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Cao K, Xu J, Cao W, Wang X, Lv W, Zeng M, Zou X, Liu J, Feng Z. Assembly of mitochondrial succinate dehydrogenase in human health and disease. Free Radic Biol Med 2023; 207:247-259. [PMID: 37490987 DOI: 10.1016/j.freeradbiomed.2023.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
Mitochondrial succinate dehydrogenase (SDH), also known as electron transport chain (ETC) Complex II, is the only enzyme complex engaged in both oxidative phosphorylation and the tricarboxylic acid (TCA) cycle. SDH has received increasing attention due to its crucial role in regulating mitochondrial metabolism and human health. Despite having the fewest subunits among the four ETC complexes, functional SDH is formed via a sequential and well-coordinated assembly of subunits. Along with the discovery of subunit-specific assembly factors, the dynamic involvement of the SDH assembly process in a broad range of diseases has been revealed. Recently, we reported that perturbation of SDH assembly in different tissues leads to interesting and distinct pathophysiological changes in mice, indicating a need to understand the intricate SDH assembly process in human health and diseases. Thus, in this review, we summarize recent findings on SDH pathogenesis with respect to disease and a focus on SDH assembly.
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Affiliation(s)
- Ke Cao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China; Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jie Xu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China
| | - Wenli Cao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China
| | - Xueqiang Wang
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, 266071, China
| | - Weiqiang Lv
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China
| | - Mengqi Zeng
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, 266071, China
| | - Xuan Zou
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China; School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, 266071, China.
| | - Zhihui Feng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, 266071, China.
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2
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How an assembly factor enhances covalent FAD attachment to the flavoprotein subunit of complex II. J Biol Chem 2022; 298:102472. [PMID: 36089066 PMCID: PMC9557727 DOI: 10.1016/j.jbc.2022.102472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 01/25/2023] Open
Abstract
The membrane-bound complex II family of proteins is composed of enzymes that catalyze succinate and fumarate interconversion coupled with reduction or oxidation of quinones within the membrane domain. The majority of complex II enzymes are protein heterotetramers with the different subunits harboring a variety of redox centers. These redox centers are used to transfer electrons between the site of succinate-fumarate oxidation/reduction and the membrane domain harboring the quinone. A covalently bound FAD cofactor is present in the flavoprotein subunit, and the covalent flavin linkage is absolutely required to enable the enzyme to oxidize succinate. Assembly of the covalent flavin linkage in eukaryotic cells and many bacteria requires additional protein assembly factors. Here, we provide mechanistic details for how the assembly factors work to enhance covalent flavinylation. Both prokaryotic SdhE and mammalian SDHAF2 enhance FAD binding to their respective apoprotein of complex II. These assembly factors also increase the affinity for dicarboxylates to the apoprotein-noncovalent FAD complex and stabilize the preassembly complex. These findings are corroborated by previous investigations of the roles of SdhE in enhancing covalent flavinylation in both bacterial succinate dehydrogenase and fumarate reductase flavoprotein subunits and of SDHAF2 in performing the same function for the human mitochondrial succinate dehydrogenase flavoprotein. In conclusion, we provide further insight into assembly factor involvement in building complex II flavoprotein subunit active site required for succinate oxidation.
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3
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Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress. mSystems 2021; 6:e0118921. [PMID: 34874779 PMCID: PMC8651089 DOI: 10.1128/msystems.01189-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation. IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.
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Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways. Int J Mol Sci 2020; 21:ijms21113820. [PMID: 32481479 PMCID: PMC7312649 DOI: 10.3390/ijms21113820] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
The assembly of mitochondrial oxidative phosphorylation (OXPHOS) complexes is an intricate process, which—given their dual-genetic control—requires tight co-regulation of two evolutionarily distinct gene expression machineries. Moreover, fine-tuning protein synthesis to the nascent assembly of OXPHOS complexes requires regulatory mechanisms such as translational plasticity and translational activators that can coordinate mitochondrial translation with the import of nuclear-encoded mitochondrial proteins. The intricacy of OXPHOS complex biogenesis is further evidenced by the requirement of many tightly orchestrated steps and ancillary factors. Early-stage ancillary chaperones have essential roles in coordinating OXPHOS assembly, whilst late-stage assembly factors—also known as the LYRM (leucine–tyrosine–arginine motif) proteins—together with the mitochondrial acyl carrier protein (ACP)—regulate the incorporation and activation of late-incorporating OXPHOS subunits and/or co-factors. In this review, we describe recent discoveries providing insights into the mechanisms required for optimal OXPHOS biogenesis, including the coordination of mitochondrial gene expression with the availability of nuclear-encoded factors entering via mitochondrial protein import systems.
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Light SH, Méheust R, Ferrell JL, Cho J, Deng D, Agostoni M, Iavarone AT, Banfield JF, D’Orazio SEF, Portnoy DA. Extracellular electron transfer powers flavinylated extracellular reductases in Gram-positive bacteria. Proc Natl Acad Sci U S A 2019; 116:26892-26899. [PMID: 31818955 PMCID: PMC6936397 DOI: 10.1073/pnas.1915678116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mineral-respiring bacteria use a process called extracellular electron transfer to route their respiratory electron transport chain to insoluble electron acceptors on the exterior of the cell. We recently characterized a flavin-based extracellular electron transfer system that is present in the foodborne pathogen Listeria monocytogenes, as well as many other Gram-positive bacteria, and which highlights a more generalized role for extracellular electron transfer in microbial metabolism. Here we identify a family of putative extracellular reductases that possess a conserved posttranslational flavinylation modification. Phylogenetic analyses suggest that divergent flavinylated extracellular reductase subfamilies possess distinct and often unidentified substrate specificities. We show that flavinylation of a member of the fumarate reductase subfamily allows this enzyme to receive electrons from the extracellular electron transfer system and support L. monocytogenes growth. We demonstrate that this represents a generalizable mechanism by finding that a L. monocytogenes strain engineered to express a flavinylated extracellular urocanate reductase uses urocanate by a related mechanism and to a similar effect. These studies thus identify an enzyme family that exploits a modular flavin-based electron transfer strategy to reduce distinct extracellular substrates and support a multifunctional view of the role of extracellular electron transfer activities in microbial physiology.
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Affiliation(s)
- Samuel H. Light
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, Berkeley, CA 94704
| | - Jessica L. Ferrell
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - Jooyoung Cho
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - David Deng
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Marco Agostoni
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA 94720
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, Berkeley, CA 94704
| | - Sarah E. F. D’Orazio
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky, Lexington, KY 40536-0298
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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Moosavi B, Berry EA, Zhu XL, Yang WC, Yang GF. The assembly of succinate dehydrogenase: a key enzyme in bioenergetics. Cell Mol Life Sci 2019; 76:4023-4042. [PMID: 31236625 PMCID: PMC11105593 DOI: 10.1007/s00018-019-03200-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
Succinate dehydrogenase (SDH) also known as complex II or succinate:quinone oxidoreductase is an enzyme involved in both oxidative phosphorylation and tricarboxylic acid cycle; the processes that generate energy. SDH is a multi-subunit enzyme which requires a series of proteins for its proper assembly at several steps. This enzyme has medical significance as there is a broad range of human diseases from cancers to neurodegeneration related to SDH malfunction. Some of these disorders have recently been linked to defective assembly factors, reinvigorating further research in this area. Apart from that this enzyme has agricultural importance as many fungicides have been/will be designed targeting specifically this enzyme in plant fungal pathogens. In addition, we speculate it might be possible to design novel fungicides specifically targeting fungal assembly factors. Considering the medical and agricultural implications of SDH, the aim of this review is an overview of the SDH assembly factors and critical analysis of controversial issues around them.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.
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7
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Sharma P, Maklashina E, Cecchini G, Iverson TM. Maturation of the respiratory complex II flavoprotein. Curr Opin Struct Biol 2019; 59:38-46. [PMID: 30851631 DOI: 10.1016/j.sbi.2019.01.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022]
Abstract
Respiratory complexes are complicated multi-subunit cofactor-containing machines that allow cells to harvest energy from the environment. Maturation of these complexes requires protein folding, cofactor insertion, and assembly of multiple subunits into a final, functional complex. Because the intermediate states in complex maturation are transitory, these processes are poorly understood. This review gives an overview of the process of maturation in respiratory complex II with a focus on recent structural studies on intermediates formed during covalent flavinylation of the catalytic subunit, SDHA. Covalent flavinylation has an evolutionary significance because variants of complex II enzymes with the covalent ligand removed by mutagenesis cannot oxidize succinate, but can still perform the reverse reaction and reduce fumarate. Since succinate oxidation is a key step of aerobic respiration, the covalent bond of complex II appears to be important for aerobic life.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, United States
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, United States; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, United States; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, United States; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, United States; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States.
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8
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Maklashina E, Rajagukguk S, Iverson TM, Cecchini G. The unassembled flavoprotein subunits of human and bacterial complex II have impaired catalytic activity and generate only minor amounts of ROS. J Biol Chem 2018; 293:7754-7765. [PMID: 29610278 PMCID: PMC5961047 DOI: 10.1074/jbc.ra118.001977] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Complex II (SdhABCD) is a membrane-bound component of mitochondrial and bacterial electron transport chains, as well as of the TCA cycle. In this capacity, it catalyzes the reversible oxidation of succinate. SdhABCD contains the SDHA protein harboring a covalently bound FAD redox center and the iron-sulfur protein SDHB, containing three distinct iron-sulfur centers. When assembly of this complex is compromised, the flavoprotein SDHA may accumulate in the mitochondrial matrix or bacterial cytoplasm. Whether the unassembled SDHA has any catalytic activity, for example in succinate oxidation, fumarate reduction, reactive oxygen species (ROS) generation, or other off-pathway reactions, is not known. Therefore, here we investigated whether unassembled Escherichia coli SdhA flavoprotein, its homolog fumarate reductase (FrdA), and the human SDHA protein have succinate oxidase or fumarate reductase activity and can produce ROS. Using recombinant expression in E. coli, we found that the free flavoproteins from these divergent biological sources have inherently low catalytic activity and generate little ROS. These results suggest that the iron-sulfur protein SDHB in complex II is necessary for robust catalytic activity. Our findings are consistent with those reported for single-subunit flavoprotein homologs that are not associated with iron-sulfur or heme partner proteins.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and
| | - Sany Rajagukguk
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121
| | - T. M. Iverson
- the Departments of Pharmacology and ,Biochemistry, ,the Center for Structural Biology, and ,the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and , Recipient of Senior Research Career Scientist Award IK6BX004215 from the Department of Veterans Affairs. To whom correspondence should be addressed:
Molecular Biology Division (151-S), San Francisco Veterans Affairs Healthcare System, 4150 Clement St., San Francisco, CA 94121. Tel.:
415-221-4810, Ext. 24416; E-mail:
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9
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Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE. Proc Natl Acad Sci U S A 2018. [PMID: 29514959 DOI: 10.1073/pnas.1800195115] [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: 02/07/2023] Open
Abstract
Succinate:quinone oxidoreductase (SQR) functions in energy metabolism, coupling the tricarboxylic acid cycle and electron transport chain in bacteria and mitochondria. The biogenesis of flavinylated SdhA, the catalytic subunit of SQR, is assisted by a highly conserved assembly factor termed SdhE in bacteria via an unknown mechanism. By using X-ray crystallography, we have solved the structure of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Our structure shows that SdhE makes a direct interaction with the flavin adenine dinucleotide-linked residue His45 in SdhA and maintains the capping domain of SdhA in an "open" conformation. This displaces the catalytic residues of the succinate dehydrogenase active site by as much as 9.0 Å compared with SdhA in the assembled SQR complex. These data suggest that bacterial SdhE proteins, and their mitochondrial homologs, are assembly chaperones that constrain the conformation of SdhA to facilitate efficient flavinylation while regulating succinate dehydrogenase activity for productive biogenesis of SQR.
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10
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Sharma P, Maklashina E, Cecchini G, Iverson TM. Crystal structure of an assembly intermediate of respiratory Complex II. Nat Commun 2018; 9:274. [PMID: 29348404 PMCID: PMC5773532 DOI: 10.1038/s41467-017-02713-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Flavin is covalently attached to the protein scaffold in ~10% of flavoenzymes. However, the mechanism of covalent modification is unclear, due in part to challenges in stabilizing assembly intermediates. Here, we capture the structure of an assembly intermediate of the Escherichiacoli Complex II (quinol:fumarate reductase (FrdABCD)). The structure contains the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor, SdhE. The structure contains two global conformational changes as compared to prior structures of the mature protein: the rotation of a domain within the FrdA subunit, and the destabilization of two large loops of the FrdA subunit, which may create a tunnel to the active site. We infer a mechanism for covalent flavinylation. As supported by spectroscopic and kinetic analyses, we suggest that SdhE shifts the conformational equilibrium of the FrdA active site to disfavor succinate/fumarate interconversion and enhance covalent flavinylation. The mechanism for covalent flavinylation of flavoenzymes is still unclear. Here, the authors propose a mechanism based on the crystal structure of a flavinylation assembly intermediate of the E. coli respiratory Complex II comprising the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor SdhE.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA. .,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA. .,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA. .,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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11
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Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, Tsukazaki T, Narita SI, Akiyama Y. The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex. Mol Microbiol 2017; 106:760-776. [PMID: 28960545 DOI: 10.1111/mmi.13844] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 01/21/2023]
Abstract
BepA (formerly YfgC) is an Escherichia coli periplasmic protein consisting of an N-terminal protease domain and a C-terminal tetratricopeptide repeat (TPR) domain. We have previously shown that BepA is a dual functional protein with chaperone-like and proteolytic activities involved in membrane assembly and proteolytic quality control of LptD, a major component of the outer membrane lipopolysaccharide translocon. Intriguingly, BepA can associate with the BAM complex: the β-barrel assembly machinery (BAM) driving integration of β-barrel proteins into the outer membrane. However, the molecular mechanism of BepA function and its association with the BAM complex remains unclear. Here, we determined the crystal structure of the BepA TPR domain, which revealed the presence of two subdomains formed by four TPR motifs. Systematic site-directed in vivo photo-cross-linking was used to map the protein-protein interactions mediated by the BepA TPR domain, showing that this domain interacts both with a substrate and with the BAM complex. Mutational analysis indicated that these interactions are important for the BepA functions. These results suggest that the TPR domain plays critical roles in BepA functions through interactions both with substrates and with the BAM complex. Our findings provide insights into the mechanism of biogenesis and quality control of the outer membrane.
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Affiliation(s)
- Yasushi Daimon
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Chigusa Iwama-Masui
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshiki Tanaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Takuya Shiota
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Saitama 351-0198, Japan
| | - Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroto Sakurada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Trevor Lithgow
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Saitama 351-0198, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Tomoya Tsukazaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Shin-Ichiro Narita
- Faculty of Nutritional Sciences, University of Morioka, Iwate 020-0694, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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12
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Starbird CA, Maklashina E, Sharma P, Qualls-Histed S, Cecchini G, Iverson TM. Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase. J Biol Chem 2017; 292:12921-12933. [PMID: 28615448 DOI: 10.1074/jbc.m117.795120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.
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Affiliation(s)
- C A Starbird
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Susan Qualls-Histed
- Departments of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232.
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13
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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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14
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Leys D, Scrutton NS. Sweating the assets of flavin cofactors: new insight of chemical versatility from knowledge of structure and mechanism. Curr Opin Struct Biol 2016; 41:19-26. [DOI: 10.1016/j.sbi.2016.05.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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15
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Bezawork-Geleta A, Dong L, Rohlena J, Neuzil J. The Assembly Factor SDHAF2 Is Dispensable for Flavination of the Catalytic Subunit of Mitochondrial Complex II in Breast Cancer Cells. J Biol Chem 2016; 291:21414-21420. [PMID: 27587393 DOI: 10.1074/jbc.c116.755017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 08/27/2016] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial complex II or succinate dehydrogenase (SDH) is at the crossroads of oxidative phosphorylation and the tricarboxylic acid cycle. It has been shown that Sdh5 (SDHAF2/SDH5 in mammals) is required for flavination of the subunit Sdh1 (SDHA in human cells) in yeast. Here we demonstrate that in human breast cancer cells, SDHAF2/SDH5 is dispensable for SDHA flavination. In contrast to yeast, CRISPR-Cas9 nickase-mediated SDHAF2 KO breast cancer cells feature flavinated SDHA and retain fully assembled and functional complex II, as well as normal mitochondrial respiration. Our data show that SDHA flavination is independent of SDHAF2 in breast cancer cells, employing an alternative mechanism.
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Affiliation(s)
| | - Lanfeng Dong
- From the School of Medical Science, Griffith University, Southport, 4222 Queensland, Australia and
| | - Jakub Rohlena
- the Institute of Biotechnology, Czech Academy of Sciences, 252 50 Prague-West, Czech Republic
| | - Jiri Neuzil
- From the School of Medical Science, Griffith University, Southport, 4222 Queensland, Australia and .,the Institute of Biotechnology, Czech Academy of Sciences, 252 50 Prague-West, Czech Republic
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16
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Zafreen L, Walker-Kopp N, Huang LS, Berry E. In-vitro, SDH5-dependent flavinylation of immobilized human respiratory complex II flavoprotein. Arch Biochem Biophys 2016; 604:47-56. [PMID: 27296776 DOI: 10.1016/j.abb.2016.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/03/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
Mitochondrial Complex II (Succinate: ubiquinone oxidoreductase) has a covalently bound FAD cofactor in its largest subunit (SDHA), which accepts electrons from oxidation of succinate during catalysis. The mechanism of flavin attachment, and factors involved, have not been fully elucidated. The recent report of an assembly factor SDH5 (SDHAF2, SDHE) required for flavinylation (Hao et al., 2009 Science 325, 1139-1142) raises the prospect of achieving flavinylation in a completely defined system, which would facilitate elucidation of the precise role played by SDH5 and other factors. At this time that goal has not been achieved, and the actual function of SDH5 is still unknown. We have developed a procedure for in-vitro flavinylation of recombinant human apo-SDHA, immobilized on Ni-IMAC resin by a His tag, in a chemically defined medium. In this system flavinylation has a pH optimum of 6.5 and is completely dependent on added SDH5. The results suggest that FAD interacts noncovalently with SDHA in the absence of SDH5. This system will be useful in understanding the process of flavinylation of SDHA and the role of SDH5 in this process.
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Affiliation(s)
- Lala Zafreen
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Nancy Walker-Kopp
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Li-Shar Huang
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Edward Berry
- Dept. of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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