1
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Pires PM, Santos D, Calisto F, Pereira M. The monotopic quinone reductases from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149488. [PMID: 38950690 DOI: 10.1016/j.bbabio.2024.149488] [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: 04/30/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
Staphylococcus aureus, a Gram-positive bacterium, is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial infections that has become a major public health threat due to the increased incidence of its drug resistance. Although being a prominent pathogen, its energetic metabolism is still underexplored, and its respiratory enzymes have been escaping attention. S. aureus can adapt to different environmental conditions by performing both aerobic and anaerobic respirations, which is particularly important as it frequently colonizes niches with different oxygen concentrations. This adaptability is derived from the composition of its respiratory chain, specifically from the presence of terminal electron acceptor reductases. The plasticity of S. aureus energy metabolism is enlarged by the ten quinone reductases encoded in its genome, eight of them being monotopic proteins. The role of these proteins is critical as they connect the different catabolic pathways to the respiratory chain. In this work, we identify, describe, and revise the monotopic quinone reductases present in S. aureus, providing an integrated view of its respiratory chain.
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Affiliation(s)
- Patrícia M Pires
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - David Santos
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Filipa Calisto
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Manuela Pereira
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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2
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Sena FV, Sousa FM, Pereira AR, Catarino T, Cabrita EJ, Pinho MG, Pinto FR, Pereira MM. The two alternative NADH:quinone oxidoreductases from Staphylococcus aureus: two players with different molecular and cellular roles. Microbiol Spectr 2024; 12:e0415223. [PMID: 39012110 DOI: 10.1128/spectrum.04152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/01/2024] [Indexed: 07/17/2024] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that has emerged as a major public health threat due to the increased incidence of its drug resistance. S. aureus presents a remarkable capacity to adapt to different niches due to the plasticity of its energy metabolism. In this work, we investigated the energy metabolism of S. aureus, focusing on the alternative NADH:quinone oxidoreductases, NDH-2s. S. aureus presents two genes encoding NDH-2s (NDH-2A and NDH-2B) and lacks genes coding for Complex I, the canonical respiratory NADH:quinone oxidoreductase. This observation makes the action of NDH-2s crucial for the regeneration of NAD+ and, consequently, for the progression of metabolism. Our study involved the comprehensive biochemical characterization of NDH-2B and the exploration of the cellular roles of NDH-2A and NDH-2B, utilizing knockout mutants (Δndh-2a and Δndh-2b). We show that NDH-2B uses NADPH instead of NADH, does not establish a charge-transfer complex in the presence of NADPH, and its reduction by this substrate is the catalytic rate-limiting step. In the case of NDH-2B, the reduction of the flavin is inherently slow, and we suggest the establishment of a charge transfer complex between NADP+ and FADH2, as previously observed for NDH-2A, to slow down quinone reduction and, consequently, prevent the overproduction of reactive oxygen species, which is potentially unnecessary. Furthermore, we observed that the lack of NDH-2A or NDH-2B impacts cell growth, volume, and division differently. The absence of these enzymes results in distinct metabolic phenotypes, emphasizing the unique cellular roles of each NDH-2 in energy metabolism.IMPORTANCEStaphylococcus aureus is an opportunistic pathogen, posing a global challenge in clinical medicine due to the increased incidence of its drug resistance. For this reason, it is essential to explore and understand the mechanisms behind its resistance, as well as the fundamental biological features such as energy metabolism and the respective players that allow S. aureus to live and survive. Despite its prominence as a pathogen, the energy metabolism of S. aureus remains underexplored, with its respiratory enzymes often escaping thorough investigation. S. aureus bioenergetic plasticity is illustrated by its ability to use different respiratory enzymes, two of which are investigated in the present study. Understanding the metabolic adaptation strategies of S. aureus to bioenergetic challenges may pave the way for the design of therapeutic approaches that interfere with the ability of the pathogen to successfully adapt when it invades different niches within its host.
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Affiliation(s)
- Filipa V Sena
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipe M Sousa
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana R Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Francisco R Pinto
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Manuela M Pereira
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
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3
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Chen M, Wang Y, Dalal R, Du J, Vollrath D. Alternative oxidase blunts pseudohypoxia and photoreceptor degeneration due to RPE mitochondrial dysfunction. Proc Natl Acad Sci U S A 2024; 121:e2402384121. [PMID: 38865272 PMCID: PMC11194566 DOI: 10.1073/pnas.2402384121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
Loss of mitochondrial electron transport complex (ETC) function in the retinal pigment epithelium (RPE) in vivo results in RPE dedifferentiation and progressive photoreceptor degeneration, and has been implicated in the pathogenesis of age-related macular degeneration. Xenogenic expression of alternative oxidases in mammalian cells and tissues mitigates phenotypes arising from some mitochondrial electron transport defects, but can exacerbate others. We expressed an alternative oxidase from Ciona intestinalis (AOX) in ETC-deficient murine RPE in vivo to assess the retinal consequences of stimulating coenzyme Q oxidation and respiration without ATP generation. RPE-restricted expression of AOX in this context is surprisingly beneficial. This focused intervention mitigates RPE mTORC1 activation, dedifferentiation, hypertrophy, stress marker expression, pseudohypoxia, and aerobic glycolysis. These RPE cell autonomous changes are accompanied by increased glucose delivery to photoreceptors with attendant improvements in photoreceptor structure and function. RPE-restricted AOX expression normalizes accumulated levels of succinate and 2-hydroxyglutarate in ETC-deficient RPE, and counteracts deficiencies in numerous neural retinal metabolites. These features can be attributed to the activation of mitochondrial inner membrane flavoproteins such as succinate dehydrogenase and proline dehydrogenase, and alleviation of inhibition of 2-oxyglutarate-dependent dioxygenases such as prolyl hydroxylases and epigenetic modifiers. Our work underscores the importance to outer retinal health of coenzyme Q oxidation in the RPE and identifies a metabolic network critical for photoreceptor survival in the context of RPE mitochondrial dysfunction.
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Affiliation(s)
- Ming Chen
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA94305
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV26506
| | - Roopa Dalal
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA94305
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV26506
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV26506
| | - Douglas Vollrath
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA94305
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA94305
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4
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Eldeeb MH, Camacho Lopez LJ, Fontanesi F. Mitochondrial respiratory supercomplexes of the yeast Saccharomyces cerevisiae. IUBMB Life 2024. [PMID: 38529880 DOI: 10.1002/iub.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
The functional and structural relationship among the individual components of the mitochondrial respiratory chain constitutes a central aspect of our understanding of aerobic catabolism. This interplay has been a subject of intense debate for over 50 years. It is well established that individual respiratory enzymes associate into higher-order structures known as respiratory supercomplexes, which represent the evolutionarily conserved organizing principle of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, supercomplexes are formed by a complex III homodimer flanked by one or two complex IV monomers, and their high-resolution structures have been recently elucidated. Despite the wealth of structural information, several proposed supercomplex functions remain speculative and our understanding of their physiological relevance is still limited. Recent advances in the field were made possible by the construction of yeast strains where the association of complex III and IV into supercomplexes is impeded, leading to diminished respiratory capacity and compromised cellular competitive fitness. Here, we discuss the experimental evidence and hypotheses relative to the functional roles of yeast respiratory supercomplexes. Moreover, we review the current models of yeast complex III and IV assembly in the context of supercomplex formation and highlight the data scattered throughout the literature suggesting the existence of cross talk between their biogenetic processes.
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Affiliation(s)
- Mazzen H Eldeeb
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Lizeth J Camacho Lopez
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
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5
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Li J, Yang S, Wu Y, Wang R, Liu Y, Liu J, Ye Z, Tang R, Whiteway M, Lv Q, Yan L. Alternative Oxidase: From Molecule and Function to Future Inhibitors. ACS OMEGA 2024; 9:12478-12499. [PMID: 38524433 PMCID: PMC10955580 DOI: 10.1021/acsomega.3c09339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/26/2024]
Abstract
In the respiratory chain of the majority of aerobic organisms, the enzyme alternative oxidase (AOX) functions as the terminal oxidase and has important roles in maintaining metabolic and signaling homeostasis in mitochondria. AOX endows the respiratory system with flexibility in the coupling among the carbon metabolism pathway, electron transport chain (ETC) activity, and ATP turnover. AOX allows electrons to bypass the main cytochrome pathway to restrict the generation of reactive oxygen species (ROS). The inhibition of AOX leads to oxidative damage and contributes to the loss of adaptability and viability in some pathogenic organisms. Although AOXs have recently been identified in several organisms, crystal structures and major functions still need to be explored. Recent work on the trypanosome alternative oxidase has provided a crystal structure of an AOX protein, which contributes to the structure-activity relationship of the inhibitors of AOX. Here, we review the current knowledge on the development, structure, and properties of AOXs, as well as their roles and mechanisms in plants, animals, algae, protists, fungi, and bacteria, with a special emphasis on the development of AOX inhibitors, which will improve the understanding of respiratory regulation in many organisms and provide references for subsequent studies of AOX-targeted inhibitors.
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Affiliation(s)
- Jiye Li
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Institute
of Medicinal Biotechnology, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiyun Yang
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yujie Wu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Ruina Wang
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yu Liu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Jiacun Liu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Zi Ye
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Renjie Tang
- Beijing
South Medical District of Chinese PLA General Hospital, Beijing 100072, China
| | - Malcolm Whiteway
- Department
of Biology, Concordia University, Montreal, H4B 1R6 Quebec, Canada
| | - Quanzhen Lv
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Basic
Medicine Innovation Center for Fungal Infectious Diseases, (Naval Medical University), Ministry of Education, Shanghai 200433, China
- Key
Laboratory of Biosafety Defense (Naval Medical University), Ministry
of Education, Shanghai 200433, China
- Shanghai
Key Laboratory of Medical Biodefense, Shanghai 200433, China
| | - Lan Yan
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Basic
Medicine Innovation Center for Fungal Infectious Diseases, (Naval Medical University), Ministry of Education, Shanghai 200433, China
- Key
Laboratory of Biosafety Defense (Naval Medical University), Ministry
of Education, Shanghai 200433, China
- Shanghai
Key Laboratory of Medical Biodefense, Shanghai 200433, China
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6
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Mori A, Uehara L, Toyoda Y, Masuda F, Soejima S, Saitoh S, Yanagida M. In fission yeast, 65 non-essential mitochondrial proteins related to respiration and stress become essential in low-glucose conditions. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230404. [PMID: 37859837 PMCID: PMC10582590 DOI: 10.1098/rsos.230404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Mitochondria perform critical functions, including respiration, ATP production, small molecule metabolism, and anti-oxidation, and they are involved in a number of human diseases. While the mitochondrial genome contains a small number of protein-coding genes, the vast majority of mitochondrial proteins are encoded by nuclear genes. In fission yeast Schizosaccharomyces pombe, we screened 457 deletion (del) mutants deficient in nuclear-encoded mitochondrial proteins, searching for those that fail to form colonies in culture medium containing low glucose (0.03-0.1%; low-glucose sensitive, lgs), but that proliferate in regular 2-3% glucose medium. Sixty-five (14%) of the 457 deletion mutants displayed the lgs phenotype. Thirty-three of them are defective either in dehydrogenases, subunits of respiratory complexes, the citric acid cycle, or in one of the nine steps of the CoQ10 biosynthetic pathway. The remaining 32 lgs mutants do not seem to be directly related to respiration. Fifteen are implicated in translation, and six encode transporters. The remaining 11 function in anti-oxidation, amino acid synthesis, repair of DNA damage, microtubule cytoskeleton, intracellular mitochondrial distribution or unknown functions. These 32 diverse lgs genes collectively maintain mitochondrial functions under low (1/20-1/60× normal) glucose concentrations. Interestingly, 30 of them have homologues associated with human diseases.
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Affiliation(s)
- Ayaka Mori
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
| | - Lisa Uehara
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
| | - Yusuke Toyoda
- Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Fumie Masuda
- Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Saeko Soejima
- Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Shigeaki Saitoh
- Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Mitsuhiro Yanagida
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
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7
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Lv Y, Liang C, Sun Q, Zhu J, Xu H, Li X, Li YY, Wang Q, Yuan H, Chu B, Zhu D. Structural insights into FSP1 catalysis and ferroptosis inhibition. Nat Commun 2023; 14:5933. [PMID: 37739943 PMCID: PMC10516921 DOI: 10.1038/s41467-023-41626-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
Ferroptosis suppressor protein 1 (FSP1, also known as AIMF2, AMID or PRG3) is a recently identified glutathione-independent ferroptosis suppressor1-3, but its underlying structural mechanism remains unknown. Here we report the crystal structures of Gallus gallus FSP1 in its substrate-free and ubiquinone-bound forms. The structures reveal a FAD-binding domain and a NAD(P)H-binding domain, both of which are shared with AIF and NADH oxidoreductases4-9, and a characteristic carboxy-terminal domain as well. We demonstrate that the carboxy-terminal domain is crucial for the catalytic activity and ferroptosis inhibition of FSP1 by mediating the functional dimerization of FSP1, and the formation of two active sites located on two sides of FAD, which are responsible for ubiquinone reduction and a unique FAD hydroxylation respectively. We also identify that FSP1 can catalyze the production of H2O2 and the conversion of FAD to 6-hydroxy-FAD in the presence of oxygen and NAD(P)H in vitro, and 6-hydroxy-FAD directly inhibits ferroptosis in cells. Together, these findings further our understanding on the catalytic and ferroptosis suppression mechanisms of FSP1 and establish 6-hydroxy-FAD as an active cofactor in FSP1 and a potent radical-trapping antioxidant in ferroptosis inhibition.
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Affiliation(s)
- Yun Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chunhui Liang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Qichao Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Haiyan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xiaoqing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yao-Yao Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Qihai Wang
- School of bioengineering, Jingchu University of Technology, Jingmen, 448000, China.
| | - Huiqing Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Key Laboratory of Experimental Teratology of Ministry of Education, Institute of Medical Sciences, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China.
| | - Bo Chu
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
| | - Deyu Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
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8
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Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice. Nat Commun 2023; 14:1172. [PMID: 36859533 PMCID: PMC9977773 DOI: 10.1038/s41467-023-36894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The hypoxic ventilatory response (HVR) is a life-saving reflex, triggered by the activation of chemoreceptor glomus cells in the carotid body (CB) connected with the brainstem respiratory center. The molecular mechanisms underlying glomus cell acute oxygen (O2) sensing are unclear. Genetic disruption of mitochondrial complex I (MCI) selectively abolishes the HVR and glomus cell responsiveness to hypoxia. However, it is unknown what functions of MCI (metabolic, proton transport, or signaling) are essential for O2 sensing. Here we show that transgenic mitochondrial expression of NDI1, a single-molecule yeast NADH/quinone oxidoreductase that does not directly contribute to proton pumping, fully recovers the HVR and glomus cell sensitivity to hypoxia in MCI-deficient mice. Therefore, maintenance of mitochondrial NADH dehydrogenase activity and the electron transport chain are absolutely necessary for O2-dependent regulation of breathing. NDI1 expression also rescues other systemic defects caused by MCI deficiency. These data explain the role of MCI in acute O2 sensing by arterial chemoreceptors and demonstrate the optimal recovery of complex organismal functions by gene therapy.
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9
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Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
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Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
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10
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Lu L, Åkerbladh L, Ahmad S, Konda V, Cao S, Vocat A, Maes L, Cole ST, Hughes D, Larhed M, Brandt P, Karlén A, Mowbray SL. Synthesis and In Vitro Biological Evaluation of Quinolinyl Pyrimidines Targeting Type II NADH-Dehydrogenase (NDH-2). ACS Infect Dis 2022; 8:482-498. [PMID: 35184552 PMCID: PMC8922281 DOI: 10.1021/acsinfecdis.1c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Type II NADH dehydrogenase
(NDH-2) is an essential component of
electron transfer in many microbial pathogens but has remained largely
unexplored as a potential drug target. Previously, quinolinyl pyrimidines
were shown to inhibit Mycobacterium tuberculosis NDH-2, as well as the growth of the bacteria [ShirudeP. S.; 2012, 3, 736−74024900541]. Here, we synthesized a number of novel quinolinyl pyrimidines
and investigated their properties. In terms of inhibition of the NDH-2
enzymes from M. tuberculosis and Mycobacterium smegmatis, the best compounds were
of similar potency to previously reported inhibitors of the same class
(half-maximal inhibitory concentration (IC50) values in
the low-μM range). However, a number of the compounds had much
better activity against Gram-negative pathogens, with minimum inhibitory
concentrations (MICs) as low as 2 μg/mL. Multivariate analyses
(partial least-squares (PLS) and principle component analysis (PCA))
showed that overall ligand charge was one of the most important factors
in determining antibacterial activity, with patterns that varied depending
on the particular bacterial species. In some cases (e.g., mycobacteria), there was a clear correlation between the IC50 values and the observed MICs, while in other instances,
no such correlation was evident. When tested against a panel of protozoan
parasites, the compounds failed to show activity that was not linked
to cytotoxicity. Further, a strong correlation between hydrophobicity
(estimated as clog P) and cytotoxicity was
revealed; more hydrophobic analogues were more cytotoxic. By contrast,
antibacterial MIC values and cytotoxicity were not well correlated,
suggesting that the quinolinyl pyrimidines can be optimized further
as antimicrobial agents.
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Affiliation(s)
- Lu Lu
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Linda Åkerbladh
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Shabbir Ahmad
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Vivek Konda
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Anthony Vocat
- École Polytechnique Fédérale de Lausanne, EPFL SV/GHI/UPCOL, Global Health Institute, Station no. 19, CH-1015 Lausanne, Switzerland
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Stewart T. Cole
- École Polytechnique Fédérale de Lausanne, EPFL SV/GHI/UPCOL, Global Health Institute, Station no. 19, CH-1015 Lausanne, Switzerland
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box
596, SE-751 24 Uppsala, Sweden
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11
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Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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12
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Godoy-Hernandez A, McMillan DGG. The Profound Influence of Lipid Composition on the Catalysis of the Drug Target NADH Type II Oxidoreductase. MEMBRANES 2021; 11:membranes11050363. [PMID: 34067848 PMCID: PMC8156991 DOI: 10.3390/membranes11050363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022]
Abstract
Lipids play a pivotal role in cellular respiration, providing the natural environment in which an oxidoreductase interacts with the quinone pool. To date, it is generally accepted that negatively charged lipids play a major role in the activity of quinone oxidoreductases. By changing lipid compositions when assaying a type II NADH:quinone oxidoreductase, we demonstrate that phosphatidylethanolamine has an essential role in substrate binding and catalysis. We also reveal the importance of acyl chain composition, specifically c14:0, on membrane-bound quinone-mediated catalysis. This demonstrates that oxidoreductase lipid specificity is more diverse than originally thought and that the lipid environment plays an important role in the physiological catalysis of membrane-bound oxidoreductases.
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13
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Boes DM, Godoy-Hernandez A, McMillan DGG. Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life. MEMBRANES 2021; 11:346. [PMID: 34066904 PMCID: PMC8151925 DOI: 10.3390/membranes11050346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Membrane proteins can be classified into two main categories-integral and peripheral membrane proteins-depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5'-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.
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Affiliation(s)
- Deborah M. Boes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Albert Godoy-Hernandez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Duncan G. G. McMillan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
- School of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11 222, New Zealand
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14
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Abstract
Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na+ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.
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15
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Ukolova IV, Kondakova MA, Kondratov IG, Sidorov AV, Borovskii GB, Voinikov VK. New insights into the organisation of the oxidative phosphorylation system in the example of pea shoot mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2020; 1861:148264. [PMID: 32663476 DOI: 10.1016/j.bbabio.2020.148264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/20/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
The physical and functional organisation of the OXPHOS system in mitochondria in vivo remains elusive. At present, different models of OXPHOS arrangement, representing either highly ordered respiratory strings or, vice versa, a set of randomly dispersed supercomplexes and respiratory complexes, have been suggested. In the present study, we examined a supramolecular arrangement of the OXPHOS system in pea shoot mitochondria using digitonin solubilisation of its constituents, which were further analysed by classical BN-related techniques and a multidimensional gel electrophoresis system when required. As a result, in addition to supercomplexes I1III2, I1III2IVn and III2IV1-2, dimer V2, and individual complexes I-V previously detected in plant mitochondria, new OXPHOS structures were also revealed. Of them, (1) a megacomplex (IIxIIIyIVz)n including complex II, (2) respirasomes I2III4IVn with two copies of complex I and dimeric complex III2, (3) a minor new supercomplex IV1Va2 comigrating with I1III2, and (4) a second minor form of ATP synthase, Va, were found. The activity of singular complexes I, IV, and V was higher than the activity of the associated forms. The detection of new supercomplex IV1Va2, along with assemblies I1III2 and I1-2III2-4IVn, prompted us to suggest the occurrence of in vivo oxphosomes comprising complexes I, III2, IV, and V. The putative oxphosome's stoichiometry, historical background, assumed functional significance, and subcompartmental location are discussed herein.
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Affiliation(s)
- Irina V Ukolova
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, 132, Lermontov St., Irkutsk 664033, Russia.
| | - Marina A Kondakova
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, 132, Lermontov St., Irkutsk 664033, Russia
| | - Ilya G Kondratov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya St., Irkutsk 664033, Russia
| | - Alexander V Sidorov
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, 132, Lermontov St., Irkutsk 664033, Russia; Irkutsk State Medical University, 1, Krasnogo Vosstaniya St., Irkutsk 664003, Russia
| | - Gennadii B Borovskii
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, 132, Lermontov St., Irkutsk 664033, Russia
| | - Victor K Voinikov
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, 132, Lermontov St., Irkutsk 664033, Russia
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16
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McElroy GS, Reczek CR, Reyfman PA, Mithal DS, Horbinski CM, Chandel NS. NAD+ Regeneration Rescues Lifespan, but Not Ataxia, in a Mouse Model of Brain Mitochondrial Complex I Dysfunction. Cell Metab 2020; 32:301-308.e6. [PMID: 32574562 PMCID: PMC7415718 DOI: 10.1016/j.cmet.2020.06.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/19/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023]
Abstract
Mitochondrial complex I regenerates NAD+ and proton pumps for TCA cycle function and ATP production, respectively. Mitochondrial complex I dysfunction has been implicated in many brain pathologies including Leigh syndrome and Parkinson's disease. We sought to determine whether NAD+ regeneration or proton pumping, i.e., bioenergetics, is the dominant function of mitochondrial complex I in protection from brain pathology. We generated a mouse that conditionally expresses the yeast NADH dehydrogenase (NDI1), a single enzyme that can replace the NAD+ regeneration capability of the 45-subunit mammalian mitochondrial complex I without proton pumping. NDI1 expression was sufficient to dramatically prolong lifespan without significantly improving motor function in a mouse model of Leigh syndrome driven by the loss of NDUFS4, a subunit of mitochondrial complex I. Therefore, mitochondrial complex I activity in the brain supports organismal survival through its NAD+ regeneration capacity, while optimal motor control requires the bioenergetic function of mitochondrial complex I.
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Affiliation(s)
- Gregory S McElroy
- Northwestern University Feinberg School of Medicine, Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Colleen R Reczek
- Northwestern University Feinberg School of Medicine, Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Paul A Reyfman
- Northwestern University Feinberg School of Medicine, Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA
| | - Divakar S Mithal
- Ann and Robert H. Lurie Children's Hospital of Chicago, Pediatric Neurology, Chicago, IL 60611, USA; Northwestern University Feinberg School of Medicine, Department of Pediatrics, Chicago, IL 60611, USA
| | - Craig M Horbinski
- Northwestern University Feinberg School of Medicine, Department of Pathology, Chicago, IL 60611, USA; Northwestern University Feinberg School of Medicine, Department of Neurological Surgery, Chicago, IL 60611, USA
| | - Navdeep S Chandel
- Northwestern University Feinberg School of Medicine, Department of Medicine Division of Pulmonary and Critical Care Medicine, Chicago, IL 60611, USA; Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60611, USA.
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17
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Rasmusson AG, Escobar MA, Hao M, Podgórska A, Szal B. Mitochondrial NAD(P)H oxidation pathways and nitrate/ammonium redox balancing in plants. Mitochondrion 2020; 53:158-165. [PMID: 32485334 DOI: 10.1016/j.mito.2020.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/05/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Abstract
Plant mitochondrial oxidative phosphorylation is characterised by alternative electron transport pathways with different energetic efficiencies, allowing turnover of cellular redox compounds like NAD(P)H. These electron transport chain pathways are profoundly affected by soil nitrogen availability, most commonly as oxidized nitrate (NO3-) and/or reduced ammonium (NH4+). The bioenergetic strategies involved in assimilating different N sources can alter redox homeostasis and antioxidant systems in different cellular compartments, including the mitochondria and the cell wall. Conversely, changes in mitochondrial redox systems can affect plant responses to N. This review explores the integration between N assimilation, mitochondrial redox metabolism, and apoplast metabolism.
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Affiliation(s)
- Allan G Rasmusson
- Lund University, Department of Biology, Sölvegatan 35B, 22362 Lund, Sweden.
| | - Matthew A Escobar
- California State University San Marcos, 333 S. Twin Oaks Valley Rd., San Marcos, CA 92096, USA
| | - Mengshu Hao
- Lund University, Department of Biology, Sölvegatan 35B, 22362 Lund, Sweden
| | - Anna Podgórska
- University of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, Ilii Miecznikowa 1, 02-096 Warsaw, Poland
| | - Bożena Szal
- University of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, Ilii Miecznikowa 1, 02-096 Warsaw, Poland
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18
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Nguyen HP, Yi D, Lin F, Viscarra JA, Tabuchi C, Ngo K, Shin G, Lee AYF, Wang Y, Sul HS. Aifm2, a NADH Oxidase, Supports Robust Glycolysis and Is Required for Cold- and Diet-Induced Thermogenesis. Mol Cell 2020; 77:600-617.e4. [PMID: 31952989 PMCID: PMC7031813 DOI: 10.1016/j.molcel.2019.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/10/2019] [Accepted: 12/03/2019] [Indexed: 01/22/2023]
Abstract
Brown adipose tissue (BAT) is highly metabolically active tissue that dissipates energy via UCP1 as heat, and BAT mass is correlated negatively with obesity. The presence of BAT/BAT-like tissue in humans renders BAT as an attractive target against obesity and insulin resistance. Here, we identify Aifm2, a NADH oxidoreductase domain containing flavoprotein, as a lipid droplet (LD)-associated protein highly enriched in BAT. Aifm2 is induced by cold as well as by diet. Upon cold or β-adrenergic stimulation, Aifm2 associates with the outer side of the mitochondrial inner membrane. As a unique BAT-specific first mammalian NDE (external NADH dehydrogenase)-like enzyme, Aifm2 oxidizes NADH to maintain high cytosolic NAD levels in supporting robust glycolysis and to transfer electrons to the electron transport chain (ETC) for fueling thermogenesis. Aifm2 in BAT and subcutaneous white adipose tissue (WAT) promotes oxygen consumption, uncoupled respiration, and heat production during cold- and diet-induced thermogenesis. Aifm2, thus, can ameliorate diet-induced obesity and insulin resistance.
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Affiliation(s)
- Hai P Nguyen
- Endocrinology Program, University of California, Berkeley, Berkeley, CA, USA; Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Danielle Yi
- Endocrinology Program, University of California, Berkeley, Berkeley, CA, USA; Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Frances Lin
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Jose A Viscarra
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Chihiro Tabuchi
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Katina Ngo
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Gawon Shin
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Angus Yiu-Fai Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Yuhui Wang
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Hei Sook Sul
- Endocrinology Program, University of California, Berkeley, Berkeley, CA, USA; Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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19
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Lencina AM, Gennis RB, Schurig-Briccio LA. The oligomeric state of the Caldivirga maquilingensis type III sulfide:Quinone Oxidoreductase is required for membrane binding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148132. [PMID: 31816290 DOI: 10.1016/j.bbabio.2019.148132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/11/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022]
Abstract
Sulfide:quinone oxidoreductase (SQR) is a monotopic membrane flavoprotein present in all domains of life, with multiple roles including sulfide detoxification, homeostasis and energy generation by providing electrons to respiratory or photosynthetic electron transport chains. A type III SQR from the hyperthermophilic archeon Caldivirga maquilingensis has been previously characterized, and its C-terminal amphipathic helices were demonstrated to be responsible for membrane binding. Here, the oligomeric state of this protein was experimentally evaluated by size exclusion chromatography, native gels and crosslinking, and found to be a monomer-dimer-trimer equilibrium. Remarkably, mutant and truncated variants unable to bind to the membrane are able to maintain their oligomeric association. Thus, unlike other related monotopic membrane proteins, the region involved in membrane binding does not influence oligomerization. Furthermore, by studying heterodimers between the WT and mutants, it was concluded that membrane binding requires an oligomer with at least two copies of the protein with intact C-terminal amphipathic helices. A structural homology model of the C. maquilingensis SQR was used to define the flavin- and quinone-binding sites. CmGly12, CmGly16, CmAla77 and CmPro44 were determined to be important for flavin binding. Unexpectedly, CmGly299 is only important for quinone reduction despite its proximity to bound FAD. CmPhe337 and CmPhe362 are also important for quinone binding apparently by direct interaction with the quinone ring, whereas CmLys359, postulated to hydrogen bond to the quinone, seems to have a more structural role. The results presented differentiate the Type III CmSQR from some of its counterparts classified as Type I, II and V.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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20
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Nakatani Y, Shimaki Y, Dutta D, Muench SP, Ireton K, Cook GM, Jeuken LJC. Unprecedented Properties of Phenothiazines Unraveled by a NDH-2 Bioelectrochemical Assay Platform. J Am Chem Soc 2020; 142:1311-1320. [PMID: 31880924 DOI: 10.1021/jacs.9b10254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) plays a crucial role in the respiratory chains of many organisms. Its absence in mammalian cells makes NDH-2 an attractive new target for developing antimicrobials and antiprotozoal agents. We established a novel bioelectrochemical platform to characterize the catalytic behavior of NDH-2 from Caldalkalibacillus thermarum and Listeria monocytogenes strain EGD-e while bound to native-like lipid membranes. Catalysis of both NADH oxidation and lipophilic quinone reduction by membrane-bound NDH-2 followed the Michaelis-Menten model; however, the maximum turnover was only achieved when a high concentration of quinone (>3 mM) was present in the membrane, suggesting that quinone availability regulates NADH-coupled respiration activity. The quinone analogue 2-heptyl-4-hydroxyquinoline-N-oxide inhibited C. thermarum NDH-2 activity, and its potency is higher in a membrane environment compared to assays performed with water-soluble quinone analogues, demonstrating the importance of testing compounds under physiologically relevant conditions. Furthermore, when phenothiazines, one of the most commonly identified NDH-2 inhibitors, were tested, they did not inhibit membrane-bound NDH-2. Instead, our assay platform unexpectedly suggests a novel mode of phenothiazine action where chlorpromazine, a promising antitubercular agent and key medicine used to treat psychotic disorders, is able to disrupt pH gradients across bacterial membranes.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Yosuke Shimaki
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Debajyoti Dutta
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Stephen P Muench
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Keith Ireton
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Lars J C Jeuken
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
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21
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Gene Therapy with Single-Subunit Yeast NADH-Ubiquinone Oxidoreductase (NDI1) Improves the Visual Function in Experimental Autoimmune Encephalomyelitis (EAE) Mice Model of Multiple Sclerosis (MS). Mol Neurobiol 2020; 57:1952-1965. [PMID: 31900864 DOI: 10.1007/s12035-019-01857-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial dysfunction mediated loss of respiration, oxidative stress, and loss of cellular homeostasis contributes to the neuronal and axonal degenerations permanent loss of function in experimental autoimmune encephalomyelitis model (EAE) of multiple sclerosis (MS). To address the mitochondrial dysfunction mediated visual loss in EAE mice, self-complementary adeno-associated virus (scAAV) containing the NADH-dehydrogenase type-2 (NDI1) complex I gene was intravitreally injected into the mice after the onset of visual defects. Visual function assessed by pattern electroretinogram (PERGs) showed progressive loss of function in EAE mice were improved significantly in NDI1 gene therapy-treated mice. Serial optical coherence tomography (OCT) revealed that progressive thinning of inner retinal layers in EAE mice was prevented upon NDI1 expression. The 45% optic nerve axonal and 33% retinal ganglion cell (RGC) loss contributed to the permanent loss of visual function in EAE mice were ameliorated by NDI1-mediated prevention of mitochondrial cristae dissolution and improved mitochondrial homeostasis. In conclusion, targeting the dysfunctional complex I using NDI1 gene can be an approach to address axonal and neuronal loss responsible for permanent disability in MS that is unaltered by current disease modifying drugs.
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22
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Trisolini L, Gambacorta N, Gorgoglione R, Montaruli M, Laera L, Colella F, Volpicella M, De Grassi A, Pierri CL. FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function. J Clin Med 2019; 8:jcm8122117. [PMID: 31810296 PMCID: PMC6947548 DOI: 10.3390/jcm8122117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure-function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna De Grassi
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| | - Ciro Leonardo Pierri
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
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23
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Godoy-Hernandez A, Tate DJ, McMillan DGG. Revealing the Membrane-Bound Catalytic Oxidation of NADH by the Drug Target Type-II NADH Dehydrogenase. Biochemistry 2019; 58:4272-4275. [PMID: 31592658 PMCID: PMC6812066 DOI: 10.1021/acs.biochem.9b00752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Type-II NADH:quinone
oxidoreductases (NDH-2s) are an important
element of microbial pathogen electron transport chains and an attractive
drug target. Despite being widely studied, its mechanism and catalysis
are still poorly understood in a hydrophobic membrane environment.
A recent report for the Escherichia coli NDH-2 showed
NADH oxidation in a solution-based assay but apparently showed the
reverse reaction in electrochemical studies, calling into question
the validity of the electrochemical approach. Here we report electrochemical
catalysis in the well-studied NDH-2 from Caldalkalibacillus
thermarum (CthNDH-2). In agreement with
previous reports, we demonstrated CthNDH-2 NADH oxidation
in a solution assay and electrochemical assays revealed a system artifact
in the absence of quinone that was absent in a membrane system. However,
in the presence of either immobilized quinone or mobile quinone in
a membrane, NADH oxidation was observed as in solution-phase assays.
This conclusively establishes surface-based electrochemistry as a
viable approach for interrogating electron transfer chain drug targets.
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Affiliation(s)
- Albert Godoy-Hernandez
- Department of Biotechnology , Delft University of Technology , Van der Maasweg 9 , Delft 2629 HZ , The Netherlands
| | - Daniel J Tate
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
| | - Duncan G G McMillan
- Department of Biotechnology , Delft University of Technology , Van der Maasweg 9 , Delft 2629 HZ , The Netherlands.,Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , Tokyo 113-8656 , Japan
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24
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Lencina AM, Koepke J, Preu J, Muenke C, Gennis RB, Michel H, Schurig-Briccio LA. Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148080. [PMID: 31520616 DOI: 10.1016/j.bbabio.2019.148080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 09/08/2019] [Indexed: 11/25/2022]
Abstract
The crystal structure of the enzyme previously characterized as a type-2 NADH:menaquinone oxidoreductase (NDH-2) from Thermus thermophilus has been solved at a resolution of 2.9 Å and revealed that this protein is, in fact, a coenzyme A-disulfide reductase (CoADR). Coenzyme A (CoASH) replaces glutathione as the major low molecular weight thiol in Thermus thermophilus and is maintained in the reduced state by this enzyme (CoADR). Although the enzyme does exhibit NADH:menadione oxidoreductase activity expected for NDH-2 enzymes, the specific activity with CoAD as an electron acceptor is about 5-fold higher than with menadione. Furthermore, the crystal structure contains coenzyme A covalently linked Cys44, a catalytic intermediate (Cys44-S-S-CoA) reduced by NADH via the FAD cofactor. Soaking the crystals with menadione shows that menadione can bind to a site near the redox active FAD, consistent with the observed NADH:menadione oxidoreductase activity. CoADRs from other species were also examined and shown to have measurable NADH:menadione oxidoreductase activity. Although a common feature of this family of enzymes, no biological relevance is proposed. The CoADR from T. thermophilus is a soluble homodimeric enzyme. Expression of the recombinant TtCoADR at high levels in E. coli results in a small fraction that co-purifies with the membrane fraction, which was used previously to isolate the enzyme wrongly identified as a membrane-bound NDH-2. It is concluded that T. thermophilus does not contain an authentic NDH-2 component in its aerobic respiratory chain.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Juergen Koepke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Julia Preu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany.
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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25
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Bausewein T, Nussberger S, Kühlbrandt W. Cryo-EM structure of Neurospora crassa respiratory complex IV. IUCRJ 2019; 6:773-780. [PMID: 31316820 PMCID: PMC6608615 DOI: 10.1107/s2052252519007486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 05/13/2023]
Abstract
In fungi, the mitochondrial respiratory chain complexes (complexes I-IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from Neurospora crassa in lipid nanodiscs as cytochrome c oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from Saccharomyces cerevisiae. Its ten subunits are conserved in S. cerevisiae and Bos taurus, but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to N. crassa.
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Affiliation(s)
- Thomas Bausewein
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Stephan Nussberger
- Abteilung Biophysik, Institut für Biomaterialien und biomolekulare Systeme, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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26
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Nawrocki WJ, Bailleul B, Picot D, Cardol P, Rappaport F, Wollman FA, Joliot P. The mechanism of cyclic electron flow. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:433-438. [PMID: 30827891 DOI: 10.1016/j.bbabio.2018.12.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 12/08/2018] [Accepted: 12/08/2018] [Indexed: 12/16/2022]
Abstract
Apart from the canonical light-driven linear electron flow (LEF) from water to CO2, numerous regulatory and alternative electron transfer pathways exist in chloroplasts. One of them is the cyclic electron flow around Photosystem I (CEF), contributing to photoprotection of both Photosystem I and II (PSI, PSII) and supplying extra ATP to fix atmospheric carbon. Nonetheless, CEF remains an enigma in the field of functional photosynthesis as we lack understanding of its pathway. Here, we address the discrepancies between functional and genetic/biochemical data in the literature and formulate novel hypotheses about the pathway and regulation of CEF based on recent structural and kinetic information.
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Affiliation(s)
- W J Nawrocki
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France; Laboratoire de Génétique et Physiologie des Microalgues, Institut de Botanique, Université de Liège, 4, Chemin de la Vallée, B-4000 Liège, Belgium.
| | - B Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France
| | - D Picot
- Institut de Biologie Physico-Chimique, UMR 7099 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France
| | - P Cardol
- Laboratoire de Génétique et Physiologie des Microalgues, Institut de Botanique, Université de Liège, 4, Chemin de la Vallée, B-4000 Liège, Belgium
| | - F Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France
| | - F-A Wollman
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France
| | - P Joliot
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P. et M. Curie, 75005 Paris, France
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27
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Alternative NAD(P)H dehydrogenase and alternative oxidase: Proposed physiological roles in animals. Mitochondrion 2019; 45:7-17. [DOI: 10.1016/j.mito.2018.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/01/2017] [Accepted: 01/26/2018] [Indexed: 12/12/2022]
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28
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Antos-Krzeminska N, Jarmuszkiewicz W. Alternative Type II NAD(P)H Dehydrogenases in the Mitochondria of Protists and Fungi. Protist 2018; 170:21-37. [PMID: 30553126 DOI: 10.1016/j.protis.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/12/2018] [Accepted: 11/04/2018] [Indexed: 01/11/2023]
Abstract
Plants, fungi, and some protists possess a more branched electron transport chain in their mitochondria compared to canonical one. In these organisms, the electron transport chain contains several rotenone-insensitive NAD(P)H dehydrogenases. Some are located on the outer surface, and others are located on the inner surface of the inner mitochondrial membrane. The putative role of these enzymes still remains elusive, but they may prevent the overreduction of the electron transport chain components and decrease the production of reaction oxygen species as a consequence. The last two decades resulted in the discovery of alternative rotenone-insensitive NAD(P)H dehydrogenases present in representatives of fungi and protozoa. The aim of this review is to gather and focus on current information concerning molecular and functional properties, regulation, and the physiological role of fungal and protozoan alternative NAD(P)H dehydrogenases.
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Affiliation(s)
- Nina Antos-Krzeminska
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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29
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Sukumar N, Liu S, Li W, Mathews FS, Mitra B, Kandavelu P. Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2 Å resolution. Biochimie 2018; 154:45-54. [PMID: 30071260 DOI: 10.1016/j.biochi.2018.07.017] [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: 01/16/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
Abstract
The x-ray structure of the monotopic membrane protein (S)-mandelate dehydrogenase (MDH) from Pseudomonas putida reveals an inherent flexibility of its membrane binding segment that might be important for its biological activity. The surface of MDH exhibits a concentration of the positive charges on one side and the negative charges on the other side. The putative membrane binding surface of MDH has a concentric circular ridge, formed by positively charged residues, which projects away from the protein surface by ∼4 Å; this is an unique structural feature and not observed in other monotopic membrane proteins to our knowledge. There are three α-helixes in the membrane binding region. Based on the structure of MDH, it is possible to propose that the interaction of MDH with the membrane is stabilized by coplanar electrostatic interactions, between the positively charged concentric circular ridge and the negatively charged head-groups of the phospholipid bilayer, along with three α-helixes that provide additional stability by inserting into the membrane. The structure reveals the possible orientation of these helixes along with possible roles for the individual residues which form those helixes. These α-helixes may play a role in the enzyme's mobility. A detergent molecule, N-Dodecyl-β-maltoside, is inserted between the membrane binding region and rest of the molecule and may provide structural stability to intra-protein regions by forming hydrogen bonds and close contacts. From the average B-factor of the MDH structure, it is likely that MDH is highly mobile, which might be essential for its interaction in membrane and non-membrane environments, as its substrate (S)-mandelate, is from the cytoplasm, while its electron acceptor is a component of the membrane electron transport chain.
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Affiliation(s)
- N Sukumar
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - S Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - W Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - F S Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - B Mitra
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - P Kandavelu
- SER-CAT and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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30
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Matuz-Mares D, Matus-Ortega G, Cárdenas-Monroy C, Romero-Aguilar L, Villalobos-Rocha JC, Vázquez-Meza H, Guerra-Sánchez G, Peña-Díaz A, Pardo JP. Expression of alternative NADH dehydrogenases (NDH-2) in the phytopathogenic fungus Ustilago maydis. FEBS Open Bio 2018; 8:1267-1279. [PMID: 30221129 PMCID: PMC6134880 DOI: 10.1002/2211-5463.12475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/27/2018] [Accepted: 06/11/2018] [Indexed: 11/17/2022] Open
Abstract
Type 2 alternative NADH dehydrogenases (NDH‐2) participate indirectly in the generation of the electrochemical proton gradient by transferring electrons from NADH and NADPH into the ubiquinone pool. Due to their structural simplicity, alternative NADH dehydrogenases have been proposed as useful tools for gene therapy of cells with defects in the respiratory complex I. In this work, we report the presence of three open reading frames, which correspond to NDH‐2 genes in the genome of Ustilago maydis. These three genes were constitutively transcribed in cells cultured in YPD and minimal medium with glucose, ethanol, or lactate as carbon sources. Proteomic analysis showed that only two of the three NDH‐2 were associated with isolated mitochondria in all culture media. Oxygen consumption by permeabilized cells using NADH or NADPH was different for each condition, opening the possibility of posttranslational regulation. We confirmed the presence of both external and internal NADH dehydrogenases, as well as an external NADPH dehydrogenase insensitive to calcium. Higher oxygen consumption rates were observed during the exponential growth phase, suggesting that the activity of NADH and NADPH dehydrogenases is coupled to the dynamics of cell growth.
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Affiliation(s)
- Deyamira Matuz-Mares
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Genaro Matus-Ortega
- Departamento de Genética Molecular Instituto de Fisiología Celular Universidad Nacional Autónoma de México Ciudad de México México
| | - Christian Cárdenas-Monroy
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Lucero Romero-Aguilar
- Bioquímica de hongos Escuela Nacional de Ciencias Biológicas Instituto Politécnico Nacional Ciudad de México México
| | | | - Héctor Vázquez-Meza
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Guadalupe Guerra-Sánchez
- Bioquímica de hongos Escuela Nacional de Ciencias Biológicas Instituto Politécnico Nacional Ciudad de México México
| | - Antonio Peña-Díaz
- Departamento de Genética Molecular Instituto de Fisiología Celular Universidad Nacional Autónoma de México Ciudad de México México
| | - Juan Pablo Pardo
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
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31
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Type 2 NADH Dehydrogenase Is the Only Point of Entry for Electrons into the Streptococcus agalactiae Respiratory Chain and Is a Potential Drug Target. mBio 2018; 9:mBio.01034-18. [PMID: 29970468 PMCID: PMC6030563 DOI: 10.1128/mbio.01034-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The opportunistic pathogen Streptococcus agalactiae is the major cause of meningitis and sepsis in a newborn’s first week, as well as a considerable cause of pneumonia, urinary tract infections, and sepsis in immunocompromised adults. This pathogen respires aerobically if heme and quinone are available in the environment, and a functional respiratory chain is required for full virulence. Remarkably, it is shown here that the entire respiratory chain of S. agalactiae consists of only two enzymes, a type 2 NADH dehydrogenase (NDH-2) and a cytochrome bd oxygen reductase. There are no respiratory dehydrogenases other than NDH-2 to feed electrons into the respiratory chain, and there is only one respiratory oxygen reductase to reduce oxygen to water. Although S. agalactiae grows well in vitro by fermentative metabolism, it is shown here that the absence of NDH-2 results in attenuated virulence, as observed by reduced colonization in heart and kidney in a mouse model of systemic infection. The lack of NDH-2 in mammalian mitochondria and its important role for virulence suggest this enzyme may be a potential drug target. For this reason, in this study, S. agalactiae NDH-2 was purified and biochemically characterized, and the isolated enzyme was used to screen for inhibitors from libraries of FDA-approved drugs. Zafirlukast was identified to successfully inhibit both NDH-2 activity and aerobic respiration in intact cells. This compound may be useful as a laboratory tool to inhibit respiration in S. agalactiae and, since it has few side effects, it might be considered a lead compound for therapeutics development. S. agalactiae is part of the human intestinal microbiota and is present in the vagina of ~30% of healthy women. Although a commensal, it is also the leading cause of septicemia and meningitis in neonates and immunocompromised adults. This organism can aerobically respire, but only using external sources of heme and quinone, required to have a functional electron transport chain. Although bacteria usually have a branched respiratory chain with multiple dehydrogenases and terminal oxygen reductases, here we establish that S. agalactiae utilizes only one type 2 NADH dehydrogenase (NDH-2) and one cytochrome bd oxygen reductase to perform respiration. NADH-dependent respiration plays a critical role in the pathogen in maintaining NADH/NAD+ redox balance in the cell, optimizing ATP production, and tolerating oxygen. In summary, we demonstrate the essential role of NDH-2 in respiration and its contribution to S. agalactiae virulence and propose it as a potential drug target.
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In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum. Molecules 2018; 23:molecules23040772. [PMID: 29584709 PMCID: PMC6017605 DOI: 10.3390/molecules23040772] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite’s respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1–UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum. The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.
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33
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Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation. Proc Natl Acad Sci U S A 2018; 115:3048-3053. [PMID: 29507228 DOI: 10.1073/pnas.1712061115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 1 (Rcf1) protein is located in the mitochondrial inner membrane where it is involved in formation of supercomplexes composed of respiratory complexes III and IV. We report the solution structure of Rcf1, which forms a dimer in dodecylphosphocholine (DPC) micelles, where each monomer consists of a bundle of five transmembrane (TM) helices and a short flexible soluble helix (SH). Three TM helices are unusually charged and provide the dimerization interface consisting of 10 putative salt bridges, defining a "charge zipper" motif. The dimer structure is supported by molecular dynamics (MD) simulations in DPC, although the simulations show a more dynamic dimer interface than the NMR data. Furthermore, CD and NMR data indicate that Rcf1 undergoes a structural change when reconstituted in liposomes, which is supported by MD data, suggesting that the dimer structure is unstable in a planar membrane environment. Collectively, these data indicate a dynamic monomer-dimer equilibrium. Furthermore, the Rcf1 dimer interacts with cytochrome c, suggesting a role as an electron-transfer bridge between complexes III and IV. The Rcf1 structure will help in understanding its functional roles at a molecular level.
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34
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Yamashita T, Inaoka DK, Shiba T, Oohashi T, Iwata S, Yagi T, Kosaka H, Miyoshi H, Harada S, Kita K, Hirano K. Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors. Sci Rep 2018; 8:2427. [PMID: 29402945 PMCID: PMC5799168 DOI: 10.1038/s41598-018-20775-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Yeast Ndi1 is a monotopic alternative NADH dehydrogenase. Its crystal structure in complex with the electron acceptor, ubiquinone, has been determined. However, there has been controversy regarding the ubiquinone binding site. To address these points, we identified the first competitive inhibitor of Ndi1, stigmatellin, along with new mixed-type inhibitors, AC0-12 and myxothiazol, and thereby determined the crystal structures of Ndi1 in complexes with the inhibitors. Two separate binding sites of stigmatellin, STG-1 and STG-2, were observed. The electron density at STG-1, located at the vicinity of the FAD cofactor, further demonstrated two binding modes: STG-1a and STG-1b. AC0-12 and myxothiazol are also located at the vicinity of FAD. The comparison of the binding modes among stigmatellin at STG-1, AC0-12, and myxothiazol revealed a unique position for the aliphatic tail of stigmatellin at STG-1a. Mutations of amino acid residues that interact with this aliphatic tail at STG-1a reduced the affinity of Ndi1 for ubiquinone. In conclusion, the position of the aliphatic tail of stigmatellin at STG-1a provides a structural basis for its competitive inhibition of Ndi1. The inherent binding site of ubiquinone is suggested to overlap with STG-1a that is distinct from the binding site for NADH.
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Affiliation(s)
- Tetsuo Yamashita
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Takumi Oohashi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - So Iwata
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire, OX11 0DE, UK
- Japan Science and Technology Agency, Exploratory Research for Advanced Technology, Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-Ku, Kyoto, 606-8501, Japan
- Systems and Structural Biology Centre, RIKEN, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takao Yagi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Hiroaki Kosaka
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
- Osaka Jikei College, 1-2-8 Miyahara, Yodogawa-Ku, Osaka, 532-0003, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan.
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Katsuya Hirano
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
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A Role for the Respiratory Chain in Regulating Meiosis Initiation in Saccharomyces cerevisiae. Genetics 2018; 208:1181-1194. [PMID: 29301906 DOI: 10.1534/genetics.118.300689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Meiosis is a specific type of cell division that is essential for sexual reproduction in most eukaryotes. Mitochondria are crucial cellular organelles that play important roles in reproduction, though the detailed mechanism by which the mitochondrial respiratory chain functions during meiosis remains elusive. Here, we show that components of the respiratory chain (Complexes I-V) play essential roles in meiosis initiation during the sporulation of budding yeast, Saccharomyces cerevisiae Any functional defects in the Complex I component Ndi1p resulted in the abolishment of sporulation. Further studies revealed that respiratory deficiency resulted in the failure of premeiotic DNA replication due to insufficient IME1 expression. In addition, respiration promoted the expression of RIM101, whose product inhibits Smp1p, a negative transcriptional regulator of IME1, to promote meiosis initiation. In summary, our studies unveiled the close relationship between mitochondria and sporulation, and uncover a novel meiosis initiation pathway that is regulated by the respiratory chain.
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Gao X, Sun T, Wu L, Chen L, Zhang W. Co-overexpression of response regulator genes slr1037 and sll0039 improves tolerance of Synechocystis sp. PCC 6803 to 1-butanol. BIORESOURCE TECHNOLOGY 2017; 245:1476-1483. [PMID: 28533065 DOI: 10.1016/j.biortech.2017.04.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 05/22/2023]
Abstract
In this study, two response regulator (RR) encoding genes slr1037 as well as sll0039 were co-overexpressed in Synechocystis sp. PCC 6803 by metabolic engineering and the 1-butanol tolerance was successfully improved by 133%. Aiming to explore the possible mechanisms for the enhancing 1-butanol tolerance, a quantitative iTRAQ-LC-MS/MS proteomics approach was then employed, identifying 216 up-regulated and 99 down-regulated proteins compared to wild type after 1-butanol treatment. This study mapped the potential target genes regulated by Slr1037 and Sll0039 and demonstrated the feasibility of engineering response regulators for modifying the biofuel tolerance in cyanobacteria.
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Affiliation(s)
- Xinyan Gao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Lina Wu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, PR China
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37
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Abstract
Iron-sulfur clusters (Fe/S clusters) are essential cofactors required throughout the clades of biology for performing a myriad of unique functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. Although Fe/S clusters can be synthesized in vitro and transferred to a client protein without enzymatic assistance, biology has evolved intricate mechanisms to assemble and transfer Fe/S clusters within the cellular environment. In eukaryotes, the foundation of all cellular clusters starts within the mitochondria. The focus of this review is to detail the mitochondrial Fe/S biogenesis (ISC) pathway along with the Fe/S cluster transfer steps necessary to mature Fe/S proteins. New advances in our understanding of the mitochondrial Fe/S biogenesis machinery will be highlighted. Additionally, we will address various experimental approaches that have been successful in the identification and characterization of components of the ISC pathway.
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Affiliation(s)
- Andrew Melber
- University of Utah Health Sciences Center, Salt Lake City, Utah, United States
| | - Dennis R Winge
- University of Utah Health Sciences Center, Salt Lake City, Utah, United States.
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38
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Nakatani Y, Jiao W, Aragão D, Shimaki Y, Petri J, Parker EJ, Cook GM. Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å. Acta Crystallogr F Struct Biol Commun 2017; 73:541-549. [PMID: 28994401 PMCID: PMC5633920 DOI: 10.1107/s2053230x17013073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022] Open
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - David Aragão
- Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Australia
| | - Yosuke Shimaki
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Jessica Petri
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
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39
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The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:823-832. [PMID: 28801048 DOI: 10.1016/j.bbabio.2017.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/04/2017] [Accepted: 08/05/2017] [Indexed: 11/22/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane bound enzymes that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones. In this way, these enzymes also contribute to the regeneration of NAD+, allowing several metabolic pathways to proceed. As for the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, the enzymatic mechanism of NDH-2s is still little explored and elusive. In this work we addressed the role of the conserved glutamate 172 (E172) residue in the enzymatic mechanism of NDH-2 from Staphylococcus aureus. We aimed to test our earlier hypothesis that E172 plays a key role in proton transfer to allow the protonation of the quinone. For this we performed a complete biochemical characterization of the enzyme's variants E172A, E172Q and E172S. Our steady state kinetic measurements show a clear decrease in the overall reaction rate, and our substrate interaction studies indicate the binding of the two substrates is also affected by these mutations. Interestingly our fast kinetic results show quinone reduction is more affected than NADH oxidation. We have also determined the X-ray crystal structure of the E172S mutant (2.55Ǻ) and compared it with the structure of the wild type (2.32Ǻ). Together these results support our hypothesis for E172 being of central importance in the catalytic mechanism of NDH-2, which may be extended to other members of the tDBDF superfamily.
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40
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SLC25 Family Member Genetic Interactions Identify a Role for HEM25 in Yeast Electron Transport Chain Stability. G3-GENES GENOMES GENETICS 2017; 7:1861-1873. [PMID: 28404662 PMCID: PMC5473764 DOI: 10.1534/g3.117.041194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The SLC25 family member SLC25A38 (Hem25 in yeast) was recently identified as a mitochondrial glycine transporter that provides substrate to initiate heme/hemoglobin synthesis. Mutations in the human SLC25A38 gene cause congenital sideroblastic anemia. The full extent to which SLC25 family members coregulate heme synthesis with other mitochondrial functions is not clear. In this study, we surveyed 29 nonessential SLC25 family members in Saccharomyces cerevisiae for their ability to support growth in the presence and absence of HEM25. Six SLC25 family members were identified that were required for growth or for heme synthesis in cells lacking Hem25 function. Importantly, we determined that loss of function of the SLC25 family member Flx1, which imports FAD into mitochondria, together with loss of function of Hem25, resulted in inability to grow on media that required yeast cells to supply energy using mitochondrial respiration. We report that specific components of complexes of the electron transport chain are decreased in the absence of Flx1 and Hem25 function. In addition, we show that mitochondria from flx1Δ hem25Δ cells contain uncharacterized Cox2-containing high molecular weight aggregates. The functions of Flx1 and Hem25 provide a facile explanation for the decrease in heme level, and in specific electron transport chain complex components.
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41
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Lemire BD. Evolution, structure and membrane association of NDUFAF6, an assembly factor for NADH:ubiquinone oxidoreductase (Complex I). Mitochondrion 2017; 35:13-22. [PMID: 28476317 DOI: 10.1016/j.mito.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/28/2017] [Accepted: 04/28/2017] [Indexed: 01/31/2023]
Abstract
The NADH:ubiquinone oxidoreductase (complex I) is the largest member of the mitochondrial respiratory chain. Its FMN cofactor accepts two electrons from NADH and transfers them to ubiquinone via a chain of iron-sulphur centers. A central core of 14 highly conserved subunits can couple electron transfer to proton translocation. The mammalian enzyme has an additional ~30 accessory subunits. Complex I has important bioenergetic and metabolic functions and is a known source of reactive oxygen species; these functions link it to a number of hereditary and degenerative diseases. For many complex I deficiencies, the primary defect is not in a subunit-encoding gene, but rather in an assembly factor or chaperone that participates in the biogenesis of newly synthesized complex I from individual subunits and cofactors. NDUFAF6 encodes a complex I assembly factor and mutations result in complex I deficiency, Leigh syndrome or Acadian variant Fanconi syndrome. Human NDUFAF6 is a mitochondria-targeted 333-amino acid protein belonging to the family of squalene and phytoene synthases. Sequence and structural information suggests that NDUFAF6 likely has enzymatic activity, but one that has evolved considerable differences from canonical squalene and phytoene synthases. Most but not all metazoans have an NDUFAF6 ortholog, indicating that in some organisms, complex I biogenesis does not require this protein. NDUFAF6 is a peripheral membrane protein and predictions identify a conserved C-terminal attachment site that have implications for substrate access.
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Affiliation(s)
- Bernard D Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G2H7, Canada.
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42
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Yang Y, Yu Y, Li X, Li J, Wu Y, Yu J, Ge J, Huang Z, Jiang L, Rao Y, Yang M. Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. J Med Chem 2017; 60:1994-2005. [DOI: 10.1021/acs.jmedchem.6b01733] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yiqing Yang
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - You Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolu Li
- Department
of Biochemistry and Molecular Biology, State Key Laboratory of Medical
Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Jing Li
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Wu
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingpeng Ge
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenghui Huang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lubin Jiang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Rao
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Maojun Yang
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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43
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Marreiros BC, Sena FV, Sousa FM, Oliveira ASF, Soares CM, Batista AP, Pereira MM. Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family. Sci Rep 2017; 7:42303. [PMID: 28181562 PMCID: PMC5299459 DOI: 10.1038/srep42303] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/05/2017] [Indexed: 12/29/2022] Open
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains. These proteins contribute indirectly to the establishment of the transmembrane difference of electrochemical potential by catalyzing the reduction of quinone by oxidation of NAD(P)H. NDH-2s are widespread enzymes being present in the three domains of life. In this work, we explored the catalytic mechanism of NDH-2 by investigating the common elements of all NDH-2s, based on the rationale that conservation of such elements reflects their structural/functional importance. We observed conserved sequence motifs and structural elements among 1762 NDH-2s. We identified two proton pathways possibly involved in the protonation of the quinone. Our results led us to propose the first catalytic mechanism for NDH-2 family, in which a conserved glutamate residue, E172 (in NDH-2 from Staphylococcus aureus) plays a key role in proton transfer to the quinone pocket. This catalytic mechanism may also be extended to the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, such as sulfide:quinone oxidoreductases.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - A Sofia F Oliveira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
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44
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The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Sci Rep 2017; 7:40165. [PMID: 28067272 PMCID: PMC5220320 DOI: 10.1038/srep40165] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/01/2016] [Indexed: 11/08/2022] Open
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.
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45
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Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Curr Genet 2016; 63:253-274. [DOI: 10.1007/s00294-016-0633-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 01/06/2023]
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46
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Regulatory role of the respiratory supercomplex factors in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2016; 113:E4476-85. [PMID: 27432958 DOI: 10.1073/pnas.1601196113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The respiratory supercomplex factors (Rcf) 1 and 2 mediate supramolecular interactions between mitochondrial complexes III (ubiquinol-cytochrome c reductase; cyt. bc1) and IV (cytochrome c oxidase; CytcO). In addition, removal of these polypeptides results in decreased activity of CytcO, but not of cyt. bc1 In the present study, we have investigated the kinetics of ligand binding, the single-turnover reaction of CytcO with O2, and the linked cyt. bc1-CytcO quinol oxidation-oxygen-reduction activities in mitochondria in which Rcf1 or Rcf2 were removed genetically (strains rcf1Δ and rcf2Δ, respectively). The data show that in the rcf1Δ and rcf2Δ strains, in a significant fraction of the population, ligand binding occurs over a time scale that is ∼100-fold faster (τ ≅ 100 μs) than observed with the wild-type mitochondria (τ ≅ 10 ms), indicating structural changes. This effect is specific to removal of Rcf and not dissociation of the cyt. bc1-CytcO supercomplex. Furthermore, in the rcf1Δ and rcf2Δ strains, the single-turnover reaction of CytcO with O2 was incomplete. This observation indicates that the lower activity of CytcO is caused by a fraction of inactive CytcO rather than decreased CytcO activity of the entire population. Furthermore, the data suggest that the Rcf1 polypeptide mediates formation of an electron-transfer bridge from cyt. bc1 to CytcO via a tightly bound cyt. c We discuss the significance of the proposed regulatory mechanism of Rcf1 and Rcf2 in the context of supramolecular interactions between cyt. bc1 and CytcO.
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47
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Hao MS, Rasmusson AG. The evolution of substrate specificity-associated residues and Ca(2+) -binding motifs in EF-hand-containing type II NAD(P)H dehydrogenases. PHYSIOLOGIA PLANTARUM 2016; 157:338-351. [PMID: 27079180 DOI: 10.1111/ppl.12453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
Most eukaryotic organisms, except some animal clades, have mitochondrial alternative electron transport enzymes that allow respiration to bypass the energy coupling in oxidative phosphorylation. The energy bypass enzymes in plants include the external type II NAD(P)H dehydrogenases (DHs) of the NDB family, which are characterized by an EF-hand domain for Ca(2+) binding. Here we investigate these plant enzymes by combining molecular modeling with evolutionary analysis. Molecular modeling of the Arabidopsis thaliana AtNDB1 with the yeast ScNDI1 as template revealed distinct similarities in the core catalytic parts, and highlighted the interaction between the pyridine nucleotide and residues correlating with NAD(P)H substrate specificity. The EF-hand domain of AtNDB1 has no counterpart in ScNDI1, and was instead modeled with Ca(2+) -binding signal transducer proteins. Combined models displayed a proximity of the AtNDB1 EF-hand domain to the substrate entrance side of the catalytic part. Evolutionary analysis of the eukaryotic NDB-type proteins revealed ancient and recent reversions between the motif observed in proteins specific for NADH (acidic type) and NADPH (non-acidic type), and that the clade of enzymes with acidic motifs in angiosperms derives from non-acidic-motif NDB-type proteins present in basal plants, fungi and protists. The results suggest that Ca(2+) -dependent external NADPH oxidation is an ancient process, indicating that it has a fundamental importance for eukaryotic cellular redox metabolism. In contrast, the external NADH DHs in plants are products of a recent expansion, mirroring the expansion of the alternative oxidase family.
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Affiliation(s)
- Meng-Shu Hao
- Department of Biology, Lund University, Lund, Sweden
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48
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Marreiros BC, Sena FV, Sousa FM, Batista AP, Pereira MM. Type II NADH:quinone oxidoreductase family: phylogenetic distribution, structural diversity and evolutionary divergences. Environ Microbiol 2016; 18:4697-4709. [PMID: 27105286 DOI: 10.1111/1462-2920.13352] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/17/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins, crucial for the catabolic metabolism, because they contribute to the maintenance of the NADH/NAD+ balance. In several pathogenic bacteria and protists, NDH-2s are the only enzymes performing respiratory NADH:quinone oxidoreductase activity. For this reason and for being considered absent in mammals, NDH-2s were proposed as suitable targets for novel antimicrobial therapies. We selected all sequences of genes encoding NDH-2s from fully sequenced genomes present in the KEGG database. These genes were present in 61% of the 1805 species belonging to Eukarya (83%), Bacteria (60%) and Archaea (32%). Notably sequences from mammal species including humans were retrieved in our selection as NDH-2s. The data obtained and the already available information allowed systematizing several properties of NDH-2s: (i) the existence of additional sequence motifs with putative regulatory functions, (ii) specificity towards NADH or NADPH and (iii) the type of quinone binding motif. We observed that NDH-2 family distribution is not congruent with the taxonomic tree, suggesting different origins for the eukaryotic sequences and possible lateral gene transfer among prokaryotes. We note the absence of genes coding for NDH-2 in anaerobic phyla and the presence of multiple copies in several genomes, specifically in cyanobacteria. These observations inspired us to propose a metabolic hypothesis for the appearance of NDH-2s.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
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49
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Salewski J, Batista AP, Sena FV, Millo D, Zebger I, Pereira MM, Hildebrandt P. Substrate-Protein Interactions of Type II NADH:Quinone Oxidoreductase from Escherichia coli. Biochemistry 2016; 55:2722-34. [PMID: 27109164 DOI: 10.1021/acs.biochem.6b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and responsible for the maintenance of NADH/NAD(+) balance in cells. NDH-2s are the only enzymes with NADH dehydrogenase activity present in the respiratory chain of many pathogens, and thus, they were proposed as suitable targets for antimicrobial therapies. In addition, NDH-2s were also considered key players for the treatment of complex I-related neurodegenerative disorders. In this work, we explored substrate-protein interaction in NDH-2 from Escherichia coli (EcNDH-2) combining surface-enhanced infrared absorption spectroscopic studies with electrochemical experiments, fluorescence spectroscopy assays, and quantum chemical calculations. Because of the specific stabilization of substrate complexes of EcNDH-2 immobilized on electrodes, it was possible to demonstrate the presence of two distinct substrate binding sites for NADH and the quinone and to identify a bound semiprotonated quinol as a catalytic intermediate.
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Affiliation(s)
- Johannes Salewski
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Diego Millo
- Biomolecular Spectroscopy/LaserLaB Amsterdam, Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ingo Zebger
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Marreiros BC, Calisto F, Castro PJ, Duarte AM, Sena FV, Silva AF, Sousa FM, Teixeira M, Refojo PN, Pereira MM. Exploring membrane respiratory chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1039-1067. [PMID: 27044012 DOI: 10.1016/j.bbabio.2016.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/20/2023]
Abstract
Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Paulo J Castro
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Afonso M Duarte
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.
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