 1,395

Quinones as the Redox Signal for the Arc Two-Component System of Bacteria

Georgellis, D., Kwon, O., & Lin, E. C. C. (2001) · Science · doi:10.1126/science.1059361 · Cited by 468

Characterization of the ferrous iron uptake system of Escherichia coli

Kammler, M., Schön, C., & Hantke, K. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.19.6212-6219.1993 · Cited by 460

Identification of the CRP regulon using in vitro and in vivo transcriptional profiling

Zheng, D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh908 · Cited by 410

New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress

Poole, R. K., & Hughes, M. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01889.x · Cited by 370

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome 1 1Edited by R. Ebright

Robison, K. E., Manson, A. L., & Church, G. M. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2160 · Cited by 353

The mononuclear molybdenum enzymes

Hille, R., Hall, J., & Basu, P. (2014) · Chemical Reviews · doi:10.1021/cr400443z · Cited by 1,738

Anaerobic Gene Expression in Staphylococcus aureus

Fuchs, S., Pané‐Farré, J., Köhler, C., Hecker, M., & Engelmann, S. (2007) · Journal of Bacteriology · doi:10.1128/jb.00081-07 · Cited by 326

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

van Heeswijk, W. C., Westerhoff, H. V., & Boogerd, F. C. (2013) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00025-13 · Cited by 301

Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks

Ishihama, A. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00227.x · Cited by 248

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Rodionov, D. A. (2007) · Chemical Reviews · doi:10.1021/cr068309+ · Cited by 218

Regulators of bacterial responses to nitric oxide

Spiro, S. (2007) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2006.00061.x · Cited by 208

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

Myers, K. S., Yan, H., Ong, I. M., Chung, D., Liang, K., Tran, F., Keleş, S., Landick, R. C., & Kiley, P. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003565 · Cited by 194

Bacterial Adaptation of Respiration from Oxic to Microoxic and Anoxic Conditions: Redox Control

Bueno, E., Mesa, S., Bedmar, E. J., Richardson, D. J., & Delgado, M. J. (2011) · Antioxidants and Redox Signaling · doi:10.1089/ars.2011.4051 · Cited by 206

Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health

Koch, C. D., Gladwin, M. T., Freeman, B. A., Lundberg, J. O., Weitzberg, E., & Morris, A. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.015 · Cited by 186

Anaerobic adaptation in Pseudomonas aeruginosa : definition of the Anr and Dnr regulons

Trunk, K., Benkert, B., Quäck, N., Münch, R., Scheer, M. P., Garbe, J., Jänsch, L., Trost, M., Wehland, J., Buer, J., et al. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02252.x · Cited by 186

Reprogramming of anaerobic metabolism by the FnrS small RNA

Durand, S., & Storz, G. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07044.x · Cited by 168

The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction

Oberto, J., Nabti, S., Jooste, V., Mignot, H., & Rouvière‐Yaniv, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004367 · Cited by 170

Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products

Förster, A. H., & Gescher, J. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00016 · Cited by 162

EfeUOB (YcdNOB) is a tripartite, acid‐induced and CpxAR‐regulated, low‐pH Fe2+ transporter that is cryptic in Escherichia coli K‐12 but functional in E. coli O157:H7

Cao, J., Woodhall, M. R., Alvarez, J., Cartron, M. L., & Andrews, S. C. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05802.x · Cited by 163

Functional Genomic Studies of Uropathogenic Escherichia coli and Host Urothelial Cells when Intracellular Bacterial Communities Are Assembled

Reigstad, C. S., Hultgren, S. J., & Gordon, J. I. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m611502200 · Cited by 152

Nitrate Sensing and Metabolism Modulate Motility, Biofilm Formation, and Virulence in Pseudomonas aeruginosa

Alst, N. E. V., Picardo, K. F., Iglewski, B. H., & Haidaris, C. G. (2007) · Infection and Immunity · doi:10.1128/iai.00201-07 · Cited by 151

NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility

Partridge, J. D., Bodenmiller, D. M., Humphrys, M. S., & Spiro, S. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06799.x · Cited by 147

FNR Is a Global Regulator of Virulence and Anaerobic Metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s)

Fink, R. C., Evans, M. R., Porwollik, S., Vázquez‐Torres, A., Jones‐Carson, J., Troxell, B., Libby, S. J., McClelland, M., & Hassan, H. M. (2007) · Journal of Bacteriology · doi:10.1128/jb.00726-06 · Cited by 149

Transcription factor distribution in Escherichia coli : studies with FNR protein

Grainger, D. C., Aiba, H., Hurd, D., Browning, D. F., & Busby, S. J. W. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl1023 · Cited by 147

Fe–S proteins that regulate gene expression

Mettert, E. L., & Kiley, P. J. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2014.11.018 · Cited by 148

The NsrR Regulon of Escherichia coli K-12 Includes Genes Encoding the Hybrid Cluster Protein and the Periplasmic, Respiratory Nitrite Reductase

Filenko, N. A., Spiro, S., Browning, D. F., Squire, D. J. P., Overton, T. W., Cole, J. A., & Constantinidou, C. (2007) · Journal of Bacteriology · doi:10.1128/jb.00080-07 · Cited by 143

Nitric Oxide in Chemostat-Cultured Escherichia coli Is Sensed by Fnr and Other Global Regulators: Unaltered Methionine Biosynthesis Indicates Lack of S Nitrosation

Pullan, S. T., Gidley, M. D., Jones, R. A., Barrett, J. A., Stevanin, T. M., Read, R. C., Green, J. D., & Poole, R. K. (2006) · Journal of Bacteriology · doi:10.1128/jb.01354-06 · Cited by 140

Bacterial sRNAs: Regulation in stress

Hoe, C. H., Raabe, C. A., Rozhdestvensky, T. S., & Tang, T. (2013) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2013.04.002 · Cited by 144

Transition of Escherichia coli from Aerobic to Micro-aerobic Conditions Involves Fast and Slow Reacting Regulatory Components

Partridge, J. D., Sanguinetti, G., Dibden, D. P., Roberts, R. E., Poole, R. K., & Green, J. D. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700728200 · Cited by 136

Anaerobic Respiration of Escherichia coli in the Mouse Intestine

Jones, S. A., Gibson, T., Maltby, R., Chowdhury, F. Z., Stewart, V. J., Cohen, P. S., & Conway, T. (2011) · Infection and Immunity · doi:10.1128/iai.05395-11 · Cited by 133

Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria

Kern, M., & Simon, J. (2009) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2008.12.010 · Cited by 128

Nitric Oxide Homeostasis in Salmonella typhimurium

Gilberthorpe, N. J., & Poole, R. K. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m708019200 · Cited by 130

Physiological roles of small RNA molecules

Michaux, C., Verneuil, N., Hartke, A., & Giárd, J.-C. (2014) · Microbiology · doi:10.1099/mic.0.076208-0 · Cited by 128

RpoS regulation of gene expression during exponential growth of Escherichia coli K12

Dong, T., Kirchhof, M. G., & Schellhorn, H. E. (2007) · Molecular Genetics and Genomics · doi:10.1007/s00438-007-0311-4 · Cited by 120

Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

Boysen, A., Møller‐Jensen, J., Kallipolitis, B. H., Valentin‐Hansen, P., & Overgaard, M. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.089755 · Cited by 113

Molybdenum enzymes in bacteria and their maturation

Magalon, A., Fedor, J. G., Walburger, A., & Weiner, J. H. (2011) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2010.12.031 · Cited by 120

Dynamic control of endogenous metabolism with combinatorial logic circuits

Moser, F., Borujeni, A. E., Ghodasara, A., Cameron, E., Park, Y., & Voigt, C. A. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188605 · Cited by 115

Escherichia coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions

Partridge, J. D., Scott, C. S., Tang, Y., Poole, R. K., & Green, J. D. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603450200 · Cited by 121

Reversible cycling between cysteine persulfide-ligated [2Fe-2S] and cysteine-ligated [4Fe-4S] clusters in the FNR regulatory protein

Zhang, B., Crack, J. C., Sowmya, S., Green, J. D., THOMSON, A. J., Brun, N. E. L., & Johnson, M. K. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208787109 · Cited by 109

Prokaryotic genome regulation: A revolutionary paradigm

Ishihama, A. (2012) · Proceedings of the Japan Academy Series B · doi:10.2183/pjab.88.485 · Cited by 108

Enzymology and ecology of the nitrogen cycle

Martínez‐Espinosa, R. M., Cole, J. A., Richardson, D. J., & Watmough, N. J. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390175 · Cited by 106

Iron-containing transcription factors and their roles as sensors

Fleischhacker, A. S., & Kiley, P. J. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.01.006 · Cited by 105

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

Ernst, J., Beg, Q. K., Kay, K. A., Balázsi, G., Oltvai, Z. N., & Bar‐Joseph, Z. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000044 · Cited by 103

Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria

(2016) · Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2016.02.007 · Cited by 100

Widespread Distribution in Pathogenic Bacteria of Di-Iron Proteins That Repair Oxidative and Nitrosative Damage to Iron-Sulfur Centers

Overton, T. W., Justino, M. C., Li, Y., Baptista, J. M., Melo, A. M. P., Cole, J. A., & Saraiva, L. M. (2008) · Journal of Bacteriology · doi:10.1128/jb.01733-07 · Cited by 100

The challenge of constructing, classifying, and representing metabolic pathways

Caspi, R., Dreher, K. A., & Karp, P. D. (2013) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12194 · Cited by 98

The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures of E scherichia coli against nitrosative stress

Wang, J., Vine, C. E., Balasiny, B. K., Rizk, J., Bradley, C. L. M., Tinajero‐Trejo, M., Poole, R. K., Bergaust, L. L., Bakken, L. R., & Cole, J. A. (2016) · Molecular Microbiology · doi:10.1111/mmi.13356 · Cited by 98

Coordinated Regulation of the Neisseria gonorrhoeae-truncated Denitrification Pathway by the Nitric Oxide-sensitive Repressor, NsrR, and Nitrite-insensitive NarQ-NarP

Overton, T. W., Whitehead, R. N., Li, Y., Snyder, L. A. S., Saunders, N. J. S. G., Smith, H. C., & Cole, J. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m607056200 · Cited by 93

Role of the ArcAB two-component system in the resistance of Escherichia colito reactive oxygen stress

Loui, C., Chang, A. C., & Lu, S. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-183 · Cited by 92

Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria

Durand, S., & Guillier, M. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.667758 · Cited by 91

Bacterial Iron–Sulfur Regulatory Proteins As Biological Sensor-Switches

Crack, J. C., Green, J. D., Hutchings, M. I., THOMSON, A. J., & Brun, N. E. L. (2012) · Antioxidants and Redox Signaling · doi:10.1089/ars.2012.4511 · Cited by 90

A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS

Merrikh, H., Ferrazzoli, A. E., Bougdour, A., Olivier-Mason, A., & Lovett, S. T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803665106 · Cited by 89

E. Coliand Oxygen: A Motility Transition

Douarche, C., Buguin, A., Salman, H., & Libchaber, A. J. (2009) · Physical Review Letters · doi:10.1103/physrevlett.102.198101 · Cited by 88

Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth

Bekker, M., Kramer, G., Hartog, A. F., Wagner, M. J., de Koster, C. G., Hellingwerf, K. J., & de Mattos, M. J. T. (2007) · Microbiology · doi:10.1099/mic.0.2007/006098-0 · Cited by 88

Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli

Lee, H., Doak, T. G., Popodi, E. M., Foster, P. L., & Tang, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw647 · Cited by 87

Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium

Bergholz, T. M., Wick, L. M., Qi, W., Riordan, J. T., Ouellette, L., & Whittam, T. S. (2007) · BMC Microbiology · doi:10.1186/1471-2180-7-97 · Cited by 86

Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae

Isabella, V. M., & Clark, V. L. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-51 · Cited by 84

Transcript Profiling and Inference of Escherichia coli K-12 ArcA Activity across the Range of Physiologically Relevant Oxygen Concentrations

Rolfe, M. D., Beek, A. T., Graham, A. I., Trotter, E. W., Asif, H. M. S., Sanguinetti, G., de Mattos, J. T., Poole, R. K., & Green, J. D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.211144 · Cited by 82

Physiological Roles of ArcA, Crp, and EtrA and Their Interactive Control on Aerobic and Anaerobic Respiration in Shewanella oneidensis

Gao, H., Wang, X., Yang, Z. K., Chen, J., Liang, Y., Chen, H., Palzkill, T. G., & Zhou, J. Z. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015295 · Cited by 82

Biofilm Formation-Gene Expression Relay System in Escherichia coli : Modulation of σ S -Dependent Gene Expression by the CsgD Regulatory Protein via σ S Protein Stabilization

Gualdi, L., Tagliabue, L., & Landini, P. (2007) · Journal of Bacteriology · doi:10.1128/jb.00900-07 · Cited by 81

Se(VI) Reduction and the Precipitation of Se(0) by the Facultative Bacterium Enterobacter cloacae SLD1a-1 Are Regulated by FNR

Yee, N., Ma, J., Dalia, A. B., Boonfueng, T., & Kobayashi, D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02542-06 · Cited by 80

The NsrR regulon in nitrosative stress resistance of Salmonella enterica serovar Typhimurium

Karlinsey, J. E., Bang, I. S., Becker, L. A., Frawley, E. R., Porwollik, S., Robbins, H. F., Thomas, V. C., Urbano, R., McClelland, M., & Fang, F. C. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08167.x · Cited by 79

The Sulfur Carrier Protein TusA Has a Pleiotropic Role in Escherichia coli That Also Affects Molybdenum Cofactor Biosynthesis*

Dahl, J., Radon, C., Bühning, M., Nimtz, M., Leichert, L. I. O., Denis, Y., Jourlin‐Castelli, C., Iobbi‐Nivol, C., Méjean, V., & Leimkühler, S. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.431569 · Cited by 75

Metabolic Deficiences Revealed in the Biotechnologically Important Model Bacterium Escherichia coli BL21(DE3)

Pinske, C., Bönn, M., Krüger, S., Lindenstrauß, U., & Sawers, R. G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022830 · Cited by 76

Mechanism of [4Fe-4S](Cys)4 Cluster Nitrosylation Is Conserved among NO-responsive Regulators

Crack, J. C., Stapleton, M. R., Green, J. D., THOMSON, A. J., & Brun, N. E. L. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.439901 · Cited by 73

An Introduction to Nitric Oxide Sensing and Response in Bacteria

Stern, A. M., & Zhu, J. (2014) · Advances in applied microbiology · doi:10.1016/b978-0-12-800261-2.00005-0 · Cited by 73

Expression of csp genes in E. coli K-12 in defined rich and defined minimal media during normal growth, and after cold-shock

Czapski, T. R., & Trun, N. J. (2014) · Gene · doi:10.1016/j.gene.2014.06.033 · Cited by 72

Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs

Ðurica-Mitić, S., Göpel, Y., & Görke, B. (2018) · Microbiology Spectrum · doi:10.1128/microbiolspec.rwr-0013-2017 · Cited by 75

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Federowicz, S., Kim, D., Ebrahim, A., Lerman, J. A., Nagarajan, H., Cho, B.-K., Zengler, K., & Palsson, B. Ø. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004264 · Cited by 71

Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons

Beauchene, N. A., Myers, K. S., Chung, D., Park, D. M., Weisnicht, A. M., Keleş, S., & Kiley, P. J. (2015) · mBio · doi:10.1128/mbio.01947-15 · Cited by 69

A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

Dong, Y., Wang, J., Fu, H., Zhou, G., Shi, M., & Gao, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051643 · Cited by 67

Increased Hydrogen Production by Genetic Engineering of Escherichia coli

Fan, Z., Yuan, L., & Chatterjee, R. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004432 · Cited by 67

Contribution of Oxygen-Limiting Conditions to Persistent Infection of Pseudomonas Aeruginosa

Schobert, M., & Tielen, P. (2010) · Future Microbiology · doi:10.2217/fmb.10.16 · Cited by 70

Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures

Kumar, R., & Shimizu, K. (2011) · Microbial Cell Factories · doi:10.1186/1475-2859-10-3 · Cited by 66

Reconstruction of the Core and Extended Regulons of Global Transcription Factors

Dufour, Y. S., Kiley, P. J., & Donohue, T. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001027 · Cited by 65

Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli

Bettenbrock, K., Bai, H., Ederer, M., Green, J. D., Hellingwerf, K. J., Holcombe, M., Kunz, S., Rolfe, M. D., Sanguinetti, G., Sawodny, O., et al. (2014) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/b978-0-12-800143-1.00002-6 · Cited by 62

Nitrate-responsive NarX-NarL represses arginine-mediated induction of the Pseudomonas aeruginosa arginine fermentation arcDABC operon

Benkert, B., Quäck, N., Schreiber, K., Jaensch, L., Jahn, D., & Schobert, M. (2008) · Microbiology · doi:10.1099/mic.0.2008/018929-0 · Cited by 62

Unresolved sources, sinks, and pathways for the recovery of enteric bacteria from nitrosative stress

Vine, C. E., & Cole, J. A. (2011) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2011.02425.x · Cited by 58

Biochemical, Spectroscopic, and Thermodynamic Properties of Flavodiiron Proteins

Vicente, J. B., Justino, M. C., Gonçalves, V. L., Saraiva, L. M., & Teixeira, M. S. (2008) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(07)37002-x · Cited by 57

Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions

Shimizu, K. (2015) · Advances in biochemical engineering, biotechnology · doi:10.1007/10_2015_320 · Cited by 54

Tuning the modular Paracoccus denitrificans respirome to adapt from aerobic respiration to anaerobic denitrification

Giannopoulos, G., Sullivan, M. J., Hartop, K. R., Rowley, G., Gates, A. J., Watmough, N. J., & Richardson, D. J. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13974 · Cited by 55

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Lemmens, K., Bie, T. D., Dhollander, T., Keersmaecker, S. C. J. D., Thijs, I. M. V., Schoofs, G., Weerdt, A. D., Moor, B. D., Vanderleyden, J., Collado‐Vides, J., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-3-r27 · Cited by 55

Global responses ofEscherichia colito adverse conditions determined by microarrays and FT-IR spectroscopy

Moen, B., Janbu, A. O., Langsrud, S., Langsrud, Ø., Hobman, J. L., Constantinidou, C., Köhler, A., & Rudi, K. (2009) · Canadian Journal of Microbiology · doi:10.1139/w09-016 · Cited by 52

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes

Sangwan, N., Lambert, C., Sharma, A., Gupta, V., Khurana, P., Khurana, J. P., Sockett, R. E., Gilbert, J. A., & Lal, R. (2015) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12297 · Cited by 50

Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR

Paul, L., Mishra, P. K., Blumenthal, R., & Matthews, R. G. (2007) · BMC Microbiology · doi:10.1186/1471-2180-7-2 · Cited by 50

The Escherichia coli yhjA gene, encoding a predicted cytochrome c peroxidase, is regulated by FNR and OxyR

Partridge, J. D., Poole, R. K., & Green, J. D. (2007) · Microbiology · doi:10.1099/mic.0.2006/004838-0 · Cited by 48

Nitrosative stress in Escherichia coli: reduction of nitric oxide

Vine, C. E., & Cole, J. A. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390213 · Cited by 49

The small FNR regulon of Neisseria gonorrhoeae: comparison with the larger Escherichia coli FNR regulon and interaction with the NarQ-NarP regulon

Whitehead, R. N., Overton, T. W., Snyder, L. A. S., McGowan, S. J., Smith, H. C., Cole, J. A., & Saunders, N. J. S. G. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-35 · Cited by 49

Conditioning of Uropathogenic Escherichia coli for Enhanced Colonization of Host

Bower, J. M., Gordon-Raagas, H. B., & Mulvey, M. A. (2009) · Infection and Immunity · doi:10.1128/iai.01200-08 · Cited by 49

Reassessing the Structure and Function Relationship of the O 2 Sensing Transcription Factor FNR

Mettert, E. L., & Kiley, P. J. (2017) · Antioxidants and Redox Signaling · doi:10.1089/ars.2017.7365 · Cited by 48

Resistance ofHaemophilus influenzaeto Reactive Nitrogen Donors and Gamma Interferon-Stimulated Macrophages Requires the Formate-Dependent Nitrite Reductase Regulator-ActivatedytfEGene

Harrington, J. C., Wong, S. M. S., Rosadini, C. V., Garifulin, O. M., Boyartchuk, V., & Akerley, B. J. (2009) · Infection and Immunity · doi:10.1128/iai.01365-08 · Cited by 47

Respiration of Nitrate and Nitrite

Cole, J. A., & Richardson, D. J. (2008) · EcoSal Plus · doi:10.1128/ecosal.3.2.5 · Cited by 48

Analysis of the Actinobacillus pleuropneumoniae HlyX (FNR) regulon and identification of iron‐regulated protein B as an essential virulence factor

Buettner, F. F. R., Bendalla, I. M., Bossé, J. T., Meens, J., Nash, J. H. E., Härtig, E., Langford, P. R., & Gerlach, G.-F. (2009) · PROTEOMICS · doi:10.1002/pmic.200800439 · Cited by 47

Fur and the Novel Regulator YqjI Control Transcription of the Ferric Reductase Gene yqjH in Escherichia coli

Wang, S., Wu, Y., & Outten, F. W. (2010) · Journal of Bacteriology · doi:10.1128/jb.01062-10 · Cited by 45

Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria

Babujee, L., Apodaca, J., Venkatesh, B., Liss, P., Kiley, P. J., Charkowski, A. O., Glasner, J. D., & Perna, N. T. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-110 · Cited by 45

Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response

Lacey, M. M., Partridge, J. D., & Green, J. D. (2010) · Microbiology · doi:10.1099/mic.0.037887-0 · Cited by 43

Role of the Escherichia coli nitrate transport protein, NarU, in survival during severe nutrient starvation and slow growth

Clegg, S. J., Jia, W., & Cole, J. A. (2006) · Microbiology · doi:10.1099/mic.0.28688-0 · Cited by 43

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

Crack, J. C., Balasiny, B. K., Bennett, S. P., Rolfe, M. D., Froes, A. V. T. D. V., MacMillan, F., Green, J. D., Cole, J. A., & Brun, N. E. L. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.1c12407 · Cited by 42

Efflux pumps mediate changes to fundamental bacterial physiology via membrane potential

Whittle, E. E., Orababa, O. Q., Osgerby, A., Siasat, P., Element, S. J., Blair, J. M. A., & Overton, T. W. (2024) · mBio · doi:10.1128/mbio.02370-24 · Cited by 42

Transcriptional Regulation of the Outer Membrane Porin Gene ompW Reveals its Physiological Role during the Transition from the Aerobic to the Anaerobic Lifestyle of Escherichia coli

Xiao, M., Lai, Y., Sun, J. P., Chen, G., & Yan, A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00799 · Cited by 42

Transcription factor NNR from Paracoccus denitrificans is a sensor of both nitric oxide and oxygen: isolation of nnr* alleles encoding effector-independent proteins and evidence for a haem-based sensing mechanism

Lee, Y.-Y., Shearer, N., & Spiro, S. (2006) · Microbiology · doi:10.1099/mic.0.28796-0 · Cited by 42

Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation

Hobmeier, K., Cantone, M., Nguyen, Q. A., Pflüger‐Grau, K., Kremling, A., Kunte, H., Pfeiffer, F., & Marı́n-Sanguino, A. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.846677 · Cited by 40

Bacterial Energy Metabolism

Ward, B. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-397169-2.00011-1 · Cited by 44

Aerobic TMAO respiration in Escherichia coli

Ansaldi, M., Théraulaz, L., Baraquet, C., Panis, G., & Méjean, V. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05936.x · Cited by 40

Distinct physiological roles for the two l-asparaginase isozymes of Escherichia coli

Srikhanta, Y. N., Atack, J. M., Beacham, I. R., & Jennings, M. P. (2013) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2013.05.066 · Cited by 39

Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology

Overton, T. W., Griffiths, L., Patel, M. D., Hobman, J. L., Penn, C. W., Cole, J. A., & Constantinidou, C. (2006) · Biochemical Society Transactions · doi:10.1042/bst0340104 · Cited by 57

Fnr, NarP, and NarL Regulation of Escherichia coli K-12 napF (Periplasmic Nitrate Reductase) Operon Transcription In Vitro

Darwin, A. J., Ziegelhoffer, E. C., Kiley, P. J., & Stewart, V. J. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.16.4192-4198.1998 · Cited by 68

FNR and its role in oxygen-regulated gene expression in Escherichia coli

Spiro, S., & Guest, J. R. (1990) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1990.tb04109.x · Cited by 416

The small FNR regulon of Neisseria gonorrhoeae: comparison with the larger Escherichia coli FNR regulon and interaction with the NarQ-NarP regulon

Whitehead, R. N., Overton, T. W., Snyder, L. A. S., McGowan, S. J., Smith, H. C., Cole, J. A., & Saunders, N. J. S. G. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-35 · Cited by 49

Regulation of Aerobic-to-Anaerobic Transitions by the FNR Cycle in Escherichia coli

Tolla, D. A., & Savageau, M. A. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.02.015 · Cited by 42