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Musatov A, Varhač R, Hosler JP, Sedlák E. Delipidation of cytochrome c oxidase from Rhodobacter sphaeroides destabilizes its quaternary structure. Biochimie 2016; 125:23-31. [PMID: 26923069 DOI: 10.1016/j.biochi.2016.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/23/2016] [Indexed: 11/28/2022]
Abstract
Delipidation of detergent-solubilized cytochrome c oxidase isolated from Rhodobacter sphaeroides (Rbs-CcO) has no apparent structural and/or functional effect on the protein, however affects its resistance against thermal or chemical denaturation. Phospholipase A2 (PLA2) hydrolysis of phospholipids that are co-purified with the enzyme removes all but two tightly bound phosphatidylethanolamines. Replacement of the removed phospholipids with nonionic detergent decreases both thermal stability of the enzyme and its resilience against the effect of chemical denaturants such as urea. In contrast to nondelipidated Rbs-CcO, the enzymatic activity of PLA2-treated Rbs-CcO is substantially diminished after exposure to high (>4 M) urea concentration at room temperature without an alteration of its secondary structure. Absorbance spectroscopy and sedimentation velocity experiments revealed a strong correlation between intact tertiary structure of heme regions and quaternary structure, respectively, and the enzymatic activity of the protein. We concluded that phospholipid environment of Rbs-CcO has the protective role for stability of its tertiary and quaternary structures.
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Affiliation(s)
- Andrej Musatov
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia.
| | - Rastislav Varhač
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biochemistry, P.J. Šafárik University, Moyzesova 11, 04001 Košice, Slovakia.
| | - Jonathan P Hosler
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Erik Sedlák
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biochemistry, P.J. Šafárik University, Moyzesova 11, 04001 Košice, Slovakia; Centre for Interdisciplinary Biosciences, P.J. Šafárik University, Jesenná 5, 04001 Košice, Slovakia.
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2
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Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Glavina Del Rio T, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin LA, Han C, Tapia R, Detter JC, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Göker M, Ivanova N, Klenk HP, Woyke T. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)). Stand Genomic Sci 2012; 7:44-58. [PMID: 23450099 PMCID: PMC3570799 DOI: 10.4056/sigs.3006378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order 'Rhizobiales', which is thus far poorly characterized at the genome level. Cultures from this species are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model organism for studying the genomic basis of regulatory networks required for the switch between consumption and production of carbon dioxide, a key component of the global carbon cycle. In addition, S. novella is of interest for its ability to grow on various inorganic sulfur compounds and several C1-compounds such as methanol. Besides Azorhizobium caulinodans, S. novella is only the second species in the family Xanthobacteraceae with a completely sequenced genome of a type strain. The current taxonomic classification of this group is in significant conflict with the 16S rRNA data. The genomic data indicate that the physiological capabilities of the organism might have been underestimated. The 4,765,023 bp long chromosome with its 4,511 protein-coding and 52 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
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Affiliation(s)
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yun-juan Chang
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
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3
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Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Glavina Del Rio T, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin LA, Han C, Tapia R, Detter JC, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Göker M, Ivanova N, Klenk HP, Woyke T. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T). Stand Genomic Sci 2012. [DOI: 10.4056/sogs.3006378] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Karen Davenport
- 2Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Susan Lucas
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Cliff Han
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C. Detter
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yun-juan Chang
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Miriam Land
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Markus Göker
- 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Hans-Peter Klenk
- 5Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- 3DOE Joint Genome Institute, Walnut Creek, California, USA
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Liu X, Zhou B, Mi S, Xue L, Shih J, Lee J, Chau J, Un F, Yen Y. An increase of cytochrome C oxidase mediated disruption of gemcitabine incorporation into DNA in a resistant KB clone. Biochem Pharmacol 2007; 73:1927-38. [PMID: 17428446 PMCID: PMC1950577 DOI: 10.1016/j.bcp.2007.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/14/2007] [Accepted: 03/15/2007] [Indexed: 12/15/2022]
Abstract
Mechanistic aberrations leading to Gemcitabine (2',2'-dFdCyd,2,2-difluorodeoxycytidine, Gem) resistance may include alteration in its transport, metabolism and incorporation into DNA. To explore the mechanism of Gem resistance, the restriction fragment differential display PCR (RFDD-PCR) was employed to compare the mRNA expression patterns of KBGem (Gem resistant), KBHURs (hydroxyurea resistant) and KBwt (parental KB cell). Nine gene fragments were overexpressed specifically in the KBGem clone. Sequencing and BLAST results showed that three fragments represent cytochrome C oxidase (CCOX, respiration complex IV) subunit III (CCOX3). The cDNA microarray confirmed that the mRNAs of CCOX and ATP synthase subunits were upregulated in KBGem as compared to KBwt and KBHURs. The increase in CCOX1 protein and activity led to the increase of free ATP concentration, which is consistent with the gene expression profile of KBGem. Furthermore, the sensitivity to Gem could be reversed by sodium azide, a CCOX inhibitor. Following the treatment of sodium azide, the cellular accumulation of [3H]-Gem increased in a dose (of azide)-dependent manner, which is associated with increase of [3H]-Gem incorporation into DNA in KBGem. In summary, an increase of CCOX activity and free ATP level may reduce the transport, metabolism and DNA incorporation of Gem, resulting in Gem resistance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yun Yen
- Correspondence: Yun Yen, M.D., Ph.D., F.A.C.P., Department of Clinical & Molecular Pharmacology, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA 91010-3000, Phone: (626) 359-8111 ext. 62867, Fax: (626) 301-8233, E-mail:
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Musatov A, Robinson NC. Cholate-induced dimerization of detergent- or phospholipid-solubilized bovine cytochrome C oxidase. Biochemistry 2002; 41:4371-6. [PMID: 11914083 DOI: 10.1021/bi016080g] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bovine heart cytochrome c oxidase (CcO), solubilized by either nonionic detergents or phospholipids, completely dimerizes upon the addition of bile salts, e.g., sodium cholate, sodium deoxycholate, or CHAPS. Bile salt induced dimerization occurs whether dodecyl maltoside, decyl maltoside, or Triton X-100 is the primary solubilizing detergent or the enzyme is dispersed in phosphatidylcholine, phosphatidylethanolamine, or mixtures thereof. In each case, complete CcO dimerization can be verified by sedimentation velocity and sedimentation equilibrium after correction for bound detergent and/or phospholipid. The relative concentration of the bile salt is critical for production of homogeneous, dimeric CcO. For example, enzyme solubilized by 2 mM detergent requires an equal molar concentration of sodium cholate. Similarly, enzyme dispersed in 20 mM phospholipid requires 50 mM sodium cholate, concentrations that are commonly used to reconstitute CcO into small unilamellar vesicles. Bile salts do more than just stabilize dimeric CcO and prevent detergent-induced dissociation into monomers. They are able to completely reverse detergent-induced monomerization and cause completely monomeric CcO to reassociate. Dimeric CcO so generated is no more stable than the original complex and easily dissociates into monomers if the bile salt is removed. The dimerization process is dependent upon a full complement of subunits; e.g., if subunits VIa and VIb are removed, the resulting monomeric CcO will not reassociate upon the addition of sodium cholate. These results support four important consequences: (1) dissociation of dimeric CcO into monomers is reversible; (2) stable dimers can be produced under solution conditions; (3) dimers can be stabilized even at relatively high pH and low enzyme concentration; and (4) subunits VIa and VIb are required for dimerization.
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Affiliation(s)
- Andrej Musatov
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
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Giudici-Orticoni MT, Leroy G, Nitschke W, Bruschi M. Characterization of a new dihemic c(4)-type cytochrome isolated from Thiobacillus ferrooxidans. Biochemistry 2000; 39:7205-11. [PMID: 10852719 DOI: 10.1021/bi992846p] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new soluble c-type cytochrome has been purified to homogeneity from the acidophilic proteobacterium Thiobacillus ferrooxidans BRGM. It is characterized by an alpha-peak wavelength of 552 nm, a molecular mass of 26 567 Da (as determined by mass spectroscopy) and a pI value of 8. Optical redox titrations at pH 4.0 revealed the presence of two distinguishable redox species with an E(m) of 510 mV and an E(m) of 430 +/- 20 mV. EPR spectra recorded for this heme protein demonstrated the presence of stoichiometric amounts of two low-spin hemes with a g(z)() of 3.08 (510 mV species) and a g(z)() of 3.22 (430 mV species). Modifications of the physicochemical properties of the cytochrome were observed on complex formation with the blue copper protein rusticyanin, another soluble electron carrier in the genus Thiobacillus. N-Terminal sequencing yielded the polypeptide sequence up to the 50th residue. The determined sequence was found to be present (at 100% amino acid identity) in the (unfinished) genome of T. ferrooxidans ATCC 23270, and the corresponding full-length protein turned out to be surprisingly similar (34.5% amino acid identity) to another c(4)-type diheme protein from T. ferrooxidans BRGM [Cavazza, C., et al. (1996) Eur. J. Biochem. 242, 308-314], the gene of which is also present (at 97% amino acid identity) in the T. ferrooxidans ATCC 23270 genome. The physicochemical properties and sequence characteristics of both c(4) cytochromes present in the same bacteria are compared, and the functional role of this new diheme protein in the iron(II)-oxidizing electron transport chain in the genus Thiobacillus is discussed.
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Affiliation(s)
- M T Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, IFR1, 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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Elbehti A, Brasseur G, Lemesle-Meunier D. First evidence for existence of an uphill electron transfer through the bc(1) and NADH-Q oxidoreductase complexes of the acidophilic obligate chemolithotrophic ferrous ion-oxidizing bacterium Thiobacillus ferrooxidans. J Bacteriol 2000; 182:3602-6. [PMID: 10852897 PMCID: PMC101977 DOI: 10.1128/jb.182.12.3602-3606.2000] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The energy-dependent electron transfer pathway involved in the reduction of pyridine nucleotides which is required for CO(2) fixation to occur in the acidophilic chemolithotrophic organism Thiobacillus ferrooxidans was investigated using ferrocytochrome c as the electron donor. The experimental results show that this uphill pathway involves a bc(1) and an NADH-Q oxidoreductase complex functioning in reverse, using an electrochemical proton gradient generated by ATP hydrolysis. Based on these results, a model is presented to explain the balance of the reducing equivalent from ferrocytochrome c between the exergonic and endergonic electron transfer pathways.
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Affiliation(s)
- A Elbehti
- Bioénergétique et Ingénierie des Proteines, CNRS, Institut de Biologie Structurale et Microbiologie, 13402 Marseille, cedex 20, France
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