Genomes and Genes
Gene Symbol: cydA
Description: cytochrome d terminal oxidase, subunit I
Alias: ECK0721, JW0722
Species: Escherichia coli str. K-12 substr. MG1655
- 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. ..
- Calhoun M, Newton G, Gennis R. E. coli map. Physical map locations of genes encoding components of the aerobic respiratory chain of Escherichia coli. J Bacteriol. 1991;173:1569-70 pubmed
- Kita K, Konishi K, Anraku Y. Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. Methods Enzymol. 1986;126:94-113 pubmed..Thus, E. coli cells can maintain efficient oxidative energy conservation over a wide range of oxygen pressures by simply changing the contents of the two terminal oxidases, each of which functions as a coupling site. ..
- 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..In contrast, expression of the aerobic pathway operons, cyoA-lacZ and cydA-lacZ, was elevated modestly...
- 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..coli plasma membrane. We hypothesize that respiration occurs in mobile membrane patches which we call 'respirazones'. ..
- Belevich I, Borisov V, Zhang J, Yang K, Konstantinov A, Gennis R, et al. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc Natl Acad Sci U S A. 2005;102:3657-62 pubmed..Presumably, E445 is one of the two redox-linked ionizable groups required for charge compensation of the di-heme oxygen-reducing site (b(595), d) upon its full reduction by two electrons. ..
- Portnoy V, Scott D, Lewis N, Tarasova Y, Osterman A, Palsson B. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl Environ Microbiol. 2010;76:6529-40 pubmed publisher..Flux and transcriptomics data were highly correlated and showed similar patterns. ..
- 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..Consistent with this interpretation, the presence of the cyo gene on a multicopy plasmid suppressed the Ts- and hydrogen peroxide-sensitive phenotypes of cyd mutants. ..
- Hoeser J, Hong S, Gehmann G, Gennis R, Friedrich T. Subunit CydX of Escherichia coli cytochrome bd ubiquinol oxidase is essential for assembly and stability of the di-heme active site. FEBS Lett. 2014;588:1537-41 pubmed publisher..The enzyme complex consists of subunits CydA and B and contains two b- and one d-type hemes as cofactors...
- Newton G, Gennis R. In vivo assembly of the cytochrome d terminal oxidase complex of Escherichia coli from genes encoding the two subunits expressed on separate plasmids. Biochim Biophys Acta. 1991;1089:8-12 pubmed..It was also shown that under heme-deficient conditions, the two polypeptide subunits are expressed and are associated with the cytoplasmic 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. ..
- 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. ..
- 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. ..
- 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
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- Borisov V, Belevich I, Bloch D, Mogi T, Verkhovsky M. Glutamate 107 in subunit I of cytochrome bd from Escherichia coli is part of a transmembrane intraprotein pathway conducting protons from the cytoplasm to the heme b595/heme d active site. Biochemistry. 2008;47:7907-14 pubmed publisher..Here we propose that E107 is either the second group or a key residue of a proposed proton delivery pathway leading from the cytoplasm toward this second group. ..
- 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. ..
- 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. ..
- Kaysser T, Ghaim J, Georgiou C, Gennis R. Methionine-393 is an axial ligand of the heme b558 component of the cytochrome bd ubiquinol oxidase from Escherichia coli. Biochemistry. 1995;34:13491-501 pubmed..The results are consistent with recent cryogenic near-infrared magnetic circular dichroism spectra that also indicate histidine-methionine ligation of heme b558. ..
- Portnoy V, Herrgard M, Palsson B. Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Appl Environ Microbiol. 2008;74:7561-9 pubmed publisher..E. coli strains produced in this study showed the ability to produce lactate as a fermentation product from glucose and to undergo mixed-acid fermentation during aerobic growth. ..
- 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..This increase in expression of 4P(cydA-lacZ) by H2O2 was further enhanced in a cyo::kan mutant...
- 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. ..
- Schembri M, Kjaergaard K, Klemm P. Global gene expression in Escherichia coli biofilms. Mol Microbiol. 2003;48:253-67 pubmed
- Borisov V, Forte E, Sarti P, Brunori M, Konstantinov A, Giuffrè A. Redox control of fast ligand dissociation from Escherichia coli cytochrome bd. Biochem Biophys Res Commun. 2007;355:97-102 pubmed..As NO, an inhibitor of respiratory oxidases, is involved in the immune response against microbial infection, the rapid dissociation of NO from cytochrome bd may have important bearings on the patho-physiology of enterobacteria. ..
- 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. ..
- 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 ...
- 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..resulted in a 140-fold repression of cyoA'-'lacZ expression relative to aerobic growth and a 3-fold increase in cydA'-'lacZ expression...
- 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..Both nalidixic acid and novobiocin reduce cydA-lacZ expression in a concentration-dependent manner...
- 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 ..
- 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. ..
- 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. ..
- 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...
- Fu H, Iuchi S, Lin E. The requirement of ArcA and Fnr for peak expression of the cyd operon in Escherichia coli under microaerobic conditions. Mol Gen Genet. 1991;226:209-13 pubmed..It thus appears that the expression of the phi(cyd-lac) operon is under dual control by the two pleiotropic activators, ArcA and Fnr, which interact to give the peak microaerobic expression. ..
- 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. ..
- Kabir M, Shimizu K. Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements. Appl Microbiol Biotechnol. 2004;65:84-96 pubmed..activity significantly affected the respiratory system and electron transport chain, as evidenced by the significant downregulation of proteins encoded by the genes nuoE, nuoH, cydA and cyoA in icd mutant E. coli compared to the parent.
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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, 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. ..
- 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..P1 and P2, were identified by primer extension analysis and are located 288 and 173 bp upstream of the start of cydA translation respectively...
- 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. ..
- Jasaitis A, Borisov V, Belevich N, Morgan J, Konstantinov A, Verkhovsky M. Electrogenic reactions of cytochrome bd. Biochemistry. 2000;39:13800-9 pubmed
- Helling R. Speed versus efficiency in microbial growth and the role of parallel pathways. J Bacteriol. 2002;184:1041-5 pubmed
- 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. ..
- Strauss B, Kelly K, Ekiert D. Cytochrome oxidase deficiency protects Escherichia coli from cell death but not from filamentation due to thymine deficiency or DNA polymerase inactivation. J Bacteriol. 2005;187:2827-35 pubmed..mutants (dnaE) are protected from cell death on incubation at nonpermissive temperature by mutation in the cydA gene controlling cytochrome bd oxidase...
- 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..coli can compensate for the loss of cytochrome bd-I activity; cytochrome bd-II-mediated quinol oxidation prevents the accumulation of NADH, whereas GABA synthesis/antiport maintains the proton motive force for ATP production. ..
- Miller M, Gennis R. Purification and reconstitution of the cytochrome d terminal oxidase complex from Escherichia coli. Methods Enzymol. 1986;126:87-94 pubmed
- 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. ..
- 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 ..
- 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
- 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
- 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. ..
- 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. ..
- 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. ..