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Fujii S, Wilson MT, Adams HR, Mikolajek H, Svistunenko DA, Smyth P, Andrew CR, Sambongi Y, Hough MA. Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding. Biophys J 2024:S0006-3495(24)00436-3. [PMID: 38937973 DOI: 10.1016/j.bpj.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 06/29/2024] Open
Abstract
Cytochromes c'-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic Alcaligenes xylosoxidans cytochrome c'-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal penta-coordinate Fe(II)-NO (5cNO) final product. Here, we characterize a thermally stable cytochrome c'-α from thermophilic Hydrogenophilus thermoluteolus (PhCP-α) to understand how protein thermal stability affects NO binding. Electron paramagnetic and resonance Raman spectroscopies reveal the formation of a PhCP-α 5cNO product, with time-resolved (stopped-flow) UV-vis absorbance indicating the involvement of a 6cNO intermediate. Relative to AxCP-α, the rates of 6cNO and 5cNO formation in PhCP-α are ∼11- and ∼13-fold lower, respectively. Notably, x-ray crystal structures of PhCP-α in the presence and absence of NO suggest that the sluggish formation of the proximal 5cNO product results from conformational rigidity: the Arg-132 residue (adjacent to the proximal His ligand) is held in place by a salt bridge between Arg-75 and Glu-135 (an interaction not present in AxCP-α or a psychrophilic counterpart). Overall, our data provide fresh insights into structural factors controlling NO binding in heme proteins, including 5cNO complexes relevant to eukaryotic NO sensors.
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Affiliation(s)
- Sotaro Fujii
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom; Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Hannah R Adams
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Halina Mikolajek
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | | | - Peter Smyth
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom; School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Michael A Hough
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom; School of Life Sciences, University of Essex, Colchester, United Kingdom
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Fujii S, Kobayashi S, Yoshimi T, Kobayashi Y, Wakai S, Yamanaka M, Sambongi Y. Thermal stability tuning without affecting gas-binding function of Thermochromatium tepidum cytochrome c'. Biosci Biotechnol Biochem 2021; 85:1846-1852. [PMID: 34124760 DOI: 10.1093/bbb/zbab108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Hydrogenophilus thermoluteolus, Thermochromatium tepidum, and Allochromatium vinosum, which grow optimally at 52, 49, and 25 °C, respectively, have homologous cytochromes c' (PHCP, TTCP, and AVCP, respectively) exhibiting at least 50% amino acid sequence identity. Here, the thermal stability of the recombinant TTCP protein was first confirmed to be between those of PHCP and AVCP. Structure comparison of the 3 proteins and a mutagenesis study on TTCP revealed that hydrogen bonds and hydrophobic interactions between the heme and amino acid residues were responsible for their stability differences. In addition, PHCP, TTCP, and AVCP and their variants with altered stability similarly bound nitric oxide and carbon oxide, but not oxygen. Therefore, the thermal stability of TTCP together with PHCP and AVCP can be tuned through specific interactions around the heme without affecting their gas-binding function. These cytochromes c' will be useful as specific gas sensor proteins exhibiting a wide thermal stability range.
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Satoru Kobayashi
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, Japan
| | - Taisuke Yoshimi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Satoshi Wakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan
| | - Masaru Yamanaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Yamanaka M, Nakayama R, Fujii S, Wakai S, Sambongi Y, Hirota S. Conferment of CO-Controlled Dimer–Monomer Transition Property to Thermostable Cytochromec′ by Mutation in the Subunit–Subunit Interface. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Ryoko Nakayama
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Satoshi Wakai
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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Stability of cytochromes c′ from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure. Extremophiles 2019; 23:239-248. [DOI: 10.1007/s00792-019-01077-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/13/2019] [Indexed: 10/27/2022]
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Yamane-Koshizawa D, Fujii S, Maruno T, Kobayashi Y, Yamanaka M, Wakai S, Sambongi Y. Stabilization of mesophilic Allochromatium vinosum cytochrome c′ through specific mutations modeled by a thermophilic homologue. Biosci Biotechnol Biochem 2018; 82:304-311. [DOI: 10.1080/09168451.2017.1419856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Abstract
AVCP cytochrome c′ from mesophilic Allochromatium vinosum exhibits lower stability than a thermophilic counterpart, Hydrogenophilus thermoluteolus cytochrome c′ (PHCP), in which the six specific amino acid residues that are not conserved in AVCP are responsible for its stability. Here we measured the stability of AVCP variants carrying these specific residues instead of the original AVCP ones. Among the six single AVCP variants, all of which formed a dimeric structure similar to that of the wild-type, three were successfully stabilized compared with the wild-type, while one showed lower stability than the wild-type. In addition, the most stabilized and destabilized AVCP variants could bind CO, similar to the wild-type. These results indicated that mesophilic AVCP could be stabilized through specific three mutations modeled by the thermophilic counterpart, PHCP, without changing the CO binding ability.
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Affiliation(s)
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
- Global Career Design Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, Suita, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Suita, Japan
| | - Masaru Yamanaka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Satoshi Wakai
- Graduate School of Science Technology and Innovation, Kobe University, Kobe, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
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Fujii S, Oki H, Kawahara K, Yamane D, Yamanaka M, Maruno T, Kobayashi Y, Masanari M, Wakai S, Nishihara H, Ohkubo T, Sambongi Y. Structural and functional insights into thermally stable cytochrome c' from a thermophile. Protein Sci 2017; 26:737-748. [PMID: 28097774 PMCID: PMC5368077 DOI: 10.1002/pro.3120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/10/2022]
Abstract
Thermophilic Hydrogenophilus thermoluteolus cytochrome c′ (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c′ (AVCP), which has a homo‐dimeric structure and ligand‐binding ability. To understand the thermal stability mechanism and ligand‐binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo‐dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 Å. In the PHCP structure, six specific residues appeared to strengthen the heme‐related and subunit–subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit–subunit interactions were more severely destabilized than ones having altered heme‐related interactions. The PHCP structure further revealed a ligand‐binding channel and a penta‐coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme‐related and subunit–subunit interactions with conservation of the ligand‐binding ability. Brief Summary We report the X‐ray crystal structure of cytochrome c′ (PHCP) from thermophilic Hydrogenophilus thermoluteolus. The high thermal stability of PHCP was attributed to heme‐related and subunit–subunit interactions, which were confirmed by a mutagenesis study. The ligand‐binding ability of PHCP was examined by spectrophotometry. PHCP acquired the thermal stability with conservation of the ligand‐binding ability. This study furthers the understanding of the stability and function of cytochromes c. PDB Code(s): 5B3I
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroya Oki
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Daisuke Yamane
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Masaru Yamanaka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Misa Masanari
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Satoshi Wakai
- Graduate School of Science, Technology, and Innovation, Kobe University, Rokkodai, Kobe, Hyogo, Japan
| | | | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Yamanaka M, Hoshizumi M, Nagao S, Nakayama R, Shibata N, Higuchi Y, Hirota S. Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers. Protein Sci 2017; 26:464-474. [PMID: 27883268 PMCID: PMC5326568 DOI: 10.1002/pro.3090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices αA and αB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein.
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Affiliation(s)
- Masaru Yamanaka
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Makoto Hoshizumi
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Satoshi Nagao
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Ryoko Nakayama
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
| | - Naoki Shibata
- Department of Life ScienceGraduate School of Life Science, University of Hyogo3‐2‐1 Koto, Kamigori‐cho, Ako‐gunHyogo678‐1297Japan
- RIKEN SPring‐8 Center1‐1‐1 Koto, Sayo‐cho, Sayo‐gunHyogo679‐5148Japan
| | - Yoshiki Higuchi
- Department of Life ScienceGraduate School of Life Science, University of Hyogo3‐2‐1 Koto, Kamigori‐cho, Ako‐gunHyogo678‐1297Japan
- RIKEN SPring‐8 Center1‐1‐1 Koto, Sayo‐cho, Sayo‐gunHyogo679‐5148Japan
| | - Shun Hirota
- Graduate School of Materials ScienceNara Institute of Science and Technology8916‐5 Takayama, IkomaNara630‐0192Japan
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Beese-Vasbender PF, Nayak S, Erbe A, Stratmann M, Mayrhofer KJ. Electrochemical characterization of direct electron uptake in electrical microbially influenced corrosion of iron by the lithoautotrophic SRB Desulfopila corrodens strain IS4. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.03.184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Conlan B, Cox N, Su JH, Hillier W, Messinger J, Lubitz W, Dutton PL, Wydrzynski T. Photo-catalytic oxidation of a di-nuclear manganese centre in an engineered bacterioferritin ‘reaction centre’. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1112-21. [DOI: 10.1016/j.bbabio.2009.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/16/2009] [Accepted: 04/21/2009] [Indexed: 11/15/2022]
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Bertini I, Cavallaro G, Rosato A. Evolution of mitochondrial-type cytochrome c domains and of the protein machinery for their assembly. J Inorg Biochem 2007; 101:1798-811. [PMID: 17368779 DOI: 10.1016/j.jinorgbio.2007.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Revised: 02/01/2007] [Accepted: 02/06/2007] [Indexed: 11/20/2022]
Abstract
Proteins containing mitochondrial-type cytochrome c domains, defined here as protein domains having the mitochondrial cytochrome c fold, are found in organisms from all domains of life, and constitute essential components in several different metabolic pathways. The number of cytochrome c domains present in a given organism as well as their functional roles can vary widely even for quite closely related organisms. In this work, we have analysed in detail the distribution of mitochondrial-type cytochrome c domains along the tree of life and attempted to define the evolutionary relationships among them. In parallel, we have similarly analysed also the occurrence and distribution of the different machineries for cytochrome c assembly. It is found that the first appearance of mitochondrial-type cytochrome c domains has likely happened in the bacterial world, together with the first apparatus for their assembly. Evolution of cytochrome c domains has been extensive, involving several gene duplication and gene transfer events. Of particular relevance are gene transfer events from Bacteria to Eukarya and Archaea. The transfer of genes encoding cytochrome c domains has generally co-occurred with transfer of the assembly machinery. This has occurred also in Eukarya, where however the latter machinery has been subsequently replaced by a new one. It is possible that of the three known enzymatic systems for cytochrome c assembly, system II (found, among others, in cyanobacteria and Gram-positive bacteria) is the most ancient. Archaea have inherited from Bacteria system I or, possibly, an evolutionary intermediate between system II and system I.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Uno T, Yukinari A, Moriyama Y, Ishikawa Y, Tomisugi Y, Brannigan JA, Wilkinson AJ. Engineering a ligand binding pocket into a four-helix bundle protein cytochrome b(562). J Am Chem Soc 2001; 123:512-3. [PMID: 11456561 DOI: 10.1021/ja002079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- T Uno
- Faculty of Pharmaceutical Sciences, Kumamoto University Oehonmachi, Kumamoto 862-0973, Japan
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