1
|
Dohnálek V, Doležal P. Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion. Open Biol 2024; 14:240021. [PMID: 38772414 PMCID: PMC11293456 DOI: 10.1098/rsob.240021] [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: 08/15/2023] [Accepted: 03/13/2024] [Indexed: 05/23/2024] Open
Abstract
Core mitochondrial processes such as the electron transport chain, protein translation and the formation of Fe-S clusters (ISC) are of prokaryotic origin and were present in the bacterial ancestor of mitochondria. In animal and fungal models, a family of small Leu-Tyr-Arg motif-containing proteins (LYRMs) uniformly regulates the function of mitochondrial complexes involved in these processes. The action of LYRMs is contingent upon their binding to the acylated form of acyl carrier protein (ACP). This study demonstrates that LYRMs are structurally and evolutionarily related proteins characterized by a core triplet of α-helices. Their widespread distribution across eukaryotes suggests that 12 specialized LYRMs were likely present in the last eukaryotic common ancestor to regulate the assembly and folding of the subunits that are conserved in bacteria but that lack LYRM homologues. The secondary reduction of mitochondria to anoxic environments has rendered the function of LYRMs and their interaction with acylated ACP dispensable. Consequently, these findings strongly suggest that early eukaryotes installed LYRMs in aerobic mitochondria as orchestrated switches, essential for regulating core metabolism and ATP production.
Collapse
Affiliation(s)
- Vít Dohnálek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec252 50, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec252 50, Czech Republic
| |
Collapse
|
2
|
Liu X, Wu Y, Li M. Identification of 7 mitochondria-related genes as diagnostic biomarkers of MDD and their correlation with immune infiltration: New insights from bioinformatics analysis. J Affect Disord 2024; 349:86-100. [PMID: 38199392 DOI: 10.1016/j.jad.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/23/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND Major depressive disorder (MDD) is one of the most prevalent and debilitating psychiatric disorders. It becomes more recognized that mitochondrial dysfunction contributes to the pathophysiology of depression. However, little research has systematically investigated the mitochondria-related biomarkers for MDD diagnosis. This study aimed to develop a novel diagnostic gene signature in MDD based on mitochondria-related genes. METHOD We identified the differentially expressed mitochondrial-related genes (DeMRGs) by combing the gene expression data of the GEO database with mitochondria-related gene lists obtained from the MitoCarta3.0 database. Next, three kinds of machine-learning algorithms were used to screen characteristic DeMRGs. Then, we constructed a multivariable diagnostic model based on these characteristic genes and evaluated the diagnostic ability of this model. Subsequently, the immune landscape of infiltrated immune cells between MDD patients and controls was evaluated by CIBERSORT. Using consensus clustering analysis, we divided MDD patients into different clusters based on the characteristic DeMRGs expression patterns. Finally, the variations in immune cell infiltration between different clusters, and the correlation between characteristic DeMRGs and immune cell infiltration were analyzed. RESULTS Seven characteristic genes, including PMPCB, MRPS28, LYRM2, MGST1, COX20, PTPMT1, and STX17, were identified from the 31 DeMRGs. Based on the seven characteristic genes, we successfully constructed a diagnostic model which had relatively good diagnostic performance and potential application in the clinical diagnosis of MDD. In addition, our results also imply an intimate and comprehensive association between the characteristic DeMRGs and immune infiltrating cells. CONCLUSION A novel mitochondria-related gene signature with a good diagnostic performance and a relationship with immune microenvironment were identified in major depressive disorder.
Collapse
Affiliation(s)
- Xiaolan Liu
- Psychiatric Intensive Care Unit (PICU), Wuhan Mental Health Center, Wuhan 430012, Hubei Province, China; Department of Depression, Wuhan Hospital for Psychotherapy, Wuhan 430012, Hubei Province, China.
| | - Yong Wu
- Psychiatric Intensive Care Unit (PICU), Wuhan Mental Health Center, Wuhan 430012, Hubei Province, China; Department of Depression, Wuhan Hospital for Psychotherapy, Wuhan 430012, Hubei Province, China
| | - Mingxing Li
- Psychiatric Intensive Care Unit (PICU), Wuhan Mental Health Center, Wuhan 430012, Hubei Province, China; Department of Depression, Wuhan Hospital for Psychotherapy, Wuhan 430012, Hubei Province, China.
| |
Collapse
|
3
|
Li H, Zhou L, Zhou W, Zhang X, Shang J, Feng X, Yu L, Fan J, Ren J, Zhang R, Duan X. Decoding the mitochondrial connection: development and validation of biomarkers for classifying and treating systemic lupus erythematosus through bioinformatics and machine learning. BMC Rheumatol 2023; 7:44. [PMID: 38044432 PMCID: PMC10694981 DOI: 10.1186/s41927-023-00369-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disease characterized by clinical and pathological diversity. Mitochondrial dysfunction has been identified as a critical pathogenetic factor in SLE. However, the specific molecular aspects and regulatory roles of this dysfunction in SLE are not fully understood. Our study aims to explore the molecular characteristics of mitochondria-related genes (MRGs) in SLE, with a focus on identifying reliable biomarkers for classification and therapeutic purposes. METHODS We sourced six SLE-related microarray datasets (GSE61635, GSE50772, GSE30153, GSE99967, GSE81622, and GSE49454) from the Gene Expression Omnibus (GEO) database. Three of these datasets (GSE61635, GSE50772, GSE30153) were integrated into a training set for differential analysis. The intersection of differentially expressed genes with MRGs yielded a set of differentially expressed MRGs (DE-MRGs). We employed machine learning algorithms-random forest (RF), support vector machine (SVM), and least absolute shrinkage and selection operator (LASSO) logistic regression-to select key hub genes. These genes' classifying potential was validated in the training set and three other validation sets (GSE99967, GSE81622, and GSE49454). Further analyses included differential expression, co-expression, protein-protein interaction (PPI), gene set enrichment analysis (GSEA), and immune infiltration, centered on these hub genes. We also constructed TF-mRNA, miRNA-mRNA, and drug-target networks based on these hub genes using the ChEA3, miRcode, and PubChem databases. RESULTS Our investigation identified 761 differentially expressed genes (DEGs), mainly related to viral infection, inflammatory, and immune-related signaling pathways. The interaction between these DEGs and MRGs led to the identification of 27 distinct DE-MRGs. Key among these were FAM210B, MSRB2, LYRM7, IFI27, and SCO2, designated as hub genes through machine learning analysis. Their significant role in SLE classification was confirmed in both the training and validation sets. Additional analyses included differential expression, co-expression, PPI, GSEA, immune infiltration, and the construction of TF-mRNA, miRNA-mRNA, and drug-target networks. CONCLUSIONS This research represents a novel exploration into the MRGs of SLE, identifying FAM210B, MSRB2, LYRM7, IFI27, and SCO2 as significant candidates for classifying and therapeutic targeting.
Collapse
Affiliation(s)
- Haoguang Li
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Lu Zhou
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Wei Zhou
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Xiuling Zhang
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jingjing Shang
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Xueqin Feng
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Le Yu
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jie Fan
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jie Ren
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Rongwei Zhang
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Xinwang Duan
- Department of Rheumatology and Immunology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China.
| |
Collapse
|
4
|
Pei J, Zhang J, Cong Q. Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. Bioinformatics 2022; 38:4301-4311. [PMID: 35881696 DOI: 10.1093/bioinformatics/btac527] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein-protein interactions (PPIs) and modeling protein complexes at the proteome level. RESULTS We applied RoseTTAFold and AlphaFold, two of the latest deep-learning methods for structure predictions, to analyze coevolution of human proteins residing in mitochondria, an organelle of vital importance in many cellular processes including energy production, metabolism, cell death and antiviral response. Variations in mitochondrial proteins have been linked to a plethora of human diseases and genetic conditions. RoseTTAFold, with high computational speed, was used to predict the coevolution of about 95% of mitochondrial protein pairs. Top-ranked pairs were further subject to modeling of the complex structures by AlphaFold, which also produced contact probability with high precision and in many cases consistent with RoseTTAFold. Most top-ranked pairs with high contact probability were supported by known PPIs and/or similarities to experimental structural complexes. For high-scoring pairs without experimental complex structures, our coevolution analyses and structural models shed light on the details of their interfaces, including CHCHD4-AIFM1, MTERF3-TRUB2, FMC1-ATPAF2 and ECSIT-NDUFAF1. We also identified novel PPIs (PYURF-NDUFAF5, LYRM1-MTRF1L and COA8-COX10) for several proteins without experimentally characterized interaction partners, leading to predictions of their molecular functions and the biological processes they are involved in. AVAILABILITY AND IMPLEMENTATION Data of mitochondrial proteins and their interactions are available at: http://conglab.swmed.edu/mitochondria. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
5
|
Han F, Liu J, Chu H, Cao D, Wu J, Fu H, Guo A, Chen W, Xu Y, Cheng X, Zhang Y. Knockdown of NDUFC1 inhibits cell proliferation, migration, and invasion of hepatocellular carcinoma. Front Oncol 2022; 12:860084. [PMID: 36119539 PMCID: PMC9479186 DOI: 10.3389/fonc.2022.860084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023] Open
Abstract
Background NADH: ubiquinone oxidoreductase subunit C1(NDUFC1) encodes a subunit of the Complex I, which may support the structural stability of Complex I and assist in its biogenesis. The expression and functional roles of NDUFC1 in hepatocellular carcinoma (HCC) remain unknown. Result We knocked down the expression of NDUFC1 in HCC cell lines to explore the effects of NDUFC1 downregulation on HCC in vitro. MTT assay determined that downregulation of NDUFC1 significantly inhibited cell proliferation. Flow cytometry with (propidium iodide) PI staining indicated silencing of NDUFC1 arrested cell cycle of BEL-7404 cells at G2 phase and SK-HEP-1 cells at S/G2 phase. Annexin V-PI double staining and flow cytometric analysis showed that the downregulation of NDUFC1 significantly increased the population of apoptotic cells. Wound-healing assay and transwell assay indicated that the downregulation of NDUFC1 suppressed the migration and invasion of HCC cells. According to the detection of complex1 activity, we found that the activity of NDUFC1 silenced group decreased, whereas the content of ROS increased. Furthermore, combined with bioinformatics analysis of senescence-related genes, we found that the silence of NDUFC1 in HCC could induce senescence and inhibit autophagy. In addition, NDUFC1 could correlate positively with cancer-related pathways, among which the p53 pathways and the PI3K/Akt/mTOR pathways. Finally, NDUFC1 is high expression in HCC specimens. High NDUFC1 expression was associated with poor prognosis and was an independent risk factor for reduced overall survival (OS). Conclusions Our study indicated, for the first time, that NDUFC1 is an independent risk factor for the poor prognosis of HCC patients. NDUFC1 may promote tumor progression by inhibiting mitochondrial Complex I and up-regulating ROS through multiple cancer-related and senescence-related pathways of HCC, including p53 pathways and PI3K/Akt/mTOR pathways. We suppose that NDUFC1 might be a potential target for the mitochondrial metabolism therapy of HCC.
Collapse
Affiliation(s)
- Fang Han
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junwei Liu
- Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongwu Chu
- Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Department of Medicine, Qingdao University, Qingdao, China
| | - Dan Cao
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Jia Wu
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Hong Fu
- Hepatobiliary and Pancreatic Surgery Dept., Shaoxing Peoples’s Hospital, Shaoxing, China
| | - Anyang Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Weiqin Chen
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yingping Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiangdong Cheng
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yuhua Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- *Correspondence: Yuhua Zhang,
| |
Collapse
|
6
|
Meyer EH, Letts JA, Maldonado M. Structural insights into the assembly and the function of the plant oxidative phosphorylation system. THE NEW PHYTOLOGIST 2022; 235:1315-1329. [PMID: 35588181 DOI: 10.1111/nph.18259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 05/23/2023]
Abstract
One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. We also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.
Collapse
Affiliation(s)
- Etienne H Meyer
- Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Maria Maldonado
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| |
Collapse
|
7
|
Mitochondrial Neurodegeneration. Cells 2022; 11:cells11040637. [PMID: 35203288 PMCID: PMC8870525 DOI: 10.3390/cells11040637] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondria are cytoplasmic organelles, which generate energy as heat and ATP, the universal energy currency of the cell. This process is carried out by coupling electron stripping through oxidation of nutrient substrates with the formation of a proton-based electrochemical gradient across the inner mitochondrial membrane. Controlled dissipation of the gradient can lead to production of heat as well as ATP, via ADP phosphorylation. This process is known as oxidative phosphorylation, and is carried out by four multiheteromeric complexes (from I to IV) of the mitochondrial respiratory chain, carrying out the electron flow whose energy is stored as a proton-based electrochemical gradient. This gradient sustains a second reaction, operated by the mitochondrial ATP synthase, or complex V, which condensates ADP and Pi into ATP. Four complexes (CI, CIII, CIV, and CV) are composed of proteins encoded by genes present in two separate compartments: the nuclear genome and a small circular DNA found in mitochondria themselves, and are termed mitochondrial DNA (mtDNA). Mutations striking either genome can lead to mitochondrial impairment, determining infantile, childhood or adult neurodegeneration. Mitochondrial disorders are complex neurological syndromes, and are often part of a multisystem disorder. In this paper, we divide the diseases into those caused by mtDNA defects and those that are due to mutations involving nuclear genes; from a clinical point of view, we discuss pediatric disorders in comparison to juvenile or adult-onset conditions. The complementary genetic contributions controlling organellar function and the complexity of the biochemical pathways present in the mitochondria justify the extreme genetic and phenotypic heterogeneity of this new area of inborn errors of metabolism known as ‘mitochondrial medicine’.
Collapse
|
8
|
López-López A, Keech O, Rouhier N. Maturation and Assembly of Iron-Sulfur Cluster-Containing Subunits in the Mitochondrial Complex I From Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:916948. [PMID: 35677241 PMCID: PMC9168917 DOI: 10.3389/fpls.2022.916948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 05/13/2023]
Abstract
In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.
Collapse
Affiliation(s)
- Alicia López-López
- INRAE, IAM, Université de Lorraine, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Nicolas Rouhier
- INRAE, IAM, Université de Lorraine, Nancy, France
- *Correspondence: Nicolas Rouhier,
| |
Collapse
|
9
|
Fujishiro T, Nakamura R, Kunichika K, Takahashi Y. Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis. Biophys Physicobiol 2022; 19:1-18. [PMID: 35377584 PMCID: PMC8918507 DOI: 10.2142/biophysico.bppb-v19.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.
Collapse
Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Ryosuke Nakamura
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Kouhei Kunichika
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Yasuhiro Takahashi
- Department of Biochemistry and Moecular Biology, Graduate School of Science and Engineering, Saitama University
| |
Collapse
|
10
|
Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens). Genes Genomics 2021; 43:1231-1246. [PMID: 34338989 DOI: 10.1007/s13258-021-01137-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/29/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. OBJECTIVE Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great significance to identify the genetic characteristics and yak breeding. METHODS Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze differentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identified and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. RESULTS Our results revealed that 1098, 1429, and 1645 DEGs were identified in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identified 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The significant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. CONCLUSIONS: In this study, we obtained two hypoxia-related specific modules and identified hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.
Collapse
|
11
|
Lill R. From the discovery to molecular understanding of cellular iron-sulfur protein biogenesis. Biol Chem 2021; 401:855-876. [PMID: 32229650 DOI: 10.1515/hsz-2020-0117] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/10/2020] [Indexed: 12/23/2022]
Abstract
Protein cofactors often are the business ends of proteins, and are either synthesized inside cells or are taken up from the nutrition. A cofactor that strictly needs to be synthesized by cells is the iron-sulfur (Fe/S) cluster. This evolutionary ancient compound performs numerous biochemical functions including electron transfer, catalysis, sulfur mobilization, regulation and protein stabilization. Since the discovery of eukaryotic Fe/S protein biogenesis two decades ago, more than 30 biogenesis factors have been identified in mitochondria and cytosol. They support the synthesis, trafficking and target-specific insertion of Fe/S clusters. In this review, I first summarize what led to the initial discovery of Fe/S protein biogenesis in yeast. I then discuss the function and localization of Fe/S proteins in (non-green) eukaryotes. The major part of the review provides a detailed synopsis of the three major steps of mitochondrial Fe/S protein biogenesis, i.e. the de novo synthesis of a [2Fe-2S] cluster on a scaffold protein, the Hsp70 chaperone-mediated transfer of the cluster and integration into [2Fe-2S] recipient apoproteins, and the reductive fusion of [2Fe-2S] to [4Fe-4S] clusters and their subsequent assembly into target apoproteins. Finally, I summarize the current knowledge of the mechanisms underlying the maturation of cytosolic and nuclear Fe/S proteins.
Collapse
Affiliation(s)
- Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032 Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Str., D-35043 Marburg, Germany
| |
Collapse
|
12
|
Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
Collapse
Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
| |
Collapse
|
13
|
Abstract
Mitochondria are essential in most eukaryotes and are involved in numerous biological functions including ATP production, cofactor biosyntheses, apoptosis, lipid synthesis, and steroid metabolism. Work over the past two decades has uncovered the biogenesis of cellular iron-sulfur (Fe/S) proteins as the essential and minimal function of mitochondria. This process is catalyzed by the bacteria-derived iron-sulfur cluster assembly (ISC) machinery and has been dissected into three major steps: de novo synthesis of a [2Fe-2S] cluster on a scaffold protein; Hsp70 chaperone-mediated trafficking of the cluster and insertion into [2Fe-2S] target apoproteins; and catalytic conversion of the [2Fe-2S] into a [4Fe-4S] cluster and subsequent insertion into recipient apoproteins. ISC components of the first two steps are also required for biogenesis of numerous essential cytosolic and nuclear Fe/S proteins, explaining the essentiality of mitochondria. This review summarizes the molecular mechanisms underlying the ISC protein-mediated maturation of mitochondrial Fe/S proteins and the importance for human disease.
Collapse
Affiliation(s)
- Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
- SYNMIKRO Zentrum für synthetische Mikrobiologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
| |
Collapse
|
14
|
Khan MAA, Ami JQ, Faisal K, Chowdhury R, Ghosh P, Hossain F, Abd El Wahed A, Mondal D. An immunoinformatic approach driven by experimental proteomics: in silico design of a subunit candidate vaccine targeting secretory proteins of Leishmania donovani amastigotes. Parasit Vectors 2020; 13:196. [PMID: 32295617 PMCID: PMC7160903 DOI: 10.1186/s13071-020-04064-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background Visceral leishmaniasis (VL) caused by dimorphic Leishmania species is a parasitic disease with high socioeconomic burden in endemic areas worldwide. Sustaining control of VL in terms of proper and prevailing immunity development is a global necessity amid unavailability of a prophylactic vaccine. Screening of experimental proteome of the human disease propagating form of Leishmania donovani (amastigote) can be more pragmatic for in silico mining of novel vaccine candidates. Methods By using an immunoinformatic approach, CD4+ and CD8+ T cell-specific epitopes from experimentally reported L. donovani proteins having secretory potential and increased abundance in amastigotes were screened. A chimera linked with a Toll-like receptor 4 (TLR4) peptide adjuvant was constructed and evaluated for physicochemical characteristics, binding interaction with TLR4 in simulated physiological condition and the trend of immune response following hypothetical immunization. Results Selected epitopes from physiologically important L. donovani proteins were found mostly conserved in L. infantum, covering theoretically more than 98% of the global population. The multi-epitope chimeric vaccine was predicted as stable, antigenic and non-allergenic. Structural analysis of vaccine-TLR4 receptor docked complex and its molecular dynamics simulation suggest sufficiently stable binding interface along with prospect of non-canonical receptor activation. Simulation dynamics of immune response following hypothetical immunization indicate active and memory B as well as CD4+ T cell generation potential, and likely chance of a more Th1 polarized response. Conclusions The methodological approach and results from this study could facilitate more informed screening and selection of candidate antigenic proteins for entry into vaccine production pipeline in future to control human VL.![]()
Collapse
Affiliation(s)
- Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Jenifar Quaiyum Ami
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Khaledul Faisal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Ahmed Abd El Wahed
- Microbiology and Animal Hygiene Division, Georg-August-University Goettingen, Burckhardtweg 2, 37077, Göttingen, Germany.
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh.
| |
Collapse
|
15
|
Dibley MG, Formosa LE, Lyu B, Reljic B, McGann D, Muellner-Wong L, Kraus F, Sharpe AJ, Stroud DA, Ryan MT. The Mitochondrial Acyl-carrier Protein Interaction Network Highlights Important Roles for LYRM Family Members in Complex I and Mitoribosome Assembly. Mol Cell Proteomics 2020; 19:65-77. [PMID: 31666358 PMCID: PMC6944232 DOI: 10.1074/mcp.ra119.001784] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 01/25/2023] Open
Abstract
NDUFAB1 is the mitochondrial acyl carrier protein (ACP) essential for cell viability. Through its pantetheine-4'-phosphate post-translational modification, NDUFAB1 interacts with members of the leucine-tyrosine-arginine motif (LYRM) protein family. Although several LYRM proteins have been described to participate in a variety of defined processes, the functions of others remain either partially or entirely unknown. We profiled the interaction network of NDUFAB1 to reveal associations with 9 known LYRM proteins as well as more than 20 other proteins involved in mitochondrial respiratory chain complex and mitochondrial ribosome assembly. Subsequent knockout and interaction network studies in human cells revealed the LYRM member AltMiD51 to be important for optimal assembly of the large mitoribosome subunit, consistent with recent structural studies. In addition, we used proteomics coupled with topographical heat-mapping to reveal that knockout of LYRM2 impairs assembly of the NADH-dehydrogenase module of complex I, leading to defects in cellular respiration. Together, this work adds to the catalogue of functions executed by LYRM family of proteins in building mitochondrial complexes and emphasizes the common and essential role of NDUFAB1 as a protagonist in mitochondrial metabolism.
Collapse
Affiliation(s)
- Marris G Dibley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Baobei Lyu
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Boris Reljic
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Dylan McGann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Linden Muellner-Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Felix Kraus
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| |
Collapse
|
16
|
NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis. Molecules 2018; 23:molecules23092213. [PMID: 30200358 PMCID: PMC6205161 DOI: 10.3390/molecules23092213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters, the ubiquitous protein cofactors found in all kingdoms of life, perform a myriad of functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. The biogenesis of Fe-S clusters is a multi-step process that involves the participation of many protein partners. Recent biophysical studies, involving X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and small angle X-ray scattering (SAXS), have greatly improved our understanding of these steps. In this review, after describing the biological importance of iron sulfur proteins, we focus on the contributions of NMR spectroscopy has made to our understanding of the structures, dynamics, and interactions of proteins involved in the biosynthesis of Fe-S cluster proteins.
Collapse
|
17
|
Cai K, Frederick RO, Dashti H, Markley JL. Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering. Structure 2018; 26:1127-1136.e4. [PMID: 29983374 PMCID: PMC6082693 DOI: 10.1016/j.str.2018.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 05/24/2018] [Indexed: 11/19/2022]
Abstract
Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.
Collapse
Affiliation(s)
- Kai Cai
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Ronnie O Frederick
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Hesam Dashti
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
| |
Collapse
|
18
|
Herrera MG, Pignataro MF, Noguera ME, Cruz KM, Santos J. Rescuing the Rescuer: On the Protein Complex between the Human Mitochondrial Acyl Carrier Protein and ISD11. ACS Chem Biol 2018; 13:1455-1462. [PMID: 29737835 DOI: 10.1021/acschembio.8b00184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Iron-sulfur clusters are essential cofactors in many biochemical processes. ISD11, one of the subunits of the protein complex that carries out the cluster assembly in mitochondria, is necessary for cysteine desulfurase NFS1 stability and function. Several authors have recently provided evidence showing that ISD11 interacts with the acyl carrier protein (ACP). We carried out the coexpression of human mitochondrial ACP and ISD11 in E. coli. This work shows that ACP and ISD11 form a soluble, structured, and stable complex able to bind to the human NFS1 subunit modulating its activity. Results suggest that ACP plays a key-role in ISD11 folding and stability in vitro. These findings offer the opportunity to study the mechanism of interaction between ISD11 and NFS1.
Collapse
Affiliation(s)
- María Georgina Herrera
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - María Florencia Pignataro
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Ezequiel Noguera
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Karen Magalí Cruz
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Javier Santos
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| |
Collapse
|
19
|
Cai K, Frederick RO, Tonelli M, Markley JL. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly. J Inorg Biochem 2018; 183:107-116. [PMID: 29576242 PMCID: PMC5951399 DOI: 10.1016/j.jinorgbio.2018.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/15/2022]
Abstract
Frataxin (FXN) is involved in mitochondrial iron‑sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. We have used a combination of isothermal titration calorimetry and multinuclear NMR spectroscopy to investigate interactions among the components of the biological machine that carries out the assembly of iron‑sulfur clusters in human mitochondria. Our results show that FXN tightly binds a single Fe2+ but not Fe3+. While FXN (with or without bound Fe2+) does not bind the scaffold protein ISCU directly, the two proteins interact mutually when each is bound to the cysteine desulfurase complex ([NFS1]2:[ISD11]2:[Acp]2), abbreviated as (NIA)2, where "N" represents the cysteine desulfurase (NFS1), "I" represents the accessory protein (ISD11), and "A" represents acyl carrier protein (Acp). FXN binds (NIA)2 weakly in the absence of ISCU but more strongly in its presence. Fe2+-FXN binds to the (NIA)2-ISCU2 complex without release of iron. However, upon the addition of both l-cysteine and a reductant (either reduced FDX2 or DTT), Fe2+ is released from FXN as consistent with Fe2+-FXN being the proximal source of iron for Fe-S cluster assembly.
Collapse
Affiliation(s)
- Kai Cai
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Ronnie O Frederick
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, United States.
| |
Collapse
|
20
|
Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife 2018. [PMID: 29521624 PMCID: PMC5922974 DOI: 10.7554/elife.32110] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species. Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species. To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species. Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi. The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.
Collapse
Affiliation(s)
| | - Dominic Pinel
- Energy Biosciences Institute, Berkeley, United States
| | | | - Masakazu Ito
- Energy Biosciences Institute, Berkeley, United States
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
| | - Ya-Fang Cheng
- Energy Biosciences Institute, Berkeley, United States
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel B Brem
- The Buck Institute for Research on Aging, Novato, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Adam P Arkin
- Energy Biosciences Institute, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Jeffrey M Skerker
- Energy Biosciences Institute, Berkeley, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
21
|
Cai K, Frederick RO, Tonelli M, Markley JL. ISCU(M108I) and ISCU(D39V) Differ from Wild-Type ISCU in Their Failure To Form Cysteine Desulfurase Complexes Containing Both Frataxin and Ferredoxin. Biochemistry 2018; 57:1491-1500. [PMID: 29406711 PMCID: PMC5842376 DOI: 10.1021/acs.biochem.7b01234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/06/2018] [Indexed: 01/09/2023]
Abstract
Whereas iron-sulfur (Fe-S) cluster assembly on the wild-type scaffold protein ISCU, as catalyzed by the human cysteine desulfurase complex (NIA)2, exhibits a requirement for frataxin (FXN), in yeast, ISCU variant M108I has been shown to bypass the FXN requirement. Wild-type ISCU populates two interconverting conformational states: one structured and one dynamically disordered. We show here that variants ISCU(M108I) and ISCU(D39V) of human ISCU populate only the structured state. We have compared the properties of ISCU, ISCU(M108I), and ISCU(D39V), with and without FXN, in both the cysteine desulfurase step of Fe-S cluster assembly and the overall Fe-S cluster assembly reaction catalyzed by (NIA)2. In the cysteine desulfurase step with dithiothreitol (DTT) as the reductant, FXN was found to stimulate cysteine desulfurase activity with both the wild-type and structured variants, although the effect was less prominent with ISCU(D39V) than with the wild-type or ISCU(M108I). In overall Fe-S cluster assembly, frataxin was found to stimulate cluster assembly with both the wild-type and structured variants when the reductant was DTT; however, with the physiological reductant, reduced ferredoxin 2 (rdFDX2), FXN stimulated the reaction with wild-type ISCU but not with either ISCU(M108I) or ISCU(D39V). Nuclear magnetic resonance titration experiments revealed that wild-type ISCU, FXN, and rdFDX2 all bind to (NIA)2. However, when ISCU was replaced by the fully structured variant ISCU(M108I), the addition of rdFDX2 to the [NIA-ISCU(M108I)-FXN]2 complex led to the release of FXN. Thus, the displacement of FXN by rdFDX2 explains the failure of FXN to stimulate Fe-S cluster assembly on ISCU(M108I).
Collapse
Affiliation(s)
- Kai Cai
- National Magnetic Resonance
Facility at Madison and Department of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Ronnie O. Frederick
- National Magnetic Resonance
Facility at Madison and Department of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Marco Tonelli
- National Magnetic Resonance
Facility at Madison and Department of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - John L. Markley
- National Magnetic Resonance
Facility at Madison and Department of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| |
Collapse
|
22
|
Freibert SA, Weiler BD, Bill E, Pierik AJ, Mühlenhoff U, Lill R. Biochemical Reconstitution and Spectroscopic Analysis of Iron-Sulfur Proteins. Methods Enzymol 2018; 599:197-226. [PMID: 29746240 DOI: 10.1016/bs.mie.2017.11.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly of Fe/S cofactors and their insertion into apoproteins in living cells requires complex proteinaceous machineries that are frequently highly conserved. In eukaryotes such as yeast and mammals, the mitochondrial iron-sulfur cluster assembly machinery and the cytosolic iron-sulfur protein assembly system consist of more than 30 components that cooperate in the generation of some 50 cellular Fe/S proteins. Both the mechanistic dissection of the intracellular Fe/S protein assembly pathways and the identification and characterization of Fe/S proteins rely on tool boxes of in vitro and in vivo methods. These cell biological, biochemical, and biophysical techniques help to determine the extent, stability, and type of bound Fe/S cluster. They also serve to distinguish bona fide Fe/S proteins from other metal-binding proteins containing similar cofactor coordination motifs. Here, we present a collection of in vitro methods that have proven useful for basic biochemical and biophysical characterization of Fe/S proteins. First, we describe the chemical assembly of [2Fe-2S] or [4Fe-4S] clusters on purified apoproteins. Then, we summarize a reconstitution system reproducing the de novo synthesis of a [2Fe-2S] cluster in mitochondria. Finally, we explain the use of UV-vis, CD, electron paramagnetic resonance, and Mössbauer spectroscopy for the routine characterization of Fe/S proteins.
Collapse
Affiliation(s)
| | | | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Antonio J Pierik
- Chemistry and Biochemistry, Technical University of Kaiserlautern, Kaiserlautern, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität, Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Marburg, Germany.
| |
Collapse
|
23
|
Dutkiewicz R, Nowak M. Molecular chaperones involved in mitochondrial iron-sulfur protein biogenesis. J Biol Inorg Chem 2017; 23:569-579. [PMID: 29124426 PMCID: PMC6006194 DOI: 10.1007/s00775-017-1504-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/28/2017] [Indexed: 12/16/2022]
Abstract
Iron-sulfur (FeS) clusters are prosthetic groups critical for the function of many proteins in all domains of life. FeS proteins function in processes ranging from oxidative phosphorylation and cofactor biosyntheses to DNA/RNA metabolism and regulation of gene expression. In eukaryotic cells, mitochondria play a central role in the process of FeS biogenesis and support maturation of FeS proteins localized within mitochondria and in other cellular compartments. In humans, defects in mitochondrial FeS cluster biogenesis lead to numerous pathologies, which are often fatal. The generation of FeS clusters in mitochondria is a complex process. The [2Fe-2S] cluster is first assembled on a dedicated scaffold protein (Isu1) by the action of protein factors that interact with Isu1 to form the "assembly complex". Next, the FeS cluster is transferred onto a recipient apo-protein. Genetic and biochemical evidence implicates participation of a specialized J-protein co-chaperone Jac1 and its mitochondrial (mt)Hsp70 chaperone partner, and the glutaredoxin Grx5 in the FeS cluster transfer process. Finally, various specialized ISC components assist in the generation of [4Fe-4S] clusters and cluster insertion into specific target apoproteins. Although a framework of protein components that are involved in the mitochondrial FeS cluster biogenesis has been established based on genetic and biochemical studies, detailed molecular mechanisms involved in this important and medically relevant process are not well understood. This review summarizes our molecular knowledge on chaperone proteins' functions during the FeS protein biogenesis.
Collapse
Affiliation(s)
- Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307, Gdańsk, Poland.
| | - Malgorzata Nowak
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307, Gdańsk, Poland
| |
Collapse
|
24
|
Maio N, Rouault TA. Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. Metallomics 2017; 8:1032-1046. [PMID: 27714045 DOI: 10.1039/c6mt00167j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.
Collapse
Affiliation(s)
- N Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| | - T A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| |
Collapse
|
25
|
Boniecki MT, Freibert SA, Mühlenhoff U, Lill R, Cygler M. Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat Commun 2017; 8:1287. [PMID: 29097656 PMCID: PMC5668364 DOI: 10.1038/s41467-017-01497-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023] Open
Abstract
Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.
Collapse
Affiliation(s)
- Michal T Boniecki
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5
| | - Sven A Freibert
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany.
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043, Marburg, Germany.
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5.
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3G 0B1.
| |
Collapse
|
26
|
Angerer H, Schönborn S, Gorka J, Bahr U, Karas M, Wittig I, Heidler J, Hoffmann J, Morgner N, Zickermann V. Acyl modification and binding of mitochondrial ACP to multiprotein complexes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1913-1920. [PMID: 28802701 DOI: 10.1016/j.bbamcr.2017.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
The mitochondrial acyl carrier protein (ACPM/NDUFAB1) is a central element of the mitochondrial fatty acid synthesis type II machinery. Originally ACPM was detected as a subunit of respiratory complex I but the reason for the association with the large enzyme complex remained elusive. Complex I from the aerobic yeast Yarrowia lipolytica comprises two different ACPMs, ACPM1 and ACPM2. They are anchored to the protein complex by LYR (leucine-tyrosine-arginine) motif containing protein (LYRM) subunits LYRM3 (NDUFB9) and LYRM6 (NDUFA6). The ACPM1-LYRM6 and ACPM2-LYRM3 modules are essential for complex I activity and assembly/stability, respectively. We show that in addition to the complex I bound fraction, ACPM1 is present as a free matrix protein and in complex with the soluble LYRM4(ISD11)/NFS1 complex implicated in Fe-S cluster biogenesis. We show that the presence of a long acyl chain bound to the phosphopantetheine cofactor is important for docking ACPMs to protein complexes and we propose that association of ACPMs and LYRMs is universally based on a new protein-protein interaction motif.
Collapse
Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Stefan Schönborn
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jan Gorka
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ute Bahr
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Michael Karas
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jan Hoffmann
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Nina Morgner
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Germany.
| |
Collapse
|
27
|
Bridges HR, Mohammed K, Harbour ME, Hirst J. Subunit NDUFV3 is present in two distinct isoforms in mammalian complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:197-207. [PMID: 27940020 PMCID: PMC5293009 DOI: 10.1016/j.bbabio.2016.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 01/10/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the electron transport chain in mammalian mitochondria. Extensive proteomic and structural analyses of complex I from Bos taurus heart mitochondria have shown it comprises 45 subunits encoded on both the nuclear and mitochondrial genomes; 44 of them are different and one is present in two copies. The bovine heart enzyme has provided a model for studying the composition of complex I in other mammalian species, including humans, but the possibility of additional subunits or isoforms in other species or tissues has not been explored. Here, we describe characterization of the complexes I purified from five rat tissues and from a rat hepatoma cell line. We identify a~50kDa isoform of subunit NDUFV3, for which the canonical isoform is only ~10kDa in size. We combine LC-MS and MALDI-TOF mass spectrometry data from two different purification methods (chromatography and immuno-purification) with information from blue native PAGE analyses to show the long isoform is present in the mature complex, but at substoichiometric levels. It is also present in complex I in cultured human cells. We describe evidence that the long isoform is more abundant in both the mitochondria and purified complexes from brain (relative to in heart, liver, kidney and skeletal muscle) and more abundant still in complex I in cultured cells. We propose that the long 50kDa isoform competes with its canonical 10kDa counterpart for a common binding site on the flavoprotein domain of complex I.
Collapse
Affiliation(s)
- Hannah R Bridges
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Khairunnisa Mohammed
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Michael E Harbour
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K..
| |
Collapse
|
28
|
Yan R, Friemel M, Aloisi C, Huynen M, Taylor IA, Leimkühler S, Pastore A. The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS. PLoS One 2016; 11:e0157895. [PMID: 27427956 PMCID: PMC4948766 DOI: 10.1371/journal.pone.0157895] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
Collapse
Affiliation(s)
- Robert Yan
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
| | - Martin Friemel
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Claudia Aloisi
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
| | - Martijn Huynen
- CMBI 260, Radboud University Medical Centre, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ian A. Taylor
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, United Kingdom
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Annalisa Pastore
- Maurice Wohl Institute, King’s College London, 5 Cutcombe Rd, SE5, London, United Kingdom
- * E-mail:
| |
Collapse
|
29
|
Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:902-14. [PMID: 26921811 DOI: 10.1016/j.bbabio.2016.02.013] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
Collapse
Affiliation(s)
- Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ulrich Brandt
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany.
| |
Collapse
|
30
|
Chen YM, Li X, Song GX, Liu M, Fan Y, Wu LJ, Li H, Zhang QJ, Liu YQ, Qian LM. Effect of LYRM1 knockdown on proliferation, apoptosis, differentiation and mitochondrial function in the P19 cell model of cardiac differentiation in vitro. J Bioenerg Biomembr 2016; 48:33-41. [PMID: 26759027 PMCID: PMC4733147 DOI: 10.1007/s10863-015-9638-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/17/2015] [Indexed: 12/15/2022]
Abstract
To explore the effects of LYRM1 knockdown on proliferation, apoptosis, differentiation and mitochondrial function in the embryonic carcinoma (P19) cell model of cardiac differentiation. Knockdown of LYRM1 using small interfering RNA (siRNA) was confirmed by quantitative real-time PCR. Cell Counting Kit-8(CCK-8) proliferation assays and cell cycle analysis demonstrated that LYRM1 gene silencing significantly inhibited P19 cell proliferation. Flow cytometry and measurement of their caspase-3 activities revealed that knockdown of LYRM1 increased P19 cell apoptosis. Observation of morphological changes using an inverted microscope and expression analysis of specific differentiation marker genes using quantitative real-time PCR and Western blotting revealed that knockdown of LYRM1 significantly inhibited the differentiation of P19 cells into cardiomyocytes. Furthermore, real-time quantitative PCR applied to detect mitochondrial DNA (mtDNA) copy number implied that there was no significant difference in the LYRM1 knockdown group compared with the control group. Cellular ATP production investigated by luciferase-based luminescence assay was dramatically decreased in differentiated cells transfected with LYRM1 RNAi. Fluorescence microscopy and flow cytometery were used to detect the reactive oxygen species (ROS) and the mitochondrial membrane potential (MMP) showed that the level of ROS was dramatically increased and MMP was obviously decreased in differentiated cells transfected with LYRM1 RNAi. Collectively, knockdown of LYRM1 promoted apoptosis and suppressed proliferation and differentiation in P19 cells. In addition, knockdown of LYRM1 induced mitochondrial impairment in P19 cells during differentiation, which was reflected by decreased ATP synthesis, lower MMP and increased ROS levels.
Collapse
Affiliation(s)
- Yu-Mei Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Xing Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Gui-Xian Song
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Ming Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Yi Fan
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Li-Jie Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Hua Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Qi-Jun Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China
| | - Yao-Qiu Liu
- Department of MICU, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, 210029, China.
| | - Ling-Mei Qian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, People's Republic of China.
| |
Collapse
|
31
|
Letts JA, Sazanov LA. Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Curr Opin Struct Biol 2015; 33:135-45. [PMID: 26387075 DOI: 10.1016/j.sbi.2015.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/13/2015] [Accepted: 08/25/2015] [Indexed: 02/04/2023]
Abstract
The 1MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.
Collapse
Affiliation(s)
- James A Letts
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
| |
Collapse
|
32
|
Fernández-Vizarra E, Zeviani M. Nuclear gene mutations as the cause of mitochondrial complex III deficiency. Front Genet 2015; 6:134. [PMID: 25914718 PMCID: PMC4391031 DOI: 10.3389/fgene.2015.00134] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/20/2015] [Indexed: 11/13/2022] Open
Abstract
Complex III (CIII) deficiency is one of the least common oxidative phosphorylation defects associated to mitochondrial disease. CIII constitutes the center of the mitochondrial respiratory chain, as well as a crossroad for several other metabolic pathways. For more than 10 years, of all the potential candidate genes encoding structural subunits and assembly factors, only three were known to be associated to CIII defects in human pathology. Thus, leaving many of these cases unresolved. These first identified genes were MT-CYB, the only CIII subunit encoded in the mitochondrial DNA; BCS1L, encoding an assembly factor, and UQCRB, a nuclear-encoded structural subunit. Nowadays, thanks to the fast progress that has taken place in the last 3-4 years, pathological changes in seven more genes are known to be associated to these conditions. This review will focus on the strategies that have permitted the latest discovery of mutations in factors that are necessary for a correct CIII assembly and activity, in relation with their function. In addition, new data further establishing the molecular role of LYRM7/MZM1L as a chaperone involved in CIII biogenesis are provided.
Collapse
Affiliation(s)
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council Cambridge, UK
| |
Collapse
|
33
|
Angerer H. Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes. BIOLOGY 2015; 4:133-50. [PMID: 25686363 PMCID: PMC4381221 DOI: 10.3390/biology4010133] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/04/2015] [Indexed: 01/18/2023]
Abstract
In eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. LYR (leucine/tyrosine/arginine) motif proteins (LYRMs) of the Complex1_LYR-like superfamily interact with protein complexes of bacterial origin. Many LYR proteins function as extra subunits (LYRM3 and LYRM6) or novel assembly factors (LYRM7, LYRM8, ACN9 and FMC1) of the oxidative phosphorylation (OXPHOS) core complexes. Structural insights into complex I accessory subunits LYRM6 and LYRM3 have been provided by analyses of EM and X-ray structures of complex I from bovine and the yeast Yarrowia lipolytica, respectively. Combined structural and biochemical studies revealed that LYRM6 resides at the matrix arm close to the ubiquinone reduction site. For LYRM3, a position at the distal proton-pumping membrane arm facing the matrix space is suggested. Both LYRMs are supposed to anchor an acyl-carrier protein (ACPM) independently to complex I. The function of this duplicated protein interaction of ACPM with respiratory complex I is still unknown. Analysis of protein-protein interaction screens, genetic analyses and predicted multi-domain LYRMs offer further clues on an interaction network and adaptor-like function of LYR proteins in mitochondria.
Collapse
Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Street 9, Frankfurt am Main 60438, Germany.
| |
Collapse
|
34
|
Lane DJR, Merlot AM, Huang MLH, Bae DH, Jansson PJ, Sahni S, Kalinowski DS, Richardson DR. Cellular iron uptake, trafficking and metabolism: Key molecules and mechanisms and their roles in disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1130-44. [PMID: 25661197 DOI: 10.1016/j.bbamcr.2015.01.021] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/09/2015] [Accepted: 01/28/2015] [Indexed: 01/08/2023]
Abstract
Iron is a crucial transition metal for virtually all life. Two major destinations of iron within mammalian cells are the cytosolic iron-storage protein, ferritin, and mitochondria. In mitochondria, iron is utilized in critical anabolic pathways, including: iron-storage in mitochondrial ferritin, heme synthesis, and iron-sulfur cluster (ISC) biogenesis. Although the pathways involved in ISC synthesis in the mitochondria and cytosol have begun to be characterized, many crucial details remain unknown. In this review, we discuss major aspects of the journey of iron from its initial cellular uptake, its modes of trafficking within cells, to an overview of its downstream utilization in the cytoplasm and within mitochondria. The understanding of mitochondrial iron processing and its communication with other organelles/subcellular locations, such as the cytosol, has been elucidated by the analysis of certain diseases e.g., Friedreich's ataxia. Increased knowledge of the molecules and their mechanisms of action in iron processing pathways (e.g., ISC biogenesis) will shape the investigation of iron metabolism in human health and disease.
Collapse
Affiliation(s)
- D J R Lane
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia.
| | - A M Merlot
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - M L-H Huang
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - D-H Bae
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - P J Jansson
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - S Sahni
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - D S Kalinowski
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia
| | - D R Richardson
- Department of Pathology and Bosch Institute, Molecular Pharmacology and Pathology Program, Blackburn Building, University of Sydney, Sydney, New South Wales 2006, Australia.
| |
Collapse
|
35
|
Mammalian iron-sulphur proteins: novel insights into biogenesis and function. Nat Rev Mol Cell Biol 2014; 16:45-55. [PMID: 25425402 DOI: 10.1038/nrm3909] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Iron-sulphur (Fe-S) clusters are inorganic cofactors that are found in nearly all species and are composed of various combinations of iron and sulphur atoms. Fe-S clusters can accept or donate single electrons to carry out oxidation and reduction reactions and to facilitate electron transport. Many details of how these complex modular structures are assembled and ligated to cellular proteins in the mitochondrial, nuclear and cytosolic compartments of mammalian cells remain unclear. Recent evidence indicates that a Leu-Tyr-Arg (LYR) tripeptide motif found in some Fe-S recipient proteins may facilitate the direct and shielded transfer of Fe-S clusters from a scaffold to client proteins. Fe-S clusters are probably an unrecognized and elusive cofactor of many known proteins.
Collapse
|
36
|
Maio N, Rouault TA. Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1493-512. [PMID: 25245479 DOI: 10.1016/j.bbamcr.2014.09.009] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/07/2014] [Indexed: 01/19/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. The combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables Fe-S clusters to participate in numerous biological processes. Fe-S clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i.e. cellular iron homeostasis and oxidative stress response), and to the replication and maintenance of the nuclear genome. Fe-S cluster biogenesis is a multistep process that involves a complex sequence of catalyzed protein-protein interactions and coupled conformational changes between the components of several dedicated multimeric complexes. Intensive studies of the assembly process have clarified key points in the biogenesis of Fe-S proteins. However several critical questions still remain, such as: what is the role of frataxin? Why do some defects of Fe-S cluster biogenesis cause mitochondrial iron overload? How are specific Fe-S recipient proteins recognized in the process of Fe-S transfer? This review focuses on the basic steps of Fe-S cluster biogenesis, drawing attention to recent advances achieved on the identification of molecular features that guide selection of specific subsets of nascent Fe-S recipients by the cochaperone HSC20. Additionally, it outlines the distinctive phenotypes of human diseases due to mutations in the components of the basic pathway. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA
| | - Tracey A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| |
Collapse
|
37
|
Duarte M, Tomás AM. The mitochondrial complex I of trypanosomatids--an overview of current knowledge. J Bioenerg Biomembr 2014; 46:299-311. [PMID: 24961227 DOI: 10.1007/s10863-014-9556-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/17/2014] [Indexed: 01/23/2023]
Abstract
The contribution of trypanosomatid mitochondrial complex I for energy transduction has long been debated. Herein, we summarize current knowledge on the composition and relevance of this enzyme. Bioinformatic and proteomic analyses allowed the identification of many conserved and trypanosomatid-specific subunits of NADH:ubiquinone oxidoreductase, revealing a multifunctional enzyme capable of performing bioenergetic activities and possibly, also of functioning in fatty acid metabolism. A multimeric structure organized in 5 domains of more than 2 MDa is predicted, in contrast to the 1 MDa described for mammalian complex I. The relevance of mitochondrial complex I within the Trypanosomatidae family is quite diverse with its NADH oxidation activity being dispensable for both procyclic and bloodstream Trypanosoma brucei, whereas in Phytomonas serpens the enzyme is the only respiratory complex able to sustain membrane potential. Aside from complex I, trypanosomatid mitochondria contain a type II NADH dehydrogenase and a NADH-dependent fumarate reductase as alternative electron entry points into the respiratory chain and thus, some trypanosomatids may have bypassed the need for complex I. The involvement of each of these enzymes in the maintenance of the mitochondrial redox balance in trypanosomatids is still an open question and requires further investigation.
Collapse
Affiliation(s)
- Margarida Duarte
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal,
| | | |
Collapse
|
38
|
The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity. Proc Natl Acad Sci U S A 2014; 111:5207-12. [PMID: 24706851 DOI: 10.1073/pnas.1322438111] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial complex I is the largest and most complicated enzyme of the oxidative phosphorylation system. It comprises a number of so-called accessory subunits of largely unknown structure and function. Here we studied subunit NB4M [NDUFA6, LYR motif containing protein 6 (LYRM6)], a member of the LYRM family of proteins. Chromosomal deletion of the corresponding gene in the yeast Yarrowia lipolytica caused concomitant loss of the mitochondrial acyl carrier protein subunit ACPM1 from the enzyme complex and paralyzed ubiquinone reductase activity. Exchanging the LYR motif and an associated conserved phenylalanine by alanines in subunit NB4M also abolished the activity and binding of subunit ACPM1. We show, by single-particle electron microscopy and structural modeling, that subunits NB4M and ACPM1 form a subdomain that protrudes from the peripheral arm in the vicinity of central subunit domains known to be involved in controlling the catalytic activity of complex I.
Collapse
|
39
|
Stehling O, Wilbrecht C, Lill R. Mitochondrial iron-sulfur protein biogenesis and human disease. Biochimie 2014; 100:61-77. [PMID: 24462711 DOI: 10.1016/j.biochi.2014.01.010] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/13/2014] [Indexed: 12/29/2022]
Abstract
Work during the past 14 years has shown that mitochondria are the primary site for the biosynthesis of iron-sulfur (Fe/S) clusters. In fact, it is this process that renders mitochondria essential for viability of virtually all eukaryotes, because they participate in the synthesis of the Fe/S clusters of key nuclear and cytosolic proteins such as DNA polymerases, DNA helicases, and ABCE1 (Rli1), an ATPase involved in protein synthesis. As a consequence, mitochondrial function is crucial for nuclear DNA synthesis and repair, ribosomal protein synthesis, and numerous other extra-mitochondrial pathways including nucleotide metabolism and cellular iron regulation. Within mitochondria, the synthesis of Fe/S clusters and their insertion into apoproteins is assisted by 17 proteins forming the ISC (iron-sulfur cluster) assembly machinery. Biogenesis of mitochondrial Fe/S proteins can be dissected into three main steps: First, a Fe/S cluster is generated de novo on a scaffold protein. Second, the Fe/S cluster is dislocated from the scaffold and transiently bound to transfer proteins. Third, the latter components, together with specific ISC targeting factors insert the Fe/S cluster into client apoproteins. Disturbances of the first two steps impair the maturation of extra-mitochondrial Fe/S proteins and affect cellular and systemic iron homeostasis. In line with the essential function of mitochondria, genetic mutations in a number of ISC genes lead to severe neurological, hematological and metabolic diseases, often with a fatal outcome in early childhood. In this review we briefly summarize our current functional knowledge on the ISC assembly machinery, and we present a comprehensive overview of the various Fe/S protein assembly diseases.
Collapse
Affiliation(s)
- Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Claudia Wilbrecht
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Str., 35043 Marburg, Germany.
| |
Collapse
|
40
|
Abstract
Mitochondrial complex I has a molecular mass of almost 1 MDa and comprises more than 40 polypeptides. Fourteen central subunits harbour the bioenergetic core functions. We are only beginning to understand the significance of the numerous accessory subunits. The present review addresses the role of accessory subunits for assembly, stability and regulation of complex I and for cellular functions not directly associated with redox-linked proton translocation.
Collapse
|