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Kapila R, Mehra U, Kaur J, Verma Y, Jakar S, Datta K. Insights into Mtg3-mitochondrial ribosome association in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2024; 737:150502. [PMID: 39180962 DOI: 10.1016/j.bbrc.2024.150502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
Ribosome biogenesis is a highly regulated multistep process aided by energy-consuming auxiliary factors. GTPases form the largest class of auxiliary factors used by bacterial, cytosolic, and mitochondrial ribosomes for their maturation. Mtg3, a circularly permuted YqeH family of GTPase, is implicated in the mitoribosome small subunit biogenesis. However, its precise mechanistic role has yet to be characterized. Mtg3 is likely to bind precursor mitoribosome molecules during subunit maturation in vivo. However, this interaction has yet to be observed with mitoribosomes biochemically. In this study, we delineate the specific conditions necessary for preserving the association of Mtg3 with mitoribosomes on a sucrose density gradient. We show that the C-terminal domain of Mtg3 is required for robust binding to the mitoribosome. Furthermore, point mutants likely to abrogate GTP/GDP binding and GTPase activity compromise protein function in vivo. Surprisingly, the association with the mitoribosome was not compromised in mutants likely to be deficient for nucleotide binding/hydrolysis. Thus, our finding supports a model wherein Mtg3 binds to a precursor mitoribosome through its C-terminus to facilitate a conformational change or validate a folding intermediate driven by the GTP/GDP binding and hydrolysis cycle.
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Affiliation(s)
- Ritika Kapila
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Upasana Mehra
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Jaswinder Kaur
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Yash Verma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Shweta Jakar
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Kaustuv Datta
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
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2
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Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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3
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Lavdovskaia E, Hanitsch E, Linden A, Pašen M, Challa V, Horokhovskyi Y, Roetschke HP, Nadler F, Welp L, Steube E, Heinrichs M, Mai MMQ, Urlaub H, Liepe J, Richter-Dennerlein R. A roadmap for ribosome assembly in human mitochondria. Nat Struct Mol Biol 2024:10.1038/s41594-024-01356-w. [PMID: 38992089 DOI: 10.1038/s41594-024-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
Mitochondria contain dedicated ribosomes (mitoribosomes), which synthesize the mitochondrial-encoded core components of the oxidative phosphorylation complexes. The RNA and protein components of mitoribosomes are encoded on two different genomes (mitochondrial and nuclear) and are assembled into functional complexes with the help of dedicated factors inside the organelle. Defects in mitoribosome biogenesis are associated with severe human diseases, yet the molecular pathway of mitoribosome assembly remains poorly understood. Here, we applied a multidisciplinary approach combining biochemical isolation and analysis of native mitoribosomal assembly complexes with quantitative mass spectrometry and mathematical modeling to reconstitute the entire assembly pathway of the human mitoribosome. We show that, in contrast to its bacterial and cytosolic counterparts, human mitoribosome biogenesis involves the formation of ribosomal protein-only modules, which then assemble on the appropriate ribosomal RNA moiety in a coordinated fashion. The presence of excess protein-only modules primed for assembly rationalizes how mitochondria cope with the challenge of forming a protein-rich ribonucleoprotein complex of dual genetic origin. This study provides a comprehensive roadmap of mitoribosome biogenesis, from very early to late maturation steps, and highlights the evolutionary divergence from its bacterial ancestor.
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Affiliation(s)
- Elena Lavdovskaia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin Pašen
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Venkatapathi Challa
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hanna P Roetschke
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, London, UK
- Francis Crick Institute, London, UK
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Luisa Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Emely Steube
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marleen Heinrichs
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Ricarda Richter-Dennerlein
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
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4
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Jin X, Meng L, Qi Z, Mi L. Effects of dietary selenium deficiency and supplementation on liver in grazing sheep: insights from transcriptomic and metabolomic analysis. Front Vet Sci 2024; 11:1358975. [PMID: 38962704 PMCID: PMC11220315 DOI: 10.3389/fvets.2024.1358975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Background Mineral elements play a crucial role in supporting the life activities and physiological functions of animals. However, numerous studies have revealed that in some geographical areas and certain grazing situations, grazing livestock frequently suffers from mineral element deficiencies due to the loss of mineral elements from grassland forages, such as selenium (Se). To shed fresh light on this issue, this study aims to investigate the impact of dietary Se deficiency and supplementation on the liver of grazing sheep in these challenging conditions. Method This study involved 28 grazing Mongolian Wu Ranke sheep with an average body weight of about 32.20 ± 0.37 kg, which were divided into the Se treatment group and the control group. The Se treatment group was fed with the low-Se diet for 60 days and then continued to be fed with the high-Se diet for 41 days. The liver concentration of minerals, transcriptomic analysis, and untargeted metabolomic analysis were conducted to assess the impact of Se deficiency and supplementation on the liver of grazing sheep. Results Dietary Se deficiency and supplementation significantly reduced and elevated liver concentration of Se, respectively (p < 0.05). Gene functional enrichment analysis suggested that dietary Se deficiency might impair protein synthesis efficiency, while Se supplementation was found to enhance liver protein synthesis in grazing sheep. AGAP1, ERN1, MAL2, NFIC, and RERG were identified as critical genes through the weighted gene correlation network analysis, the quantitative real-time polymerase chain reaction, and the receiver operating characteristic curve validation that could potentially serve as biomarkers. Metabolomics analysis revealed that dietary Se deficiency significantly reduced the abundance of metabolites such as 5-hydroxytryptamine, while dietary Se supplementation significantly elevated the abundance of metabolites such as 5-hydroxytryptophan (p < 0.05). Conclusion Integrative analysis of the transcriptome and metabolome revealed that dietary Se deficiency led to reduced hepatic antioxidant and anti-inflammatory capacity, whereas Se supplementation increased the hepatic antioxidant and anti-inflammatory capacity in grazing Wu Ranke sheep. These findings provide new insights into the effects of dietary Se deficiency and supplementation on the liver of grazing sheep, potentially leading to improved overall health and well-being of grazing livestock.
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Affiliation(s)
| | | | - Zhi Qi
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Lan Mi
- School of Life Sciences, Inner Mongolia University, Hohhot, China
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5
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Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
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Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
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6
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Wang L, Hilander T, Liu X, Tsang HY, Eriksson O, Jackson CB, Varjosalo M, Zhao H. GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation. Cell Mol Life Sci 2023; 80:361. [PMID: 37971521 PMCID: PMC10654211 DOI: 10.1007/s00018-023-05014-0] [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: 07/05/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Mitochondrial translation occurs on the mitochondrial ribosome, also known as the mitoribosome. The assembly of mitoribosomes is a highly coordinated process. During mitoribosome biogenesis, various assembly factors transiently associate with the nascent ribosome, facilitating the accurate and efficient construction of the mitoribosome. However, the specific factors involved in the assembly process, the precise mechanisms, and the cellular compartments involved in this vital process are not yet fully understood. In this study, we discovered a crucial role for GTP-binding protein 8 (GTPBP8) in the assembly of the mitoribosomal large subunit (mt-LSU) and mitochondrial translation. GTPBP8 is identified as a novel GTPase located in the matrix and peripherally bound to the inner mitochondrial membrane. Importantly, GTPBP8 is specifically associated with the mt-LSU during its assembly. Depletion of GTPBP8 leads to an abnormal accumulation of mt-LSU, indicating that GTPBP8 is critical for proper mt-LSU assembly. Furthermore, the absence of GTPBP8 results in reduced levels of fully assembled 55S monosomes. This impaired assembly leads to compromised mitochondrial translation and, consequently, impaired mitochondrial function. The identification of GTPBP8 as an important player in these processes provides new insights into the molecular mechanisms underlying mitochondrial protein synthesis and its regulation.
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Affiliation(s)
- Liang Wang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, #1 Keyuan Road, Gaopeng Street, High-Tech Development Zone, West China, Chengdu, 610041, China
| | - Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hoi Ying Tsang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Ove Eriksson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
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7
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Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
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Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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8
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Nadler F, Richter-Dennerlein R. Translation termination in human mitochondria - substrate specificity of mitochondrial release factors. Biol Chem 2023; 404:769-779. [PMID: 37377370 DOI: 10.1515/hsz-2023-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize in vitro and recent in vivo data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.
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Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, D-37075 Göttingen, Germany
- Goettingen Center for Molecular Biosciences, University of Göttingen, D-37077 Göttingen, Germany
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9
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Valach M, Benz C, Aguilar LC, Gahura O, Faktorová D, Zíková A, Oeffinger M, Burger G, Gray MW, Lukeš J. Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway. Nucleic Acids Res 2023; 51:6443-6460. [PMID: 37207340 PMCID: PMC10325924 DOI: 10.1093/nar/gkad422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The mitochondrial ribosome (mitoribosome) has diverged drastically from its evolutionary progenitor, the bacterial ribosome. Structural and compositional diversity is particularly striking in the phylum Euglenozoa, with an extraordinary protein gain in the mitoribosome of kinetoplastid protists. Here we report an even more complex mitoribosome in diplonemids, the sister-group of kinetoplastids. Affinity pulldown of mitoribosomal complexes from Diplonema papillatum, the diplonemid type species, demonstrates that they have a mass of > 5 MDa, contain as many as 130 integral proteins, and exhibit a protein-to-RNA ratio of 11:1. This unusual composition reflects unprecedented structural reduction of ribosomal RNAs, increased size of canonical mitoribosomal proteins, and accretion of three dozen lineage-specific components. In addition, we identified >50 candidate assembly factors, around half of which contribute to early mitoribosome maturation steps. Because little is known about early assembly stages even in model organisms, our investigation of the diplonemid mitoribosome illuminates this process. Together, our results provide a foundation for understanding how runaway evolutionary divergence shapes both biogenesis and function of a complex molecular machine.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
| | - Corinna Benz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Lisbeth C Aguilar
- Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal (IRCM), Montréal, Quebec, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Marlene Oeffinger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
- Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal (IRCM), Montréal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Institute of Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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10
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Khawaja A, Cipullo M, Krüger A, Rorbach J. Insights into mitoribosomal biogenesis from recent structural studies. Trends Biochem Sci 2023; 48:629-641. [PMID: 37169615 DOI: 10.1016/j.tibs.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
The mitochondrial ribosome (mitoribosome) is a multicomponent machine that has unique structural features. Biogenesis of the human mitoribosome includes correct maturation and folding of the mitochondria-encoded RNA components (12S and 16S mt-rRNAs, and mt-tRNAVal) and their assembly together with 82 nucleus-encoded mitoribosomal proteins. This complex process requires the coordinated action of multiple assembly factors. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided detailed insights into the specific functions of several mitoribosome assembly factors and have defined their timing. In this review we summarize mitoribosomal small (mtSSU) and large subunit (mtLSU) biogenesis based on structural findings, and we discuss potential crosstalk between mtSSU and mtLSU assembly pathways as well as coordination between mitoribosome biogenesis and other processes involved in mitochondrial gene expression.
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Affiliation(s)
- Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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11
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Conor Moran J, Del'Olio S, Choi A, Zhong H, Barrientos A. Mitoribosome Biogenesis. Methods Mol Biol 2023; 2661:23-51. [PMID: 37166630 PMCID: PMC10639111 DOI: 10.1007/978-1-0716-3171-3_3] [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] [Indexed: 05/12/2023]
Abstract
Mitoribosome biogenesis is a complex and energetically costly process that involves RNA elements encoded in the mitochondrial genome and mitoribosomal proteins most frequently encoded in the nuclear genome. The process is catalyzed by extra-ribosomal proteins, nucleus-encoded assembly factors that act in all stages of the assembly process to coordinate the processing and maturation of ribosomal RNAs with the hierarchical association of ribosomal proteins. Biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided hints regarding their assembly. In this general concept chapter, we will briefly describe the current knowledge, mainly regarding the mammalian mitoribosome biogenesis pathway and factors involved, and will emphasize the biological sources and approaches that have been applied to advance the field.
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Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Austin Choi
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Hui Zhong
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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12
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Albus CA, Berlinguer-Palmini R, Chrzanowska-Lightowlers ZM, Lightowlers RN. Four-Color STED Super-Resolution RNA Fluorescent In Situ Hybridization and Immunocytochemistry to Visualize Mitochondrial mRNAs in Context with Mitochondrial Ribosomes. Methods Mol Biol 2023; 2661:303-316. [PMID: 37166644 DOI: 10.1007/978-1-0716-3171-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
High-resolution imaging has enabled scientists to explore the mitochondrial network at remarkable resolution. This has been exploited to help increase our knowledge of how mitochondrial gene expression is compartmentalized in cultured cells. Here, we provide detailed methodology to simultaneously visualize up to four components including mtDNA-encoded transcripts, submitochondrial marker proteins, mitoribosomal subunits, or core members of the translational apparatus using STED super-resolution nanoscopy.
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Affiliation(s)
- Christin A Albus
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | | | - Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
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13
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Bertgen L, Flohr T, Herrmann JM. Methods to Study the Biogenesis of Mitoribosomal Proteins in Yeast. Methods Mol Biol 2023; 2661:143-161. [PMID: 37166637 DOI: 10.1007/978-1-0716-3171-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The biogenesis of mitoribosomes is an intricate process that relies on the coordinated synthesis of nuclear-encoded mitoribosomal proteins (MRPs) in the cytosol, their translocation across mitochondrial membranes, the transcription of rRNA molecules in the matrix as well as the assembly of the roughly 80 different constituents of the mitoribosome. Numerous chaperones, translocases, processing peptidases, and assembly factors of the cytosol and in mitochondria support this complex reaction. The budding yeast Saccharomyces cerevisiae served as a powerful model organism to unravel the different steps by which MRPs are imported into mitochondria, fold into their native structures, and assemble into functional ribosomes.In this chapter, we provide established protocols to study these different processes experimentally. In particular, we describe methods to purify mitochondria from yeast cells, to import radiolabeled MRPs into isolated mitochondria, and to elucidate the assembly reaction of MRPs by immunoprecipitation. These protocols and the list of dos and don'ts will enable beginners and experienced scientists to study the import and assembly of MRPs.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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14
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Mechanisms and players of mitoribosomal biogenesis revealed in trypanosomatids. Trends Parasitol 2022; 38:1053-1067. [PMID: 36075844 DOI: 10.1016/j.pt.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023]
Abstract
Translation in mitochondria is mediated by mitochondrial ribosomes, or mitoribosomes, complex ribonucleoprotein machines with dual genetic origin. Mitoribosomes in trypanosomatid parasites diverged markedly from their bacterial ancestors and other eukaryotic lineages in terms of protein composition, rRNA content, and overall architecture, yet their core functional elements remained conserved. Recent cryo-electron microscopy studies provided atomic models of trypanosomatid large and small mitoribosomal subunits and their precursors, making these parasites the organisms with the best-understood biogenesis of mitoribosomes. The structures revealed molecular mechanisms and players involved in the assembly of mitoribosomes not only in the parasites, but also in eukaryotes in general.
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15
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Hu Y, Xie J, Chen L, Tang Q, Wei W, Lin W, Du W, Xiang T, Yin L, Ji J. Integrated Analysis of Genomic and Transcriptomic Profiles Identified the Role of GTP Binding Protein-4 (GTPBP4) in Breast Cancer. Front Pharmacol 2022; 13:880445. [PMID: 35784753 PMCID: PMC9243593 DOI: 10.3389/fphar.2022.880445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: To explore the significance of GTP-binding protein 4 (GTPBP4) in breast cancer. Methods: Firstly, GTPBP4 expression analysis was performed in TIMER and UALCAN databases. Subsequently, the TCGA cohort and multiple Gene Expression Omnibus Cohorts were used as validation for GTPBP4 expression. Besides, we also evaluated the diagnostic value of GTPBP4 in TCGA Cohort and multiple GEO Cohorts. The predictive effect of GTPBP4 in breast cancer was then assessed using survival analysis. Then we look at the role of GTPBP4 in the immune milieu and create a Nomogram to help patients with breast cancer understand their prognosis. Finally, in vitro tests were carried out to look at GTPBP4 expression and function in breast cancer cell lines. Results: GTPBP4 is an independent breast cancer prognostic factor that is upregulated in the disease (p < 0.05). Enrichment analysis showed that GTPBP4 was associated with multiple functions and pathways. In addition, GTPBP4 is associated with a variety of immune cell types (p < 0.05). PCR assay showed that GTPBP4 expression was up-regulated in breast cancer cell lines. The activity, migration, and proliferation of breast cancer cells were considerably reduced after GTPBP4 knockdown in the CCK-8, Transwell, and Scratch assays. Conclusions: Our research discovered a new breast cancer biomarker that can be used as a guide for breast cancer diagnosis and treatment.
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Affiliation(s)
- Yiming Hu
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Qikai Tang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Wei Wei
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Wenfeng Lin
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wang Du
- Department of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Tinghong Xiang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lu Yin
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Ji
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
- *Correspondence: Jing Ji,
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16
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Gasparotto M, Lee YS, Palazzi A, Vacca M, Filippini F. Nuclear and Cytoplasmatic Players in Mitochondria-Related CNS Disorders: Chromatin Modifications and Subcellular Trafficking. Biomolecules 2022; 12:biom12050625. [PMID: 35625553 PMCID: PMC9138954 DOI: 10.3390/biom12050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Aberrant mitochondrial phenotypes are common to many central nervous system (CNS) disorders, including neurodegenerative and neurodevelopmental diseases. Mitochondrial function and homeostasis depend on proper control of several biological processes such as chromatin remodeling and transcriptional control, post-transcriptional events, vesicle and organelle subcellular trafficking, fusion, and morphogenesis. Mutation or impaired regulation of major players that orchestrate such processes can disrupt cellular and mitochondrial dynamics, contributing to neurological disorders. The first part of this review provides an overview of a functional relationship between chromatin players and mitochondria. Specifically, we relied on specific monogenic CNS disorders which share features with mitochondrial diseases. On the other hand, subcellular trafficking is coordinated directly or indirectly through evolutionarily conserved domains and proteins that regulate the dynamics of membrane compartments and organelles, including mitochondria. Among these “building blocks”, longin domains and small GTPases are involved in autophagy and mitophagy, cell reshaping, and organelle fusion. Impairments in those processes significantly impact CNS as well and are discussed in the second part of the review. Hopefully, in filling the functional gap between the nucleus and cytoplasmic organelles new routes for therapy could be disclosed.
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Affiliation(s)
- Matteo Gasparotto
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
| | - Yi-Shin Lee
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
- Pharmacology Division, Department of Neuroscience, Reproductive and Odontostomatological Sciences, Faculty of Medicine and surgery, University of Naples Federico II, Via Pansini 5, Building 19 (Biological Tower), 80131 Naples, Italy
| | - Alessandra Palazzi
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
| | - Marcella Vacca
- Institute of Genetics and Biophysics “A. Buzzati Traverso”, CNR, Via Pietro Castellino, 111, 80131 Naples, Italy; (Y.-S.L.); (A.P.); (M.V.)
| | - Francesco Filippini
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Via Ugo Bassi 58/B, 35131 Padua, Italy;
- Correspondence:
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17
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Jüttner M, Ferreira-Cerca S. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. Methods Mol Biol 2022; 2533:3-22. [PMID: 35796979 PMCID: PMC9761495 DOI: 10.1007/978-1-0716-2501-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability.Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of life . These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesis ; (b) what are the molecular impacts of the evolution history and how did they contribute to (re)shape the ribosome biogenesis pathway across the tree of life ; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticity and cellular adaptation of the ribosome biogenesis pathway?In this review, we provide a brief overview of ribosome biogenesis across the tree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
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Affiliation(s)
- Michael Jüttner
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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18
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Dennerlein S, Poerschke S, Oeljeklaus S, Wang C, Richter-Dennerlein R, Sattmann J, Bauermeister D, Hanitsch E, Stoldt S, Langer T, Jakobs S, Warscheid B, Rehling P. Defining the interactome of the human mitochondrial ribosome identifies SMIM4 and TMEM223 as respiratory chain assembly factors. eLife 2021; 10:68213. [PMID: 34969438 PMCID: PMC8719881 DOI: 10.7554/elife.68213] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Human mitochondria express a genome that encodes thirteen core subunits of the oxidative phosphorylation system (OXPHOS). These proteins insert into the inner membrane co-translationally. Therefore, mitochondrial ribosomes engage with the OXA1L-insertase and membrane-associated proteins, which support membrane insertion of translation products and early assembly steps into OXPHOS complexes. To identify ribosome-associated biogenesis factors for the OXPHOS system, we purified ribosomes and associated proteins from mitochondria. We identified TMEM223 as a ribosome-associated protein involved in complex IV biogenesis. TMEM223 stimulates the translation of COX1 mRNA and is a constituent of early COX1 assembly intermediates. Moreover, we show that SMIM4 together with C12ORF73 interacts with newly synthesized cytochrome b to support initial steps of complex III biogenesis in complex with UQCC1 and UQCC2. Our analyses define the interactome of the human mitochondrial ribosome and reveal novel assembly factors for complex III and IV biogenesis that link early assembly stages to the translation machinery.
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Affiliation(s)
- Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Sabine Poerschke
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Cong Wang
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Johannes Sattmann
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Diana Bauermeister
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Stoldt
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Langer
- Department of Mitochondrial Proteostasis, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stefan Jakobs
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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19
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Verma Y, Mehra U, Pandey DK, Kar J, Pérez-Martinez X, Jana SS, Datta K. MRX8, the conserved mitochondrial YihA GTPase family member, is required for de novo Cox1 synthesis at suboptimal temperatures in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:ar16. [PMID: 34432493 PMCID: PMC8693954 DOI: 10.1091/mbc.e20-07-0457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The synthesis of Cox1, the conserved catalytic-core subunit of Complex IV, a multisubunit machinery of the mitochondrial oxidative phosphorylation (OXPHOS) system under environmental stress, has not been sufficiently addressed. In this study, we show that the putative YihA superfamily GTPase, Mrx8, is a bona fide mitochondrial protein required for Cox1 translation initiation and elongation during suboptimal growth condition at 16°C. Mrx8 was found in a complex with mitochondrial ribosomes, consistent with a role in protein synthesis. Cells expressing mutant Mrx8 predicted to be defective in guanine nucleotide binding and hydrolysis were compromised for robust cellular respiration. We show that the requirement of Pet309 and Mss51 for cellular respiration is not bypassed by overexpression of Mrx8 and vice versa. Consistently the ribosomal association of Mss51 is independent of Mrx8. Significantly, we find that GTPBP8, the human orthologue, complements the loss of cellular respiration in Δmrx8 cells and GTPBP8 localizes to the mitochondria in mammalian cells. This strongly suggests a universal role of the MRX8 family of proteins in regulating mitochondrial function.
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Affiliation(s)
- Yash Verma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Upasana Mehra
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | | | - Joy Kar
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Xochitl Pérez-Martinez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kaustuv Datta
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
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20
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Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA, Ramakrishnan V. Visualizing formation of the active site in the mitochondrial ribosome. eLife 2021; 10:e68806. [PMID: 34609277 PMCID: PMC8492066 DOI: 10.7554/elife.68806] [Citation(s) in RCA: 8] [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: 03/25/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their Caenorhabditis elegans orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis.
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Affiliation(s)
| | - Nirupa Desai
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Hanting Yang
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Jon Price
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Eric A Miska
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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21
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Hilander T, Jackson CB, Robciuc M, Bashir T, Zhao H. The roles of assembly factors in mammalian mitoribosome biogenesis. Mitochondrion 2021; 60:70-84. [PMID: 34339868 DOI: 10.1016/j.mito.2021.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
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Affiliation(s)
- Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Finland.
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Tanzeela Bashir
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Key Laboratory of Stem Cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guangxi, China.
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22
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Hillen HS, Lavdovskaia E, Nadler F, Hanitsch E, Linden A, Bohnsack KE, Urlaub H, Richter-Dennerlein R. Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling. Nat Commun 2021; 12:3672. [PMID: 34135319 PMCID: PMC8209004 DOI: 10.1038/s41467-021-23702-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.
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Affiliation(s)
- Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany.
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
| | - Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Elisa Hanitsch
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Goettingen, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany.
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Lenarčič T, Jaskolowski M, Leibundgut M, Scaiola A, Schönhut T, Saurer M, Lee RG, Rackham O, Filipovska A, Ban N. Stepwise maturation of the peptidyl transferase region of human mitoribosomes. Nat Commun 2021; 12:3671. [PMID: 34135320 PMCID: PMC8208988 DOI: 10.1038/s41467-021-23811-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
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Affiliation(s)
- Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- Curtin Health Innovation Research Institute and Curtin Medical School, Curtin University, Bentley, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, University of Western Australia, Nedlands, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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Human Mitoribosome Biogenesis and Its Emerging Links to Disease. Int J Mol Sci 2021; 22:ijms22083827. [PMID: 33917098 PMCID: PMC8067846 DOI: 10.3390/ijms22083827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize a small subset of proteins, which are essential components of the oxidative phosphorylation machinery. Therefore, their function is of fundamental importance to cellular metabolism. The assembly of mitoribosomes is a complex process that progresses through numerous maturation and protein-binding events coordinated by the actions of several assembly factors. Dysregulation of mitoribosome production is increasingly recognized as a contributor to metabolic and neurodegenerative diseases. In recent years, mutations in multiple components of the mitoribosome assembly machinery have been associated with a range of human pathologies, highlighting their importance to cell function and health. Here, we provide a review of our current understanding of mitoribosome biogenesis, highlighting the key factors involved in this process and the growing number of mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors that lead to human disease.
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Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
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Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
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