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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; 123:2594-2603. [PMID: 38937973 PMCID: PMC11365222 DOI: 10.1016/j.bpj.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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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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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , 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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Difference in NaCl tolerance of membrane-bound 5'-nucleotidases purified from deep-sea and brackish water Shewanella species. Extremophiles 2017; 21:357-368. [PMID: 28050644 DOI: 10.1007/s00792-016-0909-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
Shewanella species are widely distributed in sea, brackish, and fresh water areas, growing psychrophilically or mesophilically, and piezophilically or piezo-sensitively. Here, membrane-bound 5'-nucleotidases (NTases) from deep-sea Shewanella violacea and brackish water Shewanella amazonensis were examined from the aspect of NaCl tolerance to gain an insight into protein stability against salt. Both NTases were single polypeptides with molecular masses of ~59 kDa, as determined on mass spectroscopy. They similarly required 10 mM MgCl2 for their activities, and they exhibited the same pH dependency and substrate specificity for 5'-nucleotides. However, S. violacea 5'-nucleotidase (SVNTase) was active enough in the presence of 2.5 M NaCl, whereas S. amazonensis 5'-nucleotidase (SANTase) exhibited significantly reduced activity with the same concentration of the salt. Although SVNTase and SANTase exhibited high sequence identity (69.7%), differences in the ratio of acidic to basic amino acid residues and the number of potential salt bridges maybe being responsible for the difference in the protein stability against salt. 5'-Nucleotidases from these Shewanella species will provide useful information regarding NaCl tolerance, which may be fundamental for understanding bacterial adaptation to growth environments.
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