Genomes and Genes
Gene Symbol: cydB
Description: cytochrome d terminal oxidase, subunit II
Alias: ECK0722, JW0723
Species: Escherichia coli str. K-12 substr. MG1655
- Shepherd M, Achard M, Idris A, Totsika M, Phan M, Peters K, et al. The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection. Sci Rep. 2016;6:35285 pubmed publisher..This respiratory complex is therefore of major importance for the accumulation of high bacterial loads during infection of the urinary tract. ..
- Oden K, Gennis R. Isolation and characterization of a new class of cytochrome d terminal oxidase mutants of Escherichia coli. J Bacteriol. 1991;173:6174-83 pubmed..It is proposed that the N terminus of subunit II may interact with subunit I to form an interface that binds the b595 and d heme centers. ..
- Mason M, Shepherd M, Nicholls P, Dobbin P, Dodsworth K, Poole R, et al. Cytochrome bd confers nitric oxide resistance to Escherichia coli. Nat Chem Biol. 2009;5:94-6 pubmed publisher..coli cells from NO-induced growth inhibition by virtue of its fast NO dissociation rate. ..
- Cotter P, Gunsalus R. Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli. FEMS Microbiol Lett. 1992;70:31-6 pubmed..coli. Additionally, the expression of the fnr regulatory gene, and regulation of the anaerobic respiratory genes, narGHJI, dmsABC and frdABCD, was found to be independent of ArcA. ..
- Kobayashi K, Tagawa S, Mogi T. Electron transfer process in cytochrome bd-type ubiquinol oxidase from Escherichia coli revealed by pulse radiolysis. Biochemistry. 1999;38:5913-7 pubmed..The following intramolecular electron transfer transformed the ferric and oxoferryl forms of heme d to the ferrous and ferric forms, respectively, with the first-order rate constants of 3.4 x 10(3) and 5.9 x 10(2) s-1, respectively. ..
- Oden K, DeVeaux L, Vibat C, Cronan J, Gennis R. Genomic replacement in Escherichia coli K-12 using covalently closed circular plasmid DNA. Gene. 1990;96:29-36 pubmed..It is reported that such mutants may be constructed without linearizing plasmid DNA, as described previously. ..
- Alexeeva S, Hellingwerf K, Teixeira De Mattos M. Quantitative assessment of oxygen availability: perceived aerobiosis and its effect on flux distribution in the respiratory chain of Escherichia coli. J Bacteriol. 2002;184:1402-6 pubmed..coli (and specifically its respiratory activity) are affected by the actual oxygen availability per unit of biomass rather than by the residual dissolved oxygen concentration of the culture. ..
- Delaney J, Wall D, Georgopoulos C. Molecular characterization of the Escherichia coli htrD gene: cloning, sequence, regulation, and involvement with cytochrome d oxidase. J Bacteriol. 1993;175:166-75 pubmed..In agreement with this conclusion, htrD mutant bacteria are unable to oxidize the cytochrome d-specific electron donor N,N,N',N'-tetramethyl-p-phenylenediamine...
- Lindqvist A, Membrillo Hernandez J, Poole R, Cook G. Roles of respiratory oxidases in protecting Escherichia coli K12 from oxidative stress. Antonie Van Leeuwenhoek. 2000;78:23-31 pubmed..Whether the effect of RpoS is direct or indirect remains to be determined. ..
- Delaney J, Georgopoulos C. Physical map locations of the trxB, htrD, cydC, and cydD genes of Escherichia coli. J Bacteriol. 1992;174:3824-5 pubmed
- Delaney J, Ang D, Georgopoulos C. Isolation and characterization of the Escherichia coli htrD gene, whose product is required for growth at high temperatures. J Bacteriol. 1992;174:1240-7 pubmed..coli. ..
- Bloch D, Borisov V, Mogi T, Verkhovsky M. Heme/heme redox interaction and resolution of individual optical absorption spectra of the hemes in cytochrome bd from Escherichia coli. Biochim Biophys Acta. 2009;1787:1246-53 pubmed publisher..The spectral contribution of heme d to the complex Soret band is much smaller than those of either hemes b; the Soret/alpha (DeltaA(430):DeltaA(629)) ratio for heme d is 1.6. ..
- Alexeeva S, de Kort B, Sawers G, Hellingwerf K, de Mattos M. Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli. J Bacteriol. 2000;182:4934-40 pubmed
- Jünemann S. Cytochrome bd terminal oxidase. Biochim Biophys Acta. 1997;1321:107-27 pubmed
- Govantes F, Orjalo A, Gunsalus R. Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon. Mol Microbiol. 2000;38:1061-73 pubmed..This allows peak gene expression and subsequent repression by Fnr under fully anaerobic conditions. ..
- Mogi T, Ui H, Shiomi K, Omura S, Kita K. Gramicidin S identified as a potent inhibitor for cytochrome bd-type quinol oxidase. FEBS Lett. 2008;582:2299-302 pubmed publisher..Our findings would provide a new insight into the development of gramicidin S analogs, which do not share the target and mechanism with conventional antibiotics. ..
- Green G, Lorence R, Gennis R. Specific overproduction and purification of the cytochrome b558 component of the cytochrome d complex from Escherichia coli. Biochemistry. 1986;25:2309-14 pubmed..The mutation on pNG10 that eliminates subunit II was mapped to a 250 base pair DNA fragment. ..
- Mogi T, Endou S, Akimoto S, Morimoto Tadokoro M, Miyoshi H. Glutamates 99 and 107 in transmembrane helix III of subunit I of cytochrome bd are critical for binding of the heme b595-d binuclear center and enzyme activity. Biochemistry. 2006;45:15785-92 pubmed..On the basis of this study and previous studies, we propose arrangement of transmembrane helices in subunit I, which may explain possible roles of conserved hydrophilic residues within the membrane. ..
- Mogi T. Probing the haem d-binding site in cytochrome bd quinol oxidase by site-directed mutagenesis. J Biochem. 2009;145:763-70 pubmed publisher..4 mM of the wild-type. Blue shifts in the alpha peak of I98F suggest that Ile98 is in the vicinity of the haem d-binding site. Our data are consistent with the proposal that Glu99 serves as a haem d ligand of cytochrome bd. ..
- Green G, Kranz J, Gennis R. Cloning the cyd gene locus coding for the cytochrome d complex of Escherichia coli. Gene. 1984;32:99-106 pubmed..Colonies of E. coli bearing the cloned cyd gene are yellow-green. The cyd gene can, therefore, be used as a vehicle for detection of inserted DNA fragments. ..
- Dueweke T, Gennis R. Epitopes of monoclonal antibodies which inhibit ubiquinol oxidase activity of Escherichia coli cytochrome d complex localize functional domain. J Biol Chem. 1990;265:4273-7 pubmed..Together, these data begin to define a functional domain in which ubiquinol is oxidized near the periplasmic surface of the membrane. ..
- Fang H, Lin R, Gennis R. Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis. J Biol Chem. 1989;264:8026-32 pubmed..A minimum of two additional axial ligands must be residues other than histidine. ..
- Lenn T, Leake M, Mullineaux C. Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo. Mol Microbiol. 2008;70:1397-407 pubmed publisher..We set out to visualize the distribution and dynamics of this complex in vivo. By exchanging cydB for cydB-gfpgcn4 on the E...
- Wall D, Delaney J, Fayet O, Lipinska B, Yamamoto T, Georgopoulos C. arc-dependent thermal regulation and extragenic suppression of the Escherichia coli cytochrome d operon. J Bacteriol. 1992;174:6554-62 pubmed..Mapping, molecular cloning, and DNA sequencing analyses showed that the mini-Tn10 insertion resides in the cydB gene, the distal gene of the cydAB operon (cytochrome d)...
- Cotter P, Darie S, Gunsalus R. The effect of iron limitation on expression of the aerobic and anaerobic electron transport pathway genes in Escherichia coli. FEMS Microbiol Lett. 1992;100:227-32 pubmed..The above findings suggest that in addition to Fur, some other cellular protein may bind iron for reporting and regulating iron-dependent cell functions. ..
- Goldman B, Gabbert K, Kranz R. The temperature-sensitive growth and survival phenotypes of Escherichia coli cydDC and cydAB strains are due to deficiencies in cytochrome bd and are corrected by exogenous catalase and reducing agents. J Bacteriol. 1996;178:6348-51 pubmed..We propose that the temperature sensitive growth phenotypes are due to a buildup of diffusible oxygen radicals brought on by the absence of cytochrome bd...
- Muller M, Webster R. Characterization of the tol-pal and cyd region of Escherichia coli K-12: transcript analysis and identification of two new proteins encoded by the cyd operon. J Bacteriol. 1997;179:2077-80 pubmed..The cyd transcript contains cydA cydB followed by two open reading frames: orfC, encoding a 37-residue peptide, and orfD, encoding a 97-residue peptide...
- Newton G, Yun C, Gennis R. Analysis of the topology of the cytochrome d terminal oxidase complex of Escherichia coli by alkaline phosphatase fusions. Mol Microbiol. 1991;5:2511-8 pubmed..Data from these fusions, in combination with information from other studies, provide the basis for two-dimensional models for each of the two subunits, defining the way in which the subunits fold in the inner membrane of E. coli. ..
- Cook G, Loder C, Søballe B, Stafford G, Membrillo Hernandez J, Poole R. A factor produced by Escherichia coli K-12 inhibits the growth of E. coli mutants defective in the cytochrome bd quinol oxidase complex: enterochelin rediscovered. Microbiology. 1998;144 ( Pt 12):3297-308 pubmed..Cyd- mutants overproduce siderophores, presumably reflecting intracellular iron deprivation. ..
- Miller M, Gennis R. The cytochrome d complex is a coupling site in the aerobic respiratory chain of Escherichia coli. J Biol Chem. 1985;260:14003-8 pubmed..Hence, scalar chemistry would yield H+/O = 2 and an electrogenic reaction by virtue of the transmembrane electron transfer between the proposed active sites. ..
- Green G, Kranz R, Lorence R, Gennis R. Identification of subunit I as the cytochrome b558 component of the cytochrome d terminal oxidase complex of Escherichia coli. J Biol Chem. 1984;259:7994-7 pubmed..Two classes of mutants which map to the cyd locus were obtained, cydA and cydB ...
- Bogachev A, Murtazine R, Shestopalov A, Skulachev V. Induction of the Escherichia coli cytochrome d by low delta mu H+ and by sodium ions. Eur J Biochem. 1995;232:304-8 pubmed..It is assumed that in the control of the cytochrome d synthesis, the Arc system is involved in the delta mu H+ sensing whereas sensing of delta mu Na+ (or of the Na+ concentration) is mediated by some other receptor system. ..
- Bebbington K, Williams H. A role for DNA supercoiling in the regulation of the cytochrome bd oxidase of Escherichia coli. Microbiology. 2001;147:591-8 pubmed..In conclusion, the authors have shown that changes in DNA supercoiling play a role in the induction of cydAB expression and may provide a general way of increasing cytochrome bd levels in the cell in response to environmental stress. ..
- Cotter P, Chepuri V, Gennis R, Gunsalus R. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol. 1990;172:6333-8 pubmed..We also examined cyoABCDE and cydAB expression in response to growth on alternative carbon compounds and to changes in the culture medium pH and osmolarity. ..
- Alvarez A, Malpica R, Contreras M, Escamilla E, Georgellis D. Cytochrome d but not cytochrome o rescues the toluidine blue growth sensitivity of arc mutants of Escherichia coli. J Bacteriol. 2010;192:391-9 pubmed publisher..Finally, a mechanism for TBO sensitivity and resistance is discussed. ..
- Georgiou C, Dueweke T, Gennis R. Beta-galactosidase gene fusions as probes for the cytoplasmic regions of subunits I and II of the membrane-bound cytochrome d terminal oxidase from Escherichia coli. J Biol Chem. 1988;263:13130-7 pubmed..These identified four cytoplasmic-facing regions within subunit II, consistent with its hydropathy profile showing eight transmembrane helices. The data with subunit I are less conclusive. ..
- Hill J, Alben J, Gennis R. Spectroscopic evidence for a heme-heme binuclear center in the cytochrome bd ubiquinol oxidase from Escherichia coli. Proc Natl Acad Sci U S A. 1993;90:5863-7 pubmed..This is analogous to the heme alpha 3-Cu(B) binuclear center in the heme-Cu oxidases. Heme b595 may play roles analogous to those proposed for the Cu(B) component of cytochrome c oxidase. ..
- Matsumoto Y, Murai M, Fujita D, Sakamoto K, Miyoshi H, Yoshida M, et al. Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli. J Biol Chem. 2006;281:1905-12 pubmed
- Matsumoto Y, Muneyuki E, Fujita D, Sakamoto K, Miyoshi H, Yoshida M, et al. Kinetic mechanism of quinol oxidation by cytochrome bd studied with ubiquinone-2 analogs. J Biochem. 2006;139:779-88 pubmed..These results indicate that the mechanism for the substrate oxidation by cytochrome bd is different from that of the heme-copper terminal quinol oxidase and is tightly coupled to dioxygen reduction chemistry. ..
- Zhang J, Barquera B, Gennis R. Gene fusions with beta-lactamase show that subunit I of the cytochrome bd quinol oxidase from E. coli has nine transmembrane helices with the O2 reactive site near the periplasmic surface. FEBS Lett. 2004;561:58-62 pubmed..The enzyme contains two subunits, CydA and CydB, which were initially predicted based on the sequence of the Escherichia coli oxidase to have seven and eight ..
- Govantes F, Albrecht J, Gunsalus R. Oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon: roles of multiple promoters and the Fnr-1 and Fnr-2 binding sites. Mol Microbiol. 2000;37:1456-69 pubmed..In conclusion, transcription of the cydAB operon is driven by a complex regulatory element containing at least five promoters that act in unison to provide adequate oxygen control of gene expression. ..
- Peercy B, Cox S, Shalel Levanon S, San K, Bennett G. A kinetic model of oxygen regulation of cytochrome production in Escherichia coli. J Theor Biol. 2006;242:547-63 pubmed..Toward this end we build and analyse a mathematical model that captures the role played by oxygen in the regulation of cytochrome production in E. coli. ..
- D Mello R, Hill S, Poole R. The cytochrome bd quinol oxidase in Escherichia coli has an extremely high oxygen affinity and two oxygen-binding haems: implications for regulation of activity in vivo by oxygen inhibition. Microbiology. 1996;142 ( Pt 4):755-63 pubmed
- Shepherd M, Sanguinetti G, Cook G, Poole R. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J Biol Chem. 2010;285:18464-72 pubmed publisher..A cydB mutant strain exhibited lower respiration rates while maintaining a wild type growth rate...
- Tseng C, Albrecht J, Gunsalus R. Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli. J Bacteriol. 1996;178:1094-8 pubmed..These two transcriptional regulators coordinate the hierarchial control of respiratory pathway gene expression in E. coli to ensure the optimal use of oxygen in the cell environment. ..
- Jasaitis A, Borisov V, Belevich N, Morgan J, Konstantinov A, Verkhovsky M. Electrogenic reactions of cytochrome bd. Biochemistry. 2000;39:13800-9 pubmed
- Miller M, Gennis R. Purification and reconstitution of the cytochrome d terminal oxidase complex from Escherichia coli. Methods Enzymol. 1986;126:87-94 pubmed
- Mogi T. Effects of replacement of low-spin haem b by haem O on Escherichia coli cytochromes bo and bd quinol oxidases. J Biochem. 2009;145:599-607 pubmed publisher..Our observations suggest that haem B is required at the low-spin haem site for the oxidation of quinols by cytochromes bo and bd. ..
- Cotter P, Melville S, Albrecht J, Gunsalus R. Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol Microbiol. 1997;25:605-15 pubmed..Based on the results of the in vitro and in vivo studies, a working model for ArcA activation and Fnr repression of cydAB transcription is proposed. ..
- Miller M, Hermodson M, Gennis R. The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits. J Biol Chem. 1988;263:5235-40 pubmed..It is concluded that the active enzyme in Triton X-100 is a heterodimer, containing one copy of each subunit. This is likely the structure of the enzyme in the E. coli membrane. ..
- Osborne J, Gennis R. Sequence analysis of cytochrome bd oxidase suggests a revised topology for subunit I. Biochim Biophys Acta. 1999;1410:32-50 pubmed..Phylogenetic analysis of the new sequences of cytochrome bd reveals considerable deviation from the 16sRNA tree, suggesting that a large amount of horizontal gene transfer has occurred in the evolution of cytochrome bd. ..
- Borisov V, Liebl U, Rappaport F, Martin J, Zhang J, Gennis R, et al. Interactions between heme d and heme b595 in quinol oxidase bd from Escherichia coli: a photoselection study using femtosecond spectroscopy. Biochemistry. 2002;41:1654-62 pubmed..In contrast to other known heme proteins, molecular oxygen cannot be photodissociated from the mixed-valence cytochrome bd at all, indicating a unique structural and electronic configuration of the diheme active site in the enzyme. ..
- Miller M, Gennis R. The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain. J Biol Chem. 1983;258:9159-65 pubmed..coli aerobic respiration are accounted for by this single complex. These results suggest that the E. coli aerobic respiratory chain is organized around a relatively small number of cytochrome-containing complexes. ..
- Hao W, Golding G. Asymmetrical evolution of cytochrome bd subunits. J Mol Evol. 2006;62:132-42 pubmed..coli due to their large divergence. Together, the two subunits of cytochrome bd reveal an interesting example of an asymmetric pattern of evolutionary change. ..
- Yang K, Borisov V, Konstantinov A, Gennis R. The fully oxidized form of the cytochrome bd quinol oxidase from E. coli does not participate in the catalytic cycle: direct evidence from rapid kinetics studies. FEBS Lett. 2008;582:3705-9 pubmed publisher..The data support models of the catalytic cycle which do not include the fully oxidized form of the enzyme as an intermediate. ..
- Kita K, Konishi K, Anraku Y. Terminal oxidases of Escherichia coli aerobic respiratory chain. II. Purification and properties of cytochrome b558-d complex from cells grown with limited oxygen and evidence of branched electron-carrying systems. J Biol Chem. 1984;259:3375-81 pubmed..From these and previous results, branched electron-carrying systems of the E. coli respiratory chain are proposed. ..