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Cipullo M, Valentín Gesé G, Gopalakrishna S, Krueger A, Lobo V, Pirozhkova MA, Marks J, Páleníková P, Shiriaev D, Liu Y, Misic J, Cai Y, Nguyen MD, Abdelbagi A, Li X, Minczuk M, Hafner M, Benhalevy D, Sarshad AA, Atanassov I, Hällberg BM, Rorbach J. GTPBP8 plays a role in mitoribosome formation in human mitochondria. Nat Commun 2024; 15:5664. [PMID: 38969660 PMCID: PMC11229512 DOI: 10.1038/s41467-024-50011-x] [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: 08/23/2023] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Genís Valentín Gesé
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, Stockholm, 17165, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Annika Krueger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Vivian Lobo
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Maria A Pirozhkova
- Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Petra Páleníková
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Dmitrii Shiriaev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Yong Liu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Yu Cai
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Abubakar Abdelbagi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Benhalevy
- Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, Stockholm, 17165, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden.
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Biktimirov A, Islamov D, Fatkhullin B, Lazarenko V, Validov S, Yusupov M, Usachev K. Crystal structure of GTPase YsxC from Staphylococcus aureus. Biochem Biophys Res Commun 2024; 699:149545. [PMID: 38277729 DOI: 10.1016/j.bbrc.2024.149545] [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: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024]
Abstract
The YsxC protein from Staphylococcus aureus is a GTP-binding protein from the TRAFAC superfamily of the TrmE-Era-EngA-EngB-Septin-like GTPase class, EngB family of GTPases. Recent structural and biochemical studies of YsxC function show that it is an integral part of the pathogenic microorganism life cycle, as it is involved in the assembly of the large 50S ribosomal subunit. Structural studies of this protein with its specific functional features make it an attractive target for further development of new selective antimicrobials. In this study, we cloned the ysxC protein gene from S. aureus, overexpressed the protein in E. coli, and subsequently purified and crystallized it. Protein crystals were successfully grown using the vapor diffusion method, yielding diffraction data with a resolution of up to 2 Å. Comparative analysis of the structure of SaYsxC with known three-dimensional structures of homologs from other microorganisms showed the presence of structural differences for the apo form.
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Affiliation(s)
- Artem Biktimirov
- Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation
| | - Daut Islamov
- Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation; Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan, 420111, Russian Federation
| | - Bulat Fatkhullin
- Institute of Genetics, Molecular and Cellular Biology, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, F-67400, France
| | - Vladimir Lazarenko
- National Research Centre Kurchatov Institute, Kurchatov Sq. 2, 123182, Moscow, Russian Federation
| | - Shamil Validov
- Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan, 420111, Russian Federation
| | - Marat Yusupov
- Institute of Genetics, Molecular and Cellular Biology, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, F-67400, France
| | - Konstantin Usachev
- Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation.
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Cipullo M, Pearce SF, Lopez Sanchez IG, Gopalakrishna S, Krüger A, Schober F, Busch JD, Li X, Wredenberg A, Atanassov I, Rorbach J. Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly. Nucleic Acids Res 2021; 49:354-370. [PMID: 33283228 PMCID: PMC7797037 DOI: 10.1093/nar/gkaa1131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Human mitoribosomes are macromolecular complexes essential for translation of 11 mitochondrial mRNAs. The large and the small mitoribosomal subunits undergo a multistep maturation process that requires the involvement of several factors. Among these factors, GTP-binding proteins (GTPBPs) play an important role as GTP hydrolysis can provide energy throughout the assembly stages. In bacteria, many GTPBPs are needed for the maturation of ribosome subunits and, of particular interest for this study, ObgE has been shown to assist in the 50S subunit assembly. Here, we characterize the role of a related human Obg-family member, GTPBP5. We show that GTPBP5 interacts specifically with the large mitoribosomal subunit (mt-LSU) proteins and several late-stage mitoribosome assembly factors, including MTERF4:NSUN4 complex, MRM2 methyltransferase, MALSU1 and MTG1. Interestingly, we find that interaction of GTPBP5 with the mt-LSU is compromised in the presence of a non-hydrolysable analogue of GTP, implying a different mechanism of action of this protein in contrast to that of other Obg-family GTPBPs. GTPBP5 ablation leads to severe impairment in the oxidative phosphorylation system, concurrent with a decrease in mitochondrial translation and reduced monosome formation. Overall, our data indicate an important role of GTPBP5 in mitochondrial function and suggest its involvement in the late-stage of mt-LSU maturation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabel G Lopez Sanchez
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, 32 Gisborne Street, East Melbourne, 3002 Victoria, Australia
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 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, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Florian Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Solna (L1:00), 171 76 Stockholm, Sweden
| | - Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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Gupta A, Gupta K, Habib S. YihA GTPases localize to the apicoplast and mitochondrion of the malaria parasite and interact with LSU of organellar ribosomes. Mol Biochem Parasitol 2020; 236:111265. [PMID: 32057832 DOI: 10.1016/j.molbiopara.2020.111265] [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: 09/09/2019] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 11/29/2022]
Abstract
The YihA TRAFAC GTPases are critical for late-stage assembly of the ribosomal large subunit (LSU). In order to explore biogenesis of the reduced organellar ribosomes of the malaria parasite, we identified three nuclear-encoded homologs of YihA in Plasmodium falciparum. PfYihA1 targeted to the parasite apicoplast, PfYihA2 to the mitochondrion, and PfYihA3 was found in both the apicoplast and cytosol. The three PfYihA, expressed as recombinant proteins, were active GTPases and interacted with surrogate E. coli ribosomes in a nucleotide-independent manner. In vivo complexation of PfYihA with parasite organellar and/or cytosolic LSU was confirmed by co-immunoprecipitation using specific antibodies. Mitochondrial PfYihA2 carries a large C-ter extension with a strongly positively charged stretch. We hypothesise that this is important in compensating for the absence of helices of the central protuberance in the fragmented rRNA of Plasmodium mitoribosomes and may provide additional contact sites to aid in complex assembly. Combined with previous reports, our results indicate that P. falciparum mitochondria are likely to assemble ribosomes with the aid of PfEngA, PfObg1 and PfYihA2 GTPases while apicoplast ribosomes might use PfYihA1 and 3 in combination with other factors.
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Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Kirti Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
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Chen L, Zhang YH, Wang S, Zhang Y, Huang T, Cai YD. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS One 2017; 12:e0184129. [PMID: 28873455 PMCID: PMC5584762 DOI: 10.1371/journal.pone.0184129] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022] Open
Abstract
Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - YunHua Zhang
- Anhui province key lab of farmland ecological conversation and pollution prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
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