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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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2
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Sakamoto J, Hayakawa A, Uehara T, Noguchi S, Sone N. Cloning of Bacillus stearothermophilus ctaA and heme A synthesis with the CtaA protein produced in Escherichia coli. Biosci Biotechnol Biochem 1999; 63:96-103. [PMID: 10052128 DOI: 10.1271/bbb.63.96] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Bacillus stearothermophilus ctaA gene, which is required for heme A synthesis, was found upstream of the ctaBCDEF/caaEABCD gene cluster as in B. subtilis and B. firmus. The deduced protein sequence indicate that CtaA is a 35-kDa intrinsic membrane protein with seven hydrophobic segments. Alignment of CtaA sequences showed conserved residues including histidines that may be involved in heme B binding and substrate binding. Expression of ctaA in E. coli resulted in increased formation of a membrane-bound b-type cytochrome, heme A production, and severe growth inhibition. Furthermore, B. stearothermophilus CtaA produced in E. coli was found to catalyze the conversion of heme O to heme A in vitro.
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Affiliation(s)
- J Sakamoto
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Fukuoka, Japan.
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3
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Kusano T, Kuge S, Sakamoto J, Noguchi S, Sone N. Nucleotide and amino acid sequences for cytochrome caa3-type oxidase of Bacillus stearothermophilus K1041 and non-Michaelis-type kinetics with cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1273:129-38. [PMID: 8611588 DOI: 10.1016/0005-2728(95)00126-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A pseudo-sigmoidal cytochrome c-dependence curve of oxidase activity was observed with cytochrome oxidase from the Bacillus stearothermophilus strain K1041, while the other thermophilic Bacillus PS3 which has been extensively studied possessed normal Michaelis-Menten type kinetics. The genes coding for four subunits of cytochrome caa3-type oxidase and for heme O synthase were isolated from a genomic DNA library of K1041 by using a PS3 DNA fragment containing the highly-conserved region of the largest subunit as a probe, and sequenced. Most residues in subunits I (COI/caaB product), III (COIII/caaC product), and IV (COIV/caaD product) of K1041 were highly conserved when compared with those of PS3. However, the sequence of K1041 subunit II (COII/caaA product) was distinctly different from that of the PS3 subunit II. These Bacillus COIIs have an additional sequence for cytochrome c after the CuA binding protein portion with two transmembrane segments which is homologous to the mitochondrial counterpart, and represents the site of electron ingress. Several charged residues in the vicinity of cytochrome c moiety are replaced by oppositely charged residues. It is likely that these amino acid replacements in subunit II are the cause of the abnormal sigmoidal saturation curve for extrinsic cytochromes c of the K1041 enzyme.
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Affiliation(s)
- T Kusano
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Japan
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4
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Murai N, Kamata H, Nagashima Y, Yagisawa H, Hirata H. A novel insertion sequence (IS)-like element of the thermophilic bacterium PS3 promotes expression of the alanine carrier protein-encoding gene. Gene 1995; 163:103-7. [PMID: 7557457 DOI: 10.1016/0378-1119(95)00384-i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A novel insertion sequence (IS)-like element was found in the 5'-upstream region of the alanine carrier protein-encoding gene (acp) in the thermophilic bacterium PS3 chromosomal DNA. The sequence contained an open reading frame (ORF) encoding a polypeptide of 369 amino acids which revealed high similarity with ORFs from IS891 from the cyanobacterium Anabaena and IS1136 from Saccharopolyspora erythraea. The direction of transcription was the same as that of acp, and typical inverted and direct repeats characteristic of IS were found in both the 5' and 3' region of the ORF. Southern hybridization analysis of the chromosomal DNA revealed that multiple copies of the ORF sequence were contained in the PS3 genome. This element might well be a member of a new IS family including IS891 and IS1136, and we have designated this element IS1341. The analysis of acp expression in Escherichia coli cells indicated that IS1341 promotes the expression of acp.
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Affiliation(s)
- N Murai
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo, Japan
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5
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Sone N, Sawa G, Sone T, Noguchi S. Thermophilic bacilli have split cytochrome b genes for cytochrome b6 and subunit IV. First cloning of cytochrome b from a gram-positive bacterium (Bacillus stearothermophilus). J Biol Chem 1995; 270:10612-7. [PMID: 7737998 DOI: 10.1074/jbc.270.18.10612] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The genes of Bacillus stearothermophilus K1041 encoding cytochrome b(6) (Bacillus cytochrome b is referred to as cytochrome b(6) for its resemblance to plastid b6) and subunit IV of the quinol:cytochrome c oxidoreductase (bc1 complex) were cloned and sequenced. For preparation of the probe for cloning, polymerase chain reaction was carried out using oligonucleotide mixtures targeting for N-terminal regions of cytochrome bc and subunit IV of the thermophilic Bacillus PS3. The deduced amino acid sequences contained 224 residues of 25,425 daltons for cytochrome b(6) and 173 residues of 19,371 daltons for subunit IV, and both open reading frames were separated by 67 base pairs. Cytochrome b and subunit IV contained 4 and 3 hydrophobic transmembrane segments, respectively, indicating that the fourth segment of subunit IV (eighth segment of cytochrome b) is lacking. Four histidine residues supposed to ligand two protohemes were conserved, but the two His in the fourth segment were separated by 14 amino acid residues like cytochrome b6, not like mitochondrial cytochrome b. The residues that might have conferred the two quinol-binding sites were mostly conserved, but especially the third His residue in the fourth segment of mitochondrial cytochrome b was replaced by Arg in Bacillus cytochrome b6 as in cytochrome b6. These characteristics and quantitative comparison of the protein sequences indicate that this Bacillus sequence is unique and meanwhile rather close to the cyanobacteria-plastids type than the purple bacteria-mitochondria type.
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Affiliation(s)
- N Sone
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Fukuoka-ken, Japan
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6
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García-Horsman JA, Barquera B, Rumbley J, Ma J, Gennis RB. The superfamily of heme-copper respiratory oxidases. J Bacteriol 1994; 176:5587-600. [PMID: 8083153 PMCID: PMC196760 DOI: 10.1128/jb.176.18.5587-5600.1994] [Citation(s) in RCA: 304] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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7
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Wilson TM, Cameron V. Replacement of a conserved glycine residue in subunit II of cytochrome c oxidase interferes with protein function. Curr Genet 1994; 25:233-8. [PMID: 7923409 DOI: 10.1007/bf00357167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this paper we describe the isolation and characterization of a respiration-deficient yeast strain which is defective in the function of subunit II of cytochrome c oxidase. This strain, VC32, carries a mutation in the mitochondrial COX2 gene which converts a conserved glycine residue to arginine. The conserved glycine is in a region implicated as important for ligating the CuA redox center and for interaction with cytochrome c. We have also characterized five revertants of VC32 which have recovered respiratory function; all five were mapped to the mitochondrial genome. In three of the five revertants the wild-type glycine codon is restored, while in two of the five the mutant arginine codon is still present. These two strains are likely to possess alterations either in components of the mitochondrial translation machinery or in mitochondrially-encoded gene products that interact directly with subunit II to assemble an active oxidase complex.
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Affiliation(s)
- T M Wilson
- Biology Department, Ithaca College, NY 14850
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8
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Fujiwara Y, Oka M, Hamamoto T, Sone N. Cytochrome c-551 of the thermophilic bacterium PS3, DNA sequence and analysis of the mature cytochrome. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1144:213-9. [PMID: 7916623 DOI: 10.1016/0005-2728(93)90175-f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structural gene for cytochrome c-551 was isolated from genomic DNA of the thermophilic bacterium PS3. The amino acid sequence of cytochrome c-551 as deduced from the DNA sequence consists of 111 amino acid residues and contains one heme c-binding site (-CASCH-) located approximately in the middle of the polypeptide. The N-terminus of isolated cytochrome c-551 was blocked, but treatment with Rhizopus lipase and molecular weight measurement of the mature and lipase-treated forms by ion spray mass spectroscopy suggest that the mature c-551 may have 93 or 94 amino acid residues with a diacylated glycerol-cysteine at the N-terminal region. The first 17 or 18 amino acid residues in the N-terminal region of the nascent polypeptide, rich in hydrophobic and basic amino acid residues, may be a signal peptide to translocate the major portion of cytochrome c-551 to the extracellular surface and to be processed. Similarity of amino acid sequence of this protein is discussed in relation to other c-type cytochromes of bacilli as well as bacterial small cytochromes c such as Pseudomonas aeruginosa cytochrome c-551 and cytochrome c6 of cyanobacteria.
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Affiliation(s)
- Y Fujiwara
- Department of Biochemistry, Jichi Medical School, Tochigi-ken, Japan
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9
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Fukaya M, Tayama K, Tamaki T, Ebisuya H, Okumura H, Kawamura Y, Horinouchi S, Beppu T. Characterization of a cytochrome a1 that functions as a ubiquinol oxidase in Acetobacter aceti. J Bacteriol 1993; 175:4307-14. [PMID: 8392509 PMCID: PMC204870 DOI: 10.1128/jb.175.14.4307-4314.1993] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The terminal oxidase for ethanol oxidation in Acetobacter aceti was purified as a complex consisting of four subunits (subunits I, II, III, and IV) with molecular masses of 72, 34, 21, and 13 kDa, respectively. Spectrophotometric analysis and catalytic properties determined with the purified enzyme showed that it belonged to a family of cytochrome a1 (ba)-type ubiquinol oxidases. A polymerase chain reaction with two oligonucleotides designed for amino acid sequences that are conserved in subunit I of the aa3-type cytochrome c oxidases from various origins and of an Escherichia coli o (bo)-type ubiquinol oxidase was used for cloning the cytochrome a1 gene. A 0.5-kb fragment thus amplified was used as the probe to clone a 4.5-kb KpnI fragment that contained a putative open reading frame for the whole subunit I gene. The molecular weight and amino acid composition of the product of this open reading frame (cyaA) were the same as those of the purified protein from A. aceti. The amino acid sequence of CyaA was homologous to that of subunit I of the E. coli o-type ubiquinol oxidase. Nucleotide sequence analysis of the region neighboring the cyaA gene revealed that the genes (cyaB, cyaC, and cyaD) encoding the other three subunits (subunits II, III, and IV) were clustered upstream and downstream of the cyaA gene in the order cyaB, cyaA, cyaC, and cyaD and with the same transcription polarity, forming an operon. As expected from the enzymatic properties, CyaB, CyaC, and CyaD showed great similarity in amino acid sequence to the corresponding sununits of the E. coli o-type ubiquinol oxidase and as(3)-type cytochrome c oxidases.
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Affiliation(s)
- M Fukaya
- Nakano Central Research Institute, Nakano Vinegar Co., Ltd., Aichi, Japan
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10
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Kamata H, Akiyama S, Morosawa H, Ohta T, Hamamoto T, Kambe T, Kagawa Y, Hirata H. Primary structure of the alanine carrier protein of thermophilic bacterium PS3. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)36661-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Netter P, Robineau S, Sirand-Pugnet P, Fauvarque MO. The unusual reversion properties of a mitochondrial mutation in the structural gene of subunit I of cytochrome oxidase of Saccharomyces cerevisiae reveal a probable histidine ligand of the redox center. Curr Genet 1992; 21:147-51. [PMID: 1314705 DOI: 10.1007/bf00318474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have analyzed a mutation in the mitochondrial gene oxi3 coding for subunit I of cytochrome-oxidase in the yeast Saccharomyces cerevisiae. This mutation replaces one of the seven invariant histidines of the polypeptide (position 378) by a tyrosine, and leads to a respiratory deficient phenotype. A total of 157 revertants, which have recovered the ability to grow on a respiratory substrate, have been selected from this mutant (tyrosine 378). The nature of the reversion has been analysed by a rapid screening procedure and 32 of the revertants have been sequenced. They are all true back-mutations reintroducing the histidine in position 378. This very exceptional situation suggests that this histidine is a ligand of the redox center of cytochrome oxidase.
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Affiliation(s)
- P Netter
- Centre de Génétique Moléculaire, Laboratoire Propre du C.N.R.S. Associé à l'Université Pierre et Marie Curie, Gif sur Yvette, France
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12
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Tano H, Ishizuka M, Sone N. The cytochrome C oxidase genes in blue-green algae and characteristics of the deduced protein sequence for subunit II of the thermophilic cyanobacterium Synechococcus vulcanus. Biochem Biophys Res Commun 1991; 181:437-42. [PMID: 1659815 DOI: 10.1016/s0006-291x(05)81438-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Blue-green algae (cyanobacteria) contain both primitive photosynthetic and respiratory systems in their membranes. The controversial genes coding for an alpha alpha 3-type cytochrome oxidase in cyanobacteria were examined. The DNA probe coding for the most conserved part of subunit I hybridized with DNA fragments from four cyanobacterial species. We have cloned the genes coding for subunits I and II from the genomic library of the thermophilic cyanobacterium Synechococcus vulcanus and determined the nucleotide sequence of the subunit II gene. The deduced protein sequence (327 amino acid residues) indicates that there are two hydrophobic segments near the N-terminus and a hydrophilic intermembrane domain containing ligands for CuA (the ESR-active Copper) similar to other subunit IIs. The S. vulcanus subunit II does not contain the cytochrome c moiety that is present in bacilli and thermophiles.
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Affiliation(s)
- H Tano
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
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13
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Gennis RB. Some recent advances relating to prokaryotic cytochrome c reductases and cytochrome c oxidases. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1058:21-4. [PMID: 1646011 DOI: 10.1016/s0005-2728(05)80260-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Prokaryotic systems provide excellent experimental opportunities for exploring structure/function relationships for the complex, membrane-bound, multisubunit enzymes responsible for the reduction and subsequent oxidation of c-type cytochromes in respiratory or photosynthetic electron transport chains. Two points are made in this mini-review: (1) The eukaryotic and prokaryotic aa3-type cytochrome c oxidases are members of an apparently large superfamily of structurally related respiratory oxidases. This superfamily displays considerable variation in terms of the heme prosthetic groups (a or b) as well as the substrate oxidized (quinol or cytochrome c). The relationships among these enzymes help to facilitate explorations of how they work. (2) Molecular biology techniques can be used to generate intact, redox-active, water-soluble domains of membrane-bound subunits. These soluble domains can be used for detailed examination, including obtaining high resolution structure by NMR techniques or by X-ray crystallography. This approach is being used to study the soluble heme-binding domain of cytochrome c1 from the bc1 complex of Rhodobacter sphaeroides.
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Affiliation(s)
- R B Gennis
- Department of Biochemistry and Chemistry, University of Illinois, Urbana 61801
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14
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Lightowlers R, Chrzanowska-Lightowlers Z, Marusich M, Capaldi RA. Subunit function in eukaryote cytochrome c oxidase. A mutation in the nuclear-coded subunit IV allows assembly but alters the function and stability of yeast cytochrome c oxidase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89503-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence and analysis of the deduced primary structure of subunit IIc of cytochrome caa3. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67751-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Saraste M, Metso T, Nakari T, Jalli T, Lauraeus M, Van der Oost J. The Bacillus subtilis cytochrome-c oxidase. Variations on a conserved protein theme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 195:517-25. [PMID: 1847686 DOI: 10.1111/j.1432-1033.1991.tb15732.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The structural genes of cytochrome-c oxidase in Bacillus subtilis have been isolated and sequenced. Five genes, ctaB-F, are closely spaced. ctaC, ctaD, ctaE and ctaF are the genes for subunits II, I, III and IVB, respectively, ctaB, which may encode an assembly factor, is separated and upstream from the others. In comparison to its mitochondrial counterparts, subunit I has an extended C-terminus with two additional transmembrane segments, whereas subunit III has lost two such segments from its N-terminus. The C-terminal extension in subunit II is a covalent cytochrome-c domain, previously characterized only in the thermophilic oxidases. Subunit IVB, a small hydrophobic protein, is a novel subunit. These predictions suggest that the B. subtilis cytochrome-c oxidase is structurally more related to the four-subunit Escherichia coli cytochrome-bo complex than, for instance, to the Paracoccus denitrificans enzyme. Cytochrome aa3, which was previously isolated from B. subtilis [de Vrij, W., Azzi, A. & Konings, W. N. (1983) Eur. J. Biochem. 131, 97-103] is not encoded by the ctaC-F genes; thus, there seems to be two different cytochrome-aa3-type oxidases in this Gram-positive bacterium.
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Affiliation(s)
- M Saraste
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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17
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Bott M, Bolliger M, Hennecke H. Genetic analysis of the cytochrome c-aa3 branch of the Bradyrhizobium japonicum respiratory chain. Mol Microbiol 1990; 4:2147-57. [PMID: 1965217 DOI: 10.1111/j.1365-2958.1990.tb00576.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Further genetic evidence is provided here that Bradyrhizobium japonicum possesses a mitochondria-like electron-transport pathway: 2[H]----UQ----bc1----c----aa3----O2. Two Tn5-induced mutants, COX122 and COX132, having cytochrome c oxidase-negative phenotypes, were obtained and characterized. Mutant COX122 was defective in a novel gene, named cycM, which was responsible for the synthesis of a c-type cytochrome with an Mr of 20,000 (20K). This 20K cytochrome c appeared to catalyse electron transport from the cytochrome bc1 complex to the aa3-type terminal oxidase and, unlike mitochondrial cytochrome c, was membrane-bound in B. japonicum. The Tn5 insertion of mutant COX132 was localized in coxA, the structural gene for subunit I of cytochrome aa3. This finding also led to the cloning and sequencing of the corresponding wild-type coxA gene that encoded a 541-amino-acid protein with a predicted Mr of 59,247. The CoxA protein shared about 60% sequence identity with the cytochrome aa3 subunit I of mitochondria. The B. japonicum cycM and coxA mutants were able to fix nitrogen in symbiosis with soybean (Fix+). In contrast, mutants described previously which lacked the bc1 complex did not develop into endosymbiotic bacteroids and were thus Fix-. The data suggest that a symbiosis-specific respiratory chain exists in B. japonicum in which the electrons branch off at the bc1 complex.
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Affiliation(s)
- M Bott
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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18
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Sone N, Takagi T. Monomer-dimer structure of cytochrome-c oxidase and cytochrome bc1 complex from the thermophilic bacterium PS3. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1020:207-12. [PMID: 2173952 DOI: 10.1016/0005-2728(90)90052-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molecular weights of three membrane proteins have been measured in the presence of 0.1% octaethylene glycol n-dodecyl ether (C12E8) by the measuring system in which a membrane protein eluted from a gel chromatography column is monitored sequentially for ultraviolet absorption, light scattering and refractive index. The relative molecular mass (Mr) and amount of bound detergent per protein (delta) can be calculated from these data, if instrumental constants are measured using a set of appropriate water-soluble proteins which does not bind nonionic surfactants. The molecular masses of cytochrome c oxidase and cytochrome bc1 complex from the thermophilic bacterium PS3 were determined to be 127 kDa and 185 kDa, respectively, indicating that the oxidase is monomeric, while the bc1 complex dimeric in the presence of C12E8. The larger apparent molecular mass of about 310 kDa of the PS3 oxidase obtained from the retention time of the gel chromatography (Sone, N., Sekimachi, M. and Kutoh, E. (1987) J. Biol. Chem. 262, 15386-15391) turned out to be due to a high binding ability with the detergent (delta = 1.25 g/g) of this very hydrophobic protein. Analyses of bovine heart cytochrome oxidase, on which monomer/dimer properties have been reported, showed that the enzyme is mainly dimeric (Mr = 374,000), while a small portion is monomeric (Mr = 191,000). Mild alkaline treatment of this enzyme caused monomerization of the enzyme with accompanying aggregate formation. These results, thus, show that this method is suitable to analyze monomer/dimer conversion of membrane protein as well as to estimate structure of membrane proteins.
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Affiliation(s)
- N Sone
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan
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19
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Abstract
This article tries to be a compact summary of some recent research on cytochromecoxidase (EC 1.9.3.1), an important enzyme in membrane bioenergetics. Cytochrome oxidase is the terminal catalyst of the mitochondrial respiratory chain. It uses the electrons flowing through the chain to reduce oxygen molecules to water. Four electrons and four protons are consumed in the reduction of O2to two molecules of water (Fig. 1). Cytochrome oxidase contains four redoxactive metal centres. Two of these are copper atoms, two haem A groups. These four centres are employed in the dioxygen-binding site and in the electron-transferring pathways from cytochromec. The enzyme is also called cytochromeaa3, because the protein-bound haems are functionally and spectroscopically different.
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Affiliation(s)
- M Saraste
- Department of Medical Chemistry, University of Helsinki, Finland
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20
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Azzi A, Müller M. Cytochrome c oxidases: polypeptide composition, role of subunits, and location of active metal centers. Arch Biochem Biophys 1990; 280:242-51. [PMID: 2164354 DOI: 10.1016/0003-9861(90)90326-t] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The general structure of the enzyme, its polypeptide composition, and a proposal for a rational nomenclature are discussed. The mitochondrially coded and bacterial cytochrome c oxidase subunits have been analyzed with more attention focused on elucidating the number of metals present in the enzyme and the ligands available for their coordination. The picture of a 2 Cu/2 Fe enzyme has been compared with that of a 3 Cu/2 Fe enzyme and a new model is proposed for the location of the metal centers in the enzyme.
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Affiliation(s)
- A Azzi
- Institut für Biochemie und Molekularbiologie, Universität Bern, Switzerland
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21
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The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38574-6] [Citation(s) in RCA: 183] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Gai WZ, Sun SM, Sone N, Chan SH. Cytochrome oxidase from thermophilic bacterium PS3 contains a fourth protein subunit. Biochem Biophys Res Commun 1990; 169:414-21. [PMID: 2162664 DOI: 10.1016/0006-291x(90)90347-p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Monoclonal antibodies prepared against subunits II and IV of beef heart cytochrome oxidase were found to cross-react with thermophilic bacterial PS3 oxidase. Each individual antibody affects the enzymatic activity. "Western" blot analyses showed that subunit II antibodies of beef heart recognized subunit II of PS3 and subunit IV antibody likewise recognized a fourth protein subunit on slab gels. This fourth subunit previously thought to be a contaminant or a degradation product has a molecular weight of about 10,500 on SDS-gels, and appears to exist in stoichiometric amount. We have extracted this subunit from slab gels and compared its amino acid composition with that of subunit III.
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Affiliation(s)
- W Z Gai
- Department of Biology, Syracuse University, NY 13244
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23
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Vrij W, Speelmans G, Heyne R, Konings W. Energy transduction and amino acid transport in thermophilic aerobic and fermentative bacteria. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04094.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Sone N, Shimada S, Ohmori T, Souma Y, Gonda M, Ishizuka M. A fourth subunit is present in cytochrome c oxidase from the thermophilic bacterium PS3. FEBS Lett 1990; 262:249-52. [PMID: 2159415 DOI: 10.1016/0014-5793(90)80202-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A new putative subunit was found in cytochrome c oxidase (aa3-type) of the thermophilic bacterium PS3. The N-terminal amino acid sequence of this approximately 12 kDa protein coincides with the deduced sequence of an open reading frame found downstream from the gene encoding subunit I of the PS3 cytochrome oxidase [(1988) J. Biochem. 103, 606-610]. This small hydrophobic protein, composed of 109 amino acid residues after the initial methionine residue has been processed, shows homology with the subunit IV (cyoD product) of cytochrome bo-type quinol oxidase of Escherichia coli.
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Affiliation(s)
- N Sone
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan
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25
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Raitio M, Pispa JM, Metso T, Saraste M. Are there isoenzymes of cytochrome c oxidase in Paracoccus denitrificans? FEBS Lett 1990; 261:431-5. [PMID: 2155830 DOI: 10.1016/0014-5793(90)80609-m] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have used a gene replacement strategy to delete the previously isolated gene [(1987) EMBO J. 6, 2825-2833] for the cytochrome c oxidase subunit I from Paracoccus denitrificans. The resulting mutant was still able to synthesize active cytochrome c oxidase. This led us to look for another locus which could completely suppress the mutation. In this study we report the isolation of a second gene encoding subunit I. An open reading frame coding for cytochrome c 550 was found upstream from this gene. We suggest that there are isoenzymes of cytochrome c oxidase (cytochrome aa3) in this bacterium.
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Affiliation(s)
- M Raitio
- Department of Medical Chemistry, University of Helsinki, Finland
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26
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Affiliation(s)
- S I Chan
- A.A. Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena 91125
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27
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Sone N, Kutoh E, Yanagita Y. Cytochrome c-551 from the thermophilic bacterium PS3 grown under air-limited conditions. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 977:329-34. [PMID: 2556182 DOI: 10.1016/s0005-2728(89)80088-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A small-sized c-type cytochrome, designated cytochrome c-551, was prepared from membrane fraction of the thermophilic bacterium PS3 grown under air-limited conditions by extraction with cholate, precipitation with polyethylene glycol, and successive chromatographies with DEAE-cellulose and Sephacryl S-200 in the presence of a detergent. The purified sample contained approximately 1 mol of heme c per 10,000 g protein; it showed absorption bands at 551, 522 and 416 nm upon reduction, and a Soret peak at 409 nm upon oxidation. This cytochrome showed a single band of 10 kDa on polyacrylamide gel electrophoresis with sodium dodecyl sulfate. The isoelectric point of this cytochrome c-551 was pH 4.0. Cytochrome c-551 was suggested to play an important role in the respiratory chain with a terminal oxidase cytochrome o, which is produced under air-limited conditions, since cytochrome c-551 could mediate electron transfer between cytochrome bc1(b6f) complex and cytochrome o, showing quinol oxidase activity.
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Affiliation(s)
- N Sone
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan
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28
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Mueller JP, Taber HW. Isolation and sequence of ctaA, a gene required for cytochrome aa3 biosynthesis and sporulation in Bacillus subtilis. J Bacteriol 1989; 171:4967-78. [PMID: 2549006 PMCID: PMC210305 DOI: 10.1128/jb.171.9.4967-4978.1989] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cytochrome aa3 is one of two terminal oxidase complexes in the Bacillus subtilis electron transport chain. A novel genetic strategy was devised which permitted the isolation of B. subtilis mutants lacking cytochrome aa3 by selection for streptomycin-resistant clones which failed to oxidize the artificial electron donor N,N,N',N'-tetramethyl-p-phenylenediamine. Two mutations were studied intensively. Spectroscopic examination showed that each mutant lacked cytochrome aa3; they were also asporogenous and unable to grow on lactate as the sole carbon and energy source. These mutations were mapped to a locus designated ctaA, located at 127 degrees between pyrD and metC on the B. subtilis chromosome. Both ctaA mutations were closely linked by transformation to the pycA locus. The ctaA locus and a portion of the pycA locus were cloned from a B. subtilis integration library constructed in Escherichia coli. A recombinant plasmid containing a 4.0-kilobase insert of B. subtilis DNA could transform both ctaA mutants to CtaA+. Gene disruption and complementation experiments with subcloned fragments revealed that the ctaA locus consisted of a single transcriptional unit about 1.35 kilobase pairs in size. The nucleotide sequence of the ctaA transcriptional unit contains a single open reading frame capable of coding for a protein with a predicted molecular weight of 34,065. The predicted protein is extremely hydrophobic, with several probable membrane-spanning domains. No sequence similiarity was found between ctaA and the highly conserved procaryotic and mitochondrial oxidase polypeptides. Cloning and sequence analysis of two ctaA mutations revealed that one allele is a nonsense mutation in the carboxy terminus and the other is a missense mutation in the amino terminus; this indicates that the pleiotropic phenotype conferred by each mutation was caused by loss of CtaA or of its activity. Genetic evidence suggests that the ctaA gene product is required as an accessory protein in the genetic expression, posttranslational biogenesis, or both, of the cytochrome aa3 complex and during an early stage of sporogenesis.
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Affiliation(s)
- J P Mueller
- Department of Microbiology and Immunology, Albany Medical College, New York 12208
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29
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Schiavo G, Bisson R. Oxygen influences the subunit structure of cytochrome c oxidase in the slime mold Dictyostelium discoideum. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83211-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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30
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Degli Esposti M, Mele N, Lenaz G. Structural analogies between different redox enzymes inserted into biological membranes. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:599-608. [PMID: 2551750 DOI: 10.1016/0020-711x(89)90378-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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31
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Saraste M, Raitio M, Jalli T, Chepuri V, Lemieux L, Gennis RB. Cytochrome o from Escherichia coli is structurally related to cytochrome aa3. Ann N Y Acad Sci 1988; 550:314-24. [PMID: 2854403 DOI: 10.1111/j.1749-6632.1988.tb35346.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M Saraste
- Department of Medical Chemistry, University of Helsinki, Finland
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32
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Fee JA, Mather MW, Springer P, Hensel S, Buse G. Isolation and partial sequence of the A-protein gene of Thermus thermophilus cytochrome c1aa3. Ann N Y Acad Sci 1988; 550:33-8. [PMID: 2854405 DOI: 10.1111/j.1749-6632.1988.tb35319.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- J A Fee
- Isotope and Structural Chemistry Group, Los Alamos National Laboratory, New Mexico 87545
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33
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Quinol-cytochrome c oxidoreductase from the thermophilic bacterium PS3. Purification and properties of a cytochrome bc1(b6f) complex. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68410-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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