1
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Mittra PK, Rahman MA, Roy SK, Kwon SJ, Yun SH, Kun C, Zhou M, Katsube-Tanaka T, Shiraiwa T, Woo SH. Deciphering proteomic mechanisms explaining the role of glutathione as an aid in improving plant fitness and tolerance against cadmium-toxicity in Brassica napus L. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134262. [PMID: 38640678 DOI: 10.1016/j.jhazmat.2024.134262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Cadmium (Cd) hazard is a serious limitation to plants, soils and environments. Cd-toxicity causes stunted growth, chlorosis, necrosis, and plant yield loss. Thus, ecofriendly strategies with understanding of molecular mechanisms of Cd-tolerance in plants is highly demandable. The Cd-toxicity caused plant growth retardation, leaf chlorosis and cellular damages, where the glutathione (GSH) enhanced plant fitness and Cd-toxicity in Brassica through Cd accumulation and antioxidant defense. A high-throughput proteome approach screened 4947 proteins, wherein 370 were differently abundant, 164 were upregulated and 206 were downregulated. These proteins involved in energy and carbohydrate metabolism, CO2 assimilation and photosynthesis, signal transduction and protein metabolism, antioxidant defense response, heavy metal detoxification, cytoskeleton and cell wall structure, and plant development in Brassica. Interestingly, several key proteins including glutathione S-transferase F9 (A0A078GBY1), ATP sulfurylase 2 (A0A078GW82), cystine lyase CORI3 (A0A078FC13), ferredoxin-dependent glutamate synthase 1 (A0A078HXC0), glutaredoxin-C5 (A0A078ILU9), glutaredoxin-C2 (A0A078HHH4) actively involved in antioxidant defense and sulfur assimilation-mediated Cd detoxification process confirmed by their interactome analyses. These candidate proteins shared common gene networks associated with plant fitness, Cd-detoxification and tolerance in Brassica. The proteome insights may encourage breeders for enhancing multi-omics assisted Cd-tolerance in Brassica, and GSH-mediated hazard free oil seed crop production for global food security.
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Affiliation(s)
- Probir Kumar Mittra
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Republic of Korea
| | - Md Atikur Rahman
- Grassland and Forage Division, Rural Development Administration, National Institute of Animal Science, Cheonan 31000, Republic of Korea
| | - Swapan Kumar Roy
- College of Agricultural Sciences, IUBAT-International University of Business Agriculture and Technology, 4 Embankment Drive Road, Sector 10 Uttara Model Town, Dhaka 1230, Bangladesh
| | - Soo-Jeong Kwon
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Republic of Korea
| | - Sung Ho Yun
- Bio-Chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Ochang, Cheong-ju 28119, Republic of Korea
| | - Cho Kun
- Bio-Chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Ochang, Cheong-ju 28119, Republic of Korea
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Haidian, Beijing 100081, China
| | - Tomoyuki Katsube-Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tatsuhiko Shiraiwa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Republic of Korea.
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2
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Mittra PK, Roy SK, Rahman MA, Naimuzzaman M, Kwon SJ, Yun SH, Cho K, Katsube-Tanaka T, Shiraiwa T, Woo SH. Proteome insights of citric acid-mediated cadmium toxicity tolerance in Brassica napus L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:115461-115479. [PMID: 37882925 DOI: 10.1007/s11356-023-30442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
Cadmium (Cd) is a toxic substance that is uptake by plants from soils, Cd easily transfers into the food chain. Considering global food security, eco-friendly, cost-effective, and metal detoxification strategies are highly demandable for sustainable food crop production. The purpose of this study was to investigate how citric acid (CA) alleviates or tolerates Cd toxicity in Brassica using a proteome approach. In this study, the global proteome level was significantly altered under Cd toxicity with or without CA supplementation in Brassica. A total of 4947 proteins were identified using the gel-free proteome approach. Out of these, 476 proteins showed differential abundance between the treatment groups, wherein 316 were upregulated and 160 were downregulated. The gene ontology analysis reveals that differentially abundant proteins were involved in different biological processes including energy and carbohydrate metabolism, CO2 assimilation and photosynthesis, signal transduction and protein metabolism, antioxidant defense, heavy metal detoxification, plant development, and cytoskeleton and cell wall structure in Brassica leaves. Interestingly, several candidate proteins such as superoxide dismutase (A0A078GZ68) L-ascorbate peroxidase 3 (A0A078HSG4), glutamine synthetase (A0A078HLB2), glutathione S-transferase DHAR1 (A0A078HPN8), glutamine synthetase (A0A078HLB2), cysteine synthase (A0A078GAD3), S-adenosylmethionine synthase 2 (A0A078JDL6), and thiosulfate/3-mercaptopyruvate sulfur transferase 2 (A0A078H905) were involved in antioxidant defense system and sulfur assimilation-involving Cd-detoxification process in Brassica. These findings provide new proteome insights into CA-mediated Cd-toxicity alleviation in Brassica, which might be useful to oilseed crop breeders for enhancing heavy metal tolerance in Brassica using the breeding program, with sustainable and smart Brassica production in a metal-toxic environment.
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Affiliation(s)
- Probir Kumar Mittra
- Department of Crop Science, Chungbuk National University, Cheong-Ju, 28644, Republic of Korea
| | - Swapan Kumar Roy
- College of Agricultural Sciences, IUBAT-International University of Business Agriculture and Technology, 4 Embankment Drive Road, Sector 10 Uttara Model Town, Dhaka, 1230, Bangladesh
| | - Md Atikur Rahman
- Grassland and Forage Division, Rural Development Administration, National Institute of Animal Science, Cheonan, 31000, Republic of Korea
| | - Mollah Naimuzzaman
- College of Agricultural Sciences, IUBAT-International University of Business Agriculture and Technology, 4 Embankment Drive Road, Sector 10 Uttara Model Town, Dhaka, 1230, Bangladesh
| | - Soo-Jeong Kwon
- Department of Crop Science, Chungbuk National University, Cheong-Ju, 28644, Republic of Korea
| | - Sung Ho Yun
- Bio-Chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Ochang, Cheong-Ju, 28119, Republic of Korea
| | - Kun Cho
- Bio-Chemical Analysis Team, Center for Research Equipment, Korea Basic Science Institute, Ochang, Cheong-Ju, 28119, Republic of Korea
| | - Tomoyuki Katsube-Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Tatsuhiko Shiraiwa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-Ju, 28644, Republic of Korea.
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3
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Grba DN, Chung I, Bridges HR, Agip ANA, Hirst J. Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. SCIENCE ADVANCES 2023; 9:eadi1359. [PMID: 37531432 PMCID: PMC10396290 DOI: 10.1126/sciadv.adi1359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023]
Abstract
Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the proton-motive force for ATP synthesis. Despite remarkable advances in structural knowledge of this complicated membrane-bound enzyme, its mechanism of catalysis remains controversial. In particular, how ubiquinone reduction is coupled to proton pumping and the pathways and mechanisms of proton translocation are contested. We present a 2.4-Å resolution cryo-EM structure of complex I from mouse heart mitochondria in the closed, active (ready-to-go) resting state, with 2945 water molecules modeled. By analyzing the networks of charged and polar residues and water molecules present, we evaluate candidate pathways for proton transfer through the enzyme, for the chemical protons for ubiquinone reduction, and for the protons transported across the membrane. Last, we compare our data to the predictions of extant mechanistic models, and identify key questions to answer in future work to test them.
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4
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Jarman OD, Hirst J. Membrane-domain mutations in respiratory complex I impede catalysis but do not uncouple proton pumping from ubiquinone reduction. PNAS NEXUS 2022; 1:pgac276. [PMID: 36712358 PMCID: PMC9802314 DOI: 10.1093/pnasnexus/pgac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022]
Abstract
Respiratory complex I [NADH:ubiquinone (UQ) oxidoreductase] captures the free energy released from NADH oxidation and UQ reduction to pump four protons across an energy-transducing membrane and power ATP synthesis. Mechanisms for long-range energy coupling in complex I have been proposed from structural data but not yet evaluated by robust biophysical and biochemical analyses. Here, we use the powerful bacterial model system Paracoccus denitrificans to investigate 14 mutations of key residues in the membrane-domain Nqo13/ND4 subunit, defining the rates and reversibility of catalysis and the number of protons pumped per NADH oxidized. We reveal new insights into the roles of highly conserved charged residues in lateral energy transduction, confirm the purely structural role of the Nqo12/ND5 transverse helix, and evaluate a proposed hydrated channel for proton uptake. Importantly, even when catalysis is compromised the enzyme remains strictly coupled (four protons are pumped per NADH oxidized), providing no evidence for escape cycles that circumvent blocked proton-pumping steps.
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Affiliation(s)
- Owen D Jarman
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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5
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Xu HX, Tang YQ, Nie Y, Wu XL. Comparative transcriptome analysis reveals different adaptation mechanisms for degradation of very long-chain and normal long-chain alkanes in Dietzia sp. DQ12-45-1b. Environ Microbiol 2022; 24:1932-1945. [PMID: 35191184 DOI: 10.1111/1462-2920.15928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/30/2022] [Indexed: 12/13/2022]
Abstract
Hydrocarbon-degrading bacteria typically metabolize a broad range of alkane substrates, but global metabolic characteristics of strains growing on alkane substrates in different chain lengths remain unclear. In this study, we analysed the transcriptional profiles of a hydrocarbon degrading bacterium, Dietzia sp. DQ12-45-1b, during growth on octacosane (C28), hexadecane (C16) and glucose as the sole carbon sources. Our results highlight that C16 and C28 induced common genes of core alkane degradation pathways in DQ12-45-1b, whereas transcriptional patterns of genes related to lipid metabolism, energy metabolism, biomass synthesis, and metal ion transportation were distinct. In addition, the transcriptional differences of genes related to glyoxylate shunt (GS) as well as growth phenotypes of mutant strain with defects in GS demonstrated that GS is essential for C16 degradation, though it is dispensable for C28 degradation in DQ12-45-1b. These results demonstrate that DQ12-45-1b cells exhibited considerable metabolic flexibility by using various mechanisms during growth on alkane substrates in different chain lengths. This study advances our knowledge of microbial hydrocarbon degradation and provides valuable information for the application of alkane-degrading bacteria in bioremediation and microbial enhanced oil recovery.
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Affiliation(s)
- Hong-Xiu Xu
- College of Architecture and Environment, Sichuan University, Chengdu, 610207, China.,College of Engineering, Peking University, Beijing, 100871, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610207, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.,Institute of Ecology, Peking University, Beijing, 100871, China.,Institute of Ocean Research, Peking University, Beijing, 100871, China
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6
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Artier J, Walker RM, Miller NT, Zhang M, Price GD, Burnap RL. Modeling and mutagenesis of amino acid residues critical for CO 2 hydration by specialized NDH-1 complexes in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148503. [PMID: 34610280 DOI: 10.1016/j.bbabio.2021.148503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The uptake of inorganic carbon in cyanobacteria is facilitated by an energetically intensive CO2-concentrating mechanism (CCM). This includes specialized Type-1 NDH complexes that function to couple photosynthetic redox energy to CO2 hydration forming the bicarbonate that accumulates to high cytoplasmic concentrations during the operation of the CCM, required for effective carbon fixation. Here we used a Synechococcus PCC7942 expression system to investigate the role of conserved histidine and cysteine residues in the CupB (also designated, ChpX) protein, which has been hypothesized to participate in a vectoral CO2 hydration reaction near the interface between CupB protein and the proton-pumping subunits of the NDH-1 complex. A homology model has been constructed and most of the targeted conserved residues are in the vicinity of a Zn ion modeled to form the catalytic site of deprotonation and CO2 hydration. Growth and CO2 uptake assays show that the most severe defects in activity among the targeted residues are due to a substitution of the predicted Zn ligand, CupB-His86. Mutations at other sites produced intermediate effects. Proteomic analysis revealed that some amino acid substitution mutations of CupB caused the induction of bicarbonate uptake proteins to a greater extent than complete deletion of CupB, despite growth under CO2-enriched conditions. The results are discussed in terms of hypotheses on the catalytic function of this unusual enzyme.
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Affiliation(s)
- Juliana Artier
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ross M Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Neil T Miller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Minquan Zhang
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - G Dean Price
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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7
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Jarman OD, Biner O, Wright JJ, Hirst J. Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I. Sci Rep 2021; 11:10143. [PMID: 33980947 PMCID: PMC8115037 DOI: 10.1038/s41598-021-89575-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.
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Affiliation(s)
- Owen D. Jarman
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Olivier Biner
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - John J. Wright
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Judy Hirst
- grid.5335.00000000121885934The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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8
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Di Luca A, Kaila VRI. Molecular strain in the active/deactive-transition modulates domain coupling in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148382. [PMID: 33513365 DOI: 10.1016/j.bbabio.2021.148382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
Complex I functions as a primary redox-driven proton pump in aerobic respiratory chains, establishing a proton motive force that powers ATP synthesis and active transport. Recent cryo-electron microscopy (cryo-EM) experiments have resolved the mammalian complex I in the biomedically relevant active (A) and deactive (D) states (Zhu et al., 2016; Fiedorczuk et al., 2016; Agip et al., 2018 [1-3]) that could regulate enzyme turnover, but it still remains unclear how the conformational state and activity are linked. We show here how global motion along the A/D transition accumulates molecular strain at specific coupling regions important for both redox chemistry and proton pumping. Our data suggest that the A/D motion modulates force propagation pathways between the substrate-binding site and the proton pumping machinery that could alter electrostatic and conformational coupling across large distances. Our findings provide a molecular basis to understand how global protein dynamics can modulate the biological activity of large molecular complexes.
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Affiliation(s)
- Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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9
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Respiratory complex I - Mechanistic insights and advances in structure determination. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148153. [PMID: 31935361 DOI: 10.1016/j.bbabio.2020.148153] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/16/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022]
Abstract
Complex I is the largest and most intricate redox-driven proton pump of the respiratory chain. The structure of bacterial and mitochondrial complex I has been determined by X-ray crystallography and cryo-EM at increasing resolution. The recent cryo-EM structures of the complex I-like NDH complex and membrane bound hydrogenase open a new and more comprehensive perspective on the complex I superfamily. Functional studies and molecular modeling approaches have greatly advanced our understanding of the catalytic cycle of complex I. However, the molecular mechanism by which energy is extracted from the redox reaction and utilized to drive proton translocation is unresolved and a matter of ongoing debate. Here, we review progress in structure determination and functional characterization of complex I and discuss current mechanistic models.
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10
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Li J, Wang J, Liu W, Hayashi T, Itoh K, Onodera S, Ikejima T. Metformin protects Escherichia coli from bleomycin-induced bactericide via enhanced generation of hydrogen peroxide. Free Radic Res 2020; 54:64-75. [PMID: 31905044 DOI: 10.1080/10715762.2019.1703968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bleomycin is a glycopeptide antibiotic that is widely employed in the therapy of a range of lymphomas and germ cell tumours. But the therapeutic efficacy of bleomycin is limited by development of lung fibrosis. The cytotoxicity of bleomycin is mostly ascribed to mitochondrial DNA (mtDNA) damage, while a protective effect of metformin against bleomycin-induced lung fibrosis results from the inhibition of mitochondrial complex I. Since mitochondria and bacteria have certain similarities in structure and function, we used Escherichia coli for simplification in the present work to investigate the relationship between metformin and bleomycin with apparently opposite effects on mitochondrial DNA damage. Bleomycin lethality to E. coli was ameliorated by metformin treatment accompanying further increase of the level of reactive oxygen species. Catalase but not superoxide dismutases attenuated the protective effect of metformin. Meanwhile, treatment with hydrogen peroxide enhanced the protection, indicating that metformin may protect E. coli from bleomycin-induced bactericide via enhanced generation of hydrogen peroxide. Moreover, silibinin, a hepatoprotective polyphenolic flavonoid attenuates the cytotoxicity of bleomycin to E. coli via enhanced generation of hydrogen peroxide as well. This bacterial model in place of mitochondria can provide us with easier screening for the molecules with capability of reducing the bleomycin side effect.
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Affiliation(s)
- Jian Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Jiaojiao Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Weiwei Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Toshihiko Hayashi
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, Hachioji, Japan
| | | | | | - Takashi Ikejima
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Shenyang Pharmaceutical University, Shenyang, P. R. China
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11
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Fiedorczuk K, Sazanov LA. Mammalian Mitochondrial Complex I Structure and Disease-Causing Mutations. Trends Cell Biol 2018; 28:835-867. [PMID: 30055843 DOI: 10.1016/j.tcb.2018.06.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Abstract
Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria; Present address: The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria.
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12
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Haapanen O, Sharma V. Role of water and protein dynamics in proton pumping by respiratory complex I. Sci Rep 2017; 7:7747. [PMID: 28798393 PMCID: PMC5552823 DOI: 10.1038/s41598-017-07930-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/05/2017] [Indexed: 11/29/2022] Open
Abstract
Membrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear. Here, based on atomistic molecular dynamics simulations performed on the entire structure of complex I from Thermus thermophilus, we studied the hydration of the quinone-binding site and the membrane-bound subunits. The data from simulations show rapid diffusion of water molecules in the protein interior, and formation of hydrated regions in the three antiporter-type subunits. An unexpected water-protein based connectivity between the middle of the Q-tunnel and the fourth proton channel is also observed. The protonation-state dependent dynamics of key acidic residues in the Nqo8 subunit suggest that the latter may be linked to redox-coupled proton pumping in complex I. We propose that in complex I the proton and electron transfer paths are not entirely separate, instead the nature of coupling may in part be ‘direct’.
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Affiliation(s)
- Outi Haapanen
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland.,Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101, Tampere, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Helsinki, Finland. .,Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101, Tampere, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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13
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Sinha PK, Castro-Guerrero N, Patki G, Sato M, Torres-Bacete J, Sinha S, Miyoshi H, Matsuno-Yagi A, Yagi T. Conserved amino acid residues of the NuoD segment important for structure and function of Escherichia coli NDH-1 (complex I). Biochemistry 2015; 54:753-64. [PMID: 25545070 PMCID: PMC4310626 DOI: 10.1021/bi501403t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The NuoD segment (homologue of mitochondrial
49 kDa subunit) of
the proton-translocating NADH:quinone oxidoreductase (complex I/NDH-1)
from Escherichia coli is in the hydrophilic domain
and bears many highly conserved amino acid residues. The three-dimensional
structural model of NDH-1 suggests that the NuoD segment, together
with the neighboring subunits, constitutes a putative quinone binding
cavity. We used the homologous DNA recombination technique to clarify
the role of selected key amino acid residues of the NuoD segment.
Among them, residues Tyr273 and His224 were considered candidates
for having important interactions with the quinone headgroup. Mutant
Y273F retained partial activity but lost sensitivity to capsaicin-40.
Mutant H224R scarcely affected the activity, suggesting that this
residue may not be essential. His224 is located in a loop near the
N-terminus of the NuoD segment (Gly217–Phe227) which is considered
to form part of the quinone binding cavity. In contrast to the His224
mutation, mutants G217V, P218A, and G225V almost completely lost the
activity. One region of this loop is positioned close to a cytosolic
loop of the NuoA subunit in the membrane domain, and together they
seem to be important in keeping the quinone binding cavity intact.
The structural role of the longest helix in the NuoD segment located
behind the quinone binding cavity was also investigated. Possible
roles of other highly conserved residues of the NuoD segment are discussed.
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Affiliation(s)
- Prem Kumar Sinha
- Deparment of Molecular and Experimental Medicine, and ‡Department of Cell and Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, MEM256, La Jolla, California 92037, United States
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