1
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Remes C, Khawaja A, Pearce SF, Dinan AM, Gopalakrishna S, Cipullo M, Kyriakidis V, Zhang J, Dopico XC, Yukhnovets O, Atanassov I, Firth AE, Cooperman B, Rorbach J. Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria. Nucleic Acids Res 2023; 51:891-907. [PMID: 36629253 PMCID: PMC9881170 DOI: 10.1093/nar/gkac1233] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It has been commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5' leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S), in a manner that requires initiator fMet-tRNAMet binding. In addition, we demonstrate that in human cells and in vitro, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Furthermore, we show that mtIF2 is indispensable for mitochondrial protein synthesis. Our results demonstrate an important evolutionary divergence of the mitochondrial translation system and further our fundamental understanding of a process central to eukaryotic metabolism.
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Affiliation(s)
- Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, 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, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Adam M Dinan
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, 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, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Vasileios Kyriakidis
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Olessya Yukhnovets
- RWTH Aachen, I. Physikalisches Institut (IA), Aachen, Germany
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- STIAS: Stellenbosch Institute for Advanced Study at Stellenbosch University, Marais Rd, Stellenbosch 7600, South Africa
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3
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Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A. Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature 2022; 606:603-608. [PMID: 35676484 PMCID: PMC9200640 DOI: 10.1038/s41586-022-04795-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/22/2022] [Indexed: 12/27/2022]
Abstract
Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Laptev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Petr Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
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Cipullo M, Gesé GV, Khawaja A, Hällberg BM, Rorbach J. Structural basis for late maturation steps of the human mitoribosomal large subunit. Nat Commun 2021; 12:3673. [PMID: 34135318 PMCID: PMC8209036 DOI: 10.1038/s41467-021-23617-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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: 01/29/2023] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Genís Valentín Gesé
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden.
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Hamburg, Germany.
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden.
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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5
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Shi Y, Yuan J, Rraklli V, Maxymovitz E, Cipullo M, Liu M, Li S, Westerlund I, Bedoya-Reina OC, Bullova P, Rorbach J, Juhlin CC, Stenman A, Larsson C, Kogner P, O’Sullivan MJ, Schlisio S, Holmberg J. Aberrant splicing in neuroblastoma generates RNA-fusion transcripts and provides vulnerability to spliceosome inhibitors. Nucleic Acids Res 2021; 49:2509-2521. [PMID: 33555349 PMCID: PMC7969022 DOI: 10.1093/nar/gkab054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
The paucity of recurrent mutations has hampered efforts to understand and treat neuroblastoma. Alternative splicing and splicing-dependent RNA-fusions represent mechanisms able to increase the gene product repertoire but their role in neuroblastoma remains largely unexplored. Here we investigate the presence and possible roles of aberrant splicing and splicing-dependent RNA-fusion transcripts in neuroblastoma. In addition, we attend to establish whether the spliceosome can be targeted to treat neuroblastoma. Through analysis of RNA-sequenced neuroblastoma we show that elevated expression of splicing factors is a strong predictor of poor clinical outcome. Furthermore, we identified >900 primarily intrachromosomal fusions containing canonical splicing sites. Fusions included transcripts from well-known oncogenes, were enriched for proximal genes and in chromosomal regions commonly gained or lost in neuroblastoma. As a proof-of-principle that these fusions can generate altered gene products, we characterized a ZNF451-BAG2 fusion, producing a truncated BAG2-protein which inhibited retinoic acid induced differentiation. Spliceosome inhibition impeded neuroblastoma fusion expression, induced apoptosis and inhibited xenograft tumor growth. Our findings elucidate a splicing-dependent mechanism generating altered gene products in neuroblastoma and show that the spliceosome is a potential target for clinical intervention.
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Affiliation(s)
- Yao Shi
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Juan Yuan
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Eva Maxymovitz
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - Mingzhi Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Shuijie Li
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Isabelle Westerlund
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Oscar C Bedoya-Reina
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Petra Bullova
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Maureen J O’Sullivan
- Department of Histopathology, Our Lady's Children's Hospital, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Susanne Schlisio
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Pearce SF, Cipullo M, Chung B, Brierley I, Rorbach J. Mitoribosome Profiling from Human Cell Culture: A High Resolution View of Mitochondrial Translation. Methods Mol Biol 2021; 2192:183-196. [PMID: 33230774 DOI: 10.1007/978-1-0716-0834-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ribosome profiling (Ribo-Seq) is a technique that allows genome-wide, quantitative analysis of translation. In recent years, it has found multiple applications in studies of translation in diverse organisms, tracking protein synthesis with single codon resolution. Traditional protocols applied for generating Ribo-Seq libraries from mammalian cell cultures are not suitable to study mitochondrial translation due to differences between eukaryotic cytosolic and mitochondrial ribosomes. Here, we present an adapted protocol enriching for mitoribosome footprints. In addition, we describe the preparation of small RNA sequencing libraries from the resultant mitochondrial ribosomal protected fragments (mtRPFs).
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Affiliation(s)
- Sarah F Pearce
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Cipullo
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Betty Chung
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Joanna Rorbach
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden. .,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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8
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Lopez Sanchez MIG, Cipullo M, Gopalakrishna S, Khawaja A, Rorbach J. Methylation of Ribosomal RNA: A Mitochondrial Perspective. Front Genet 2020; 11:761. [PMID: 32765591 PMCID: PMC7379855 DOI: 10.3389/fgene.2020.00761] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/26/2020] [Indexed: 01/02/2023] Open
Abstract
Ribosomal RNA (rRNA) from all organisms undergoes post-transcriptional modifications that increase the diversity of its composition and activity. In mitochondria, specialized mitochondrial ribosomes (mitoribosomes) are responsible for the synthesis of 13 oxidative phosphorylation proteins encoded by the mitochondrial genome. Mitoribosomal RNA is also modified, with 10 modifications thus far identified and all corresponding modifying enzymes described. This form of epigenetic regulation of mitochondrial gene expression affects mitoribosome biogenesis and function. Here, we provide an overview on rRNA methylation and highlight critical work that is beginning to elucidate its role in mitochondrial gene expression. Given the similarities between bacterial and mitochondrial ribosomes, we focus on studies involving Escherichia coli and human models. Furthermore, we highlight the use of state-of-the-art technologies, such as cryoEM in the study of rRNA methylation and its biological relevance. Understanding the mechanisms and functional relevance of this process represents an exciting frontier in the RNA biology and mitochondrial fields.
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Affiliation(s)
- M Isabel G Lopez Sanchez
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Centre for Eye Research Australia, Melbourne, VIC, Australia
| | - Miriam Cipullo
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anas Khawaja
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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9
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Gopalakrishna S, Pearce SF, Dinan AM, Schober FA, Cipullo M, Spåhr H, Khawaja A, Maffezzini C, Freyer C, Wredenberg A, Atanassov I, Firth AE, Rorbach J. C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis. Nucleic Acids Res 2019; 47:9386-9399. [PMID: 31396629 PMCID: PMC6755124 DOI: 10.1093/nar/gkz684] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 01/17/2023] Open
Abstract
In all biological systems, RNAs are associated with RNA-binding proteins (RBPs), forming complexes that control gene regulatory mechanisms, from RNA synthesis to decay. In mammalian mitochondria, post-transcriptional regulation of gene expression is conducted by mitochondrial RBPs (mt-RBPs) at various stages of mt-RNA metabolism, including polycistronic transcript production, its processing into individual transcripts, mt-RNA modifications, stability, translation and degradation. To date, only a handful of mt-RBPs have been characterized. Here, we describe a putative human mitochondrial protein, C6orf203, that contains an S4-like domain-an evolutionarily conserved RNA-binding domain previously identified in proteins involved in translation. Our data show C6orf203 to bind highly structured RNA in vitro and associate with the mitoribosomal large subunit in HEK293T cells. Knockout of C6orf203 leads to a decrease in mitochondrial translation and consequent OXPHOS deficiency, without affecting mitochondrial RNA levels. Although mitoribosome stability is not affected in C6orf203-depleted cells, mitoribosome profiling analysis revealed a global disruption of the association of mt-mRNAs with the mitoribosome, suggesting that C6orf203 may be required for the proper maturation and functioning of the mitoribosome. We therefore propose C6orf203 to be a novel RNA-binding protein involved in mitochondrial translation, expanding the repertoire of factors engaged in this process.
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Affiliation(s)
- Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Adam M Dinan
- Department of Pathology, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Florian A Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Henrik Spåhr
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 77 Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, 171 77 Stockholm, Sweden
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10
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Busch JD, Cipullo M, Atanassov I, Bratic A, Silva Ramos E, Schöndorf T, Li X, Pearce SF, Milenkovic D, Rorbach J, Larsson NG. MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. Cell Rep 2019; 29:1728-1738.e9. [PMID: 31693908 PMCID: PMC6859486 DOI: 10.1016/j.celrep.2019.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/14/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria harbor specialized ribosomes (mitoribosomes) necessary for the synthesis of key membrane proteins of the oxidative phosphorylation (OXPHOS) machinery located in the mitochondrial inner membrane. To date, no animal model exists to study mitoribosome composition and mitochondrial translation coordination in mammals in vivo. Here, we create MitoRibo-Tag mice as a tool enabling affinity purification and proteomics analyses of mitoribosomes and their interactome in different tissues. We also define the composition of an assembly intermediate formed in the absence of MTERF4, necessary for a late step in mitoribosomal biogenesis. We identify the orphan protein PUSL1, which interacts with a large subunit assembly intermediate, and demonstrate that it is an inner-membrane-associated mitochondrial matrix protein required for efficient mitochondrial translation. This work establishes MitoRibo-Tag mice as a powerful tool to study mitoribosomes in vivo, enabling future studies on the mitoribosome interactome under different physiological states, as well as in disease and aging. MitoRibo-Tag mice with a tag on mL62 were generated to study mitoribosomes in vivo The mitoribosome interactome of different mouse tissues was defined with proteomics PUSL1 was identified as a mitoribosome-interacting protein using MitoRibo-Tag mice MitoRibo-Tag mice allow mitoribosome analysis under different conditions and setups
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Affiliation(s)
- Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for 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
| | - Ana Bratic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Eduardo Silva Ramos
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Thomas Schöndorf
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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Leone A, Manna R, Verrecchia E, Cipullo M, Rigante D. Long-term treatment with anakinra and canakinumab resolves patellar subchondral erosion in neonatal-onset multisystem inflammatory disease. Reumatismo 2019; 71:53-55. [PMID: 30932446 DOI: 10.4081/reumatismo.2019.1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/28/2018] [Indexed: 11/22/2022] Open
Abstract
Not available.
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Affiliation(s)
- A Leone
- Institute of Radiology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Università Cattolica Sacro Cuore, Rome,.
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