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Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E. Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography. J Biochem 2016; 159:527-38. [PMID: 26769972 PMCID: PMC4846774 DOI: 10.1093/jb/mvv133] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/19/2015] [Indexed: 11/17/2022] Open
Abstract
Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 Å resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR.
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Affiliation(s)
- Yohta Fukuda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ka Man Tse
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Kay Diederichs
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany;
| | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan;
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan;
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan;
| | - Changyong Song
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea; and
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan;
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
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Aas FE, Li X, Edwards J, Hongrø Solbakken M, Deeudom M, Vik Å, Moir J, Koomey M, Aspholm M. Cytochrome c-based domain modularity governs genus-level diversification of electron transfer to dissimilatory nitrite reduction. Environ Microbiol 2014; 17:2114-32. [PMID: 25330335 DOI: 10.1111/1462-2920.12661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/04/2014] [Indexed: 12/19/2022]
Abstract
The genus Neisseria contains two pathogenic species (N. meningitidis and N. gonorrhoeae) in addition to a number of commensal species that primarily colonize mucosal surfaces in man. Within the genus, there is considerable diversity and apparent redundancy in the components involved in respiration. Here, we identify a unique c-type cytochrome (cN ) that is broadly distributed among commensal Neisseria, but absent in the pathogenic species. Specifically, cN supports nitrite reduction in N. gonorrhoeae strains lacking the cytochromes c5 and CcoP established to be critical to NirK nitrite reductase activity. The c-type cytochrome domain of cN shares high sequence identity with those localized c-terminally in c5 and CcoP and all three domains were shown to donate electrons directly to NirK. Thus, we identify three distinct but paralogous proteins that donate electrons to NirK. We also demonstrate functionality for a N. weaverii NirK variant with a C-terminal c-type heme extension. Taken together, modular domain distribution and gene rearrangement events related to these respiratory electron carriers within Neisseria are concordant with major transitions in the macroevolutionary history of the genus. This work emphasizes the importance of denitrification as a selectable trait that may influence speciation and adaptive diversification within this largely host-restricted bacterial genus.
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Affiliation(s)
- Finn Erik Aas
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - Xi Li
- Department of Biology, University of York, York, YO10 5DD, UK
| | - James Edwards
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Monica Hongrø Solbakken
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Manu Deeudom
- Department of Biology, University of York, York, YO10 5DD, UK.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Åshild Vik
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - James Moir
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Michael Koomey
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Marina Aspholm
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
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5
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Aspholm M, Aas FE, Harrison OB, Quinn D, Vik Å, Viburiene R, Tønjum T, Moir J, Maiden MCJ, Koomey M. Structural alterations in a component of cytochrome c oxidase and molecular evolution of pathogenic Neisseria in humans. PLoS Pathog 2010; 6:e1001055. [PMID: 20808844 PMCID: PMC2924362 DOI: 10.1371/journal.ppat.1001055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/21/2010] [Indexed: 12/26/2022] Open
Abstract
Three closely related bacterial species within the genus Neisseria are of importance to human disease and health. Neisseria meningitidis is a major cause of meningitis, while Neisseria gonorrhoeae is the agent of the sexually transmitted disease gonorrhea and Neisseria lactamica is a common, harmless commensal of children. Comparative genomics have yet to yield clear insights into which factors dictate the unique host-parasite relationships exhibited by each since, as a group, they display remarkable conservation at the levels of nucleotide sequence, gene content and synteny. Here, we discovered two rare alterations in the gene encoding the CcoP protein component of cytochrome cbb3 oxidase that are phylogenetically informative. One is a single nucleotide polymorphism resulting in CcoP truncation that acts as a molecular signature for the species N. meningitidis. We go on to show that the ancestral ccoP gene arose by a unique gene duplication and fusion event and is specifically and completely distributed within species of the genus Neisseria. Surprisingly, we found that strains engineered to express either of the two CcoP forms conditionally differed in their capacity to support nitrite-dependent, microaerobic growth mediated by NirK, a nitrite reductase. Thus, we propose that changes in CcoP domain architecture and ensuing alterations in function are key traits in successive, adaptive radiations within these metapopulations. These findings provide a dramatic example of how rare changes in core metabolic proteins can be connected to significant macroevolutionary shifts. They also show how evolutionary change at the molecular level can be linked to metabolic innovation and its reversal as well as demonstrating how genotype can be used to infer alterations of the fitness landscape within a single host. The closely related bacterial species N. meningitidis, N. gonorrhoeae and N. lactamica exclusively colonise mucosal surfaces in humans. While N. gonorrhoeae leads to gonorrhea, the other two species persist mainly in their host in the absence of disease. N. meningitidis does occasionally cause severe, life threatening illness, however. Little is known about the factors and elements that dictate the unique human interactions exhibited by each species. Moreover, the evolutionary relationships between these species are poorly characterized. Here, we describe two successive alterations in a single gene that can be linked first to all species within the genus Neisseria and then the species N. meningitidis. We also show these signature alterations have phenotypic consequences by affecting core respiratory metabolic processes. These findings have significant implications for the evolution of related bacterial species within a single host and provide a novel perspective on the episodic and reversible nature of innovative adaptation.
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Affiliation(s)
- Marina Aspholm
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Finn Erik Aas
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | | | - Diana Quinn
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | - Åshild Vik
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Raimonda Viburiene
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- Institute of Microbiology, University of Oslo, Oslo, Norway
| | - James Moir
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | | | - Michael Koomey
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- * E-mail:
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