Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
33576519
PubMed Central
PMC7957421
DOI
10.15252/embj.2020106292
Knihovny.cz E-zdroje
- Klíčová slova
- assembly, mitochondria, mitoribosome, translation, trypanosoma,
- MeSH
- elektronová kryomikroskopie MeSH
- konformace proteinů MeSH
- mitochondriální ribozomy metabolismus MeSH
- proteiny vázající GTP metabolismus MeSH
- proteosyntéza fyziologie MeSH
- RNA ribozomální genetika MeSH
- Trypanosoma brucei brucei metabolismus MeSH
- vazba proteinů fyziologie MeSH
- velké ribozomální podjednotky metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- proteiny vázající GTP MeSH
- RNA ribozomální MeSH
Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
Institute of Parasitology Biology Centre Czech Academy of Sciences Ceske Budejovice Czech Republic
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Achila D, Gulati M, Jain N, Britton RA (2012) Biochemical characterization of ribosome assembly GTPase RbgA in Bacillus subtilis. J Biol Chem 287: 8417–8423 PubMed PMC
Aibara S, Singh V, Modelska A, Amunts A (2020) Structural basis of mitochondrial translation. Elife 9: e58362 PubMed PMC
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI‐BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402 PubMed PMC
Amunts A, Brown A, Bai XC, Llacer JL, Hussain T, Emsley P, Long F, Murshudov G, Scheres SH, Ramakrishnan V (2014) Structure of the yeast mitochondrial large ribosomal subunit. Science 343: 1485–1489 PubMed PMC
Amunts A, Brown A, Toots J, Scheres SHW, Ramakrishnan V (2015) Ribosome. The structure of the human mitochondrial ribosome. Science 348: 95–98 PubMed PMC
Antonicka H, Shoubridge EA (2015) Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis. Cell Rep 10: 920–932 PubMed
Barrientos A, Korr D, Barwell KJ, Sjulsen C, Gajewski CD, Manfredi G, Ackerman S, Tzagoloff A (2003) MTG1 codes for a conserved protein required for mitochondrial translation. Mol Biol Cell 14: 2292–2302 PubMed PMC
Bogenhagen DF, Martin DW, Koller A (2014) Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metab 19: 618–629 PubMed
Brown A, Rathore S, Kimanius D, Aibara S, Bai XC, Rorbach J, Amunts A, Ramakrishnan V (2017) Structures of the human mitochondrial ribosome in native states of assembly. Nat Struct Mol Biol 24: 866–869 PubMed PMC
Couvillion MT, Soto IC, Shipkovenska G, Churchman LS (2016) Synchronized mitochondrial and cytosolic translation programs. Nature 533: 499–503 PubMed PMC
Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR (2016) Modular assembly of the bacterial large ribosomal subunit. Cell 167: 1610–1622 e15 PubMed PMC
Davis JH, Williamson JR (2017) Structure and dynamics of bacterial ribosome biogenesis. Philos Trans R Soc Lond B Biol Sci 372: 1–9 PubMed PMC
De Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk‐Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006) ScanProsite: detection of PROSITE signature matches and ProRule‐associated functional and structural residues in proteins. Nucleic Acids Res 34(Suppl_2): W362–W365 PubMed PMC
De Silva D, Tu YT, Amunts A, Fontanesi F, Barrientos A (2015) Mitochondrial ribosome assembly in health and disease. Cell Cycle 14: 2226–2250 PubMed PMC
Del Campo M, Lambowitz AM (2009) Structure of the yeast DEAD‐box protein Mss116p reveals two wedges that crimp RNA. Mol Cell 35: 598–609 PubMed PMC
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486–501 PubMed PMC
Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA (2016) Atomic structure of the entire mammalian mitochondrial complex I. Nature 538: 406–410 PubMed PMC
Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE (2018) UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci 27: 14–25 PubMed PMC
Greber BJ, Ban N (2016) Structure and Function of the Mitochondrial Ribosome. Annu Rev Biochem. 85: 103–132 PubMed
Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N (2015) Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Science 348: 303–308 PubMed
Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N (2014) The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature 515: 283–286 PubMed
Gulati M, Jain N, Anand B, Prakash B, Britton RA (2013) Mutational analysis of the ribosome assembly GTPase RbgA provides insight into ribosome interaction and ribosome‐stimulated GTPase activation. Nucleic Acids Res 41: 3217–3227 PubMed PMC
Gutgsell NS, Del Campo M, Raychaudhuri S, Ofengand J (2001) A second function for pseudouridine synthases: a point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD‐minus strain. RNA 7: 990–998 PubMed PMC
Gutgsell NS, Deutscher MP, Ofengand J (2005) The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli . RNA 11: 1141–1152 PubMed PMC
Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, Enrique M (2010) Pathway of ATP utilization and duplex rRNA unwinding by the DEAD‐box helicase, DbpA. Proc Natl Acad Sci USA 107: 4046–4050 PubMed PMC
Hori H (2017) Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA. Biomolecules 7: 23
Huang S, Aleksashin NA, Loveland AB, Klepacki D, Reier K, Kefi A, Szal T, Remme J, Jaeger L, Vázquez‐Laslop N et al (2020) Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. Nat Commun 11: 1–13 PubMed PMC
Itoh Y, Naschberger A, Mortezaei N, Herrmann J, Amunts A (2020) Analysis of translating mitoribosome reveals functional characteristics of protein synthesis in mitochondria of fungi. Nat Commun 11: 5187 PubMed PMC
Itoh Y, Andrell J, Choi A, Richter U, Maiti P, Best R, Barrientos A, Battersby B, Amunts A (2021) Mechanism of membrane‐tethered mitochondrial protein synthesis. Science 371: 846–849. PubMed PMC
Jaskolowski M, Ramrath DJF, Bieri P, Niemann M, Mattei S, Calderaro S, Leibundgut M, Horn EK, Boehringer D, Schneider A et al (2020) Structural insights into the mechanism of mitoribosomal large subunit biogenesis. Mol Cell 79: 629–644 PubMed
Jomaa A, Jain N, Davis JH, Williamson JR, Britton RA, Ortega J (2014) Functional domains of the 50S subunit mature late in the assembly process. Nucleic Acids Res 42: 3419–3435 PubMed PMC
Kandiah E, Giraud T, de Maaria Antolinos A, Dobias F, Effantin G, Flot D, Hons M, Schoehn G, Susini J, Svensson O et al (2019) CM01: a facility for cryo‐electron microscopy at the European Synchrotron. Acta Cryst D75: 528–535 PubMed PMC
Kim HJ, Barrientos A (2018) MTG1 couples mitoribosome large subunit assembly with intersubunit bridge formation. Nucleic Acids Res 46: 8435–8453 PubMed PMC
Kimanius D, Forsberg BO, Scheres SH, Lindahl E (2016) Accelerated cryo‐EM structure determination with parallelisation using GPUs in RELION‐2. Elife 5: e18722 PubMed PMC
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948 PubMed
Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N (2013) Cryo‐EM structures of the late‐stage assembly intermediates of the bacterial 50S ribosomal subunit. Nucleic Acids Res 41: 7073–7083 PubMed PMC
Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ et al (2019) Macromolecular structure determination using X‐rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75: 861–877 PubMed PMC
Liu F, Putnam A, Jankowsky E (2008) ATP hydrolysis is required for DEAD‐box protein recycling but not for duplex unwinding. Proc Natl Acad Sci USA 105: 20209–20214 PubMed PMC
Lövgren JM, Wikström PM (2001) The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli . J Bacteriol 183: 6957–6960 PubMed PMC
Masud AJ, Kastaniotis AJ, Rahman MT, Autio KJ, Hiltunen JK (2019). Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function. Biochim Biophys Acta 1866: 118540 PubMed
Ni X, Davis JH, Jain N, Razi A, Benlekbir S, McArthur AG, Rubinstein JL, Britton RA, Williamson JR, Ortega J (2016) YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit. Nucleic Acids Res 44: 8442–8455 PubMed PMC
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris‐Taube K, Nierhaus KH, Spahn CMT (2018) Structural visualization of the formation and activation of the 50S ribosomal subunit during in vitro reconstitution. Mol Cell 70: 881–893 e3 PubMed
Ott M, Amunts A, Brown A (2016) Organization and regulation of mitochondrial protein synthesis. Annu Rev Biochem 85: 77–101 PubMed
Pausch P, Steinchen W, Wieland M, Klaus T, Freibert SA, Altegoer F, Wilson DN, Bange G (2018) Structural basis for (p)ppGpp‐mediated inhibition of the GTPase RbgA. J Biol Chem. 293: 19699–19709 PubMed PMC
Pearce SF, Rebelo‐Guiomar P, D’Souza AR, Powell CA, Van Haute L, Minczuk M (2017) Regulation of mammalian mitochondrial gene expression: recent advances. Trends Biochem Sci 42: 625–639 PubMed PMC
Petrov AS, Wood EC, Bernier CR, Norris AM, Brown A, Amunts A (2019) Structural patching fosters divergence of mitochondrial ribosomes. Mol Biol Evol 36: 207–219 PubMed PMC
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25: 1605–1612 PubMed
Ramrath DJF, Niemann M, Leibundgut M, Bieri P, Prange C, Horn EK, Leitner A, Boehringer D, Schneider A, Ban N (2018) Evolutionary shift toward protein‐based architecture in trypanosomal mitochondrial ribosomes. Science 362: eaau7735 PubMed
Rorbach J, Boesch P, Gammage PA, Nicholls TJ, Pearce SF, Patel D, Hauser A, Perocchi F, Minczuk M (2014) MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome. Mol Biol Cell 25: 2542–2555 PubMed PMC
Saurer M, Ramrath DJF, Niemann M, Calderaro S, Prange C, Mattei S, Scaiola A, Leitner A, Bieri P, Horn EK et al (2019) Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Science 365: 1144–1149 PubMed
Schneider A, Charriere F, Pusnik M, Horn EK (2007) Isolation of mitochondria from procyclic Trypanosoma brucei . Methods Mol Biol 372: 67–80 PubMed
Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J (2019) Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate. Nucleic Acids Res 47: 10414–10425 PubMed PMC
Sirum‐Connolly K, Mason TL (1993) Functional requirement of a site‐specific ribose methylation in ribosomal RNA. Science 262: 1886–1889 PubMed
Soufari H, Waltz F, Parrot C, Durrieu‐Gaillard S, Bochler A, Kuhn L, Sissler M, Hashem Y (2020) Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Proc Natl Acad Sci USA 117: 29851–29861 PubMed PMC
Tegunov D, Cramer P (2019) Real‐time cryo‐electron microscopy data preprocessing with Warp. Nat Methods 16: 1146–1152 PubMed PMC
Theissen B, Karow AR, Köhler J, Gubaev A, Klostermeier D (2008) Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase. Proc Natl Acad Sci USA 105: 548–553 PubMed PMC
Tobiasson V, Amunts A (2020) Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation. Elife 9: e59264 PubMed PMC
Van Vranken JG, Jeong MY, Wei P, Chen YC, Gygi SP, Winge DR, Rutter J (2016) The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis. Elife 5: e17828 PubMed PMC
Waltz F, Soufari H, Bochler A, Giege P, Hashem Y (2020) Cryo‐EM structure of the RNA‐rich plant mitochondrial ribosome. Nat Plants 6: 377–383 PubMed
Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB et al (2018) MolProbity: more and better reference data for improved all‐atom structure validation. Protein Sci 27: 293–315 PubMed PMC
Xing Z, Ma WK, Tran EJ (2019) The DDX5/Dbp2 subfamily of DEAD‐box RNA helicases. Wiley Interdisc Rev 10: e1519 PubMed PMC
Zaganelli S, Rebelo‐Guiomar P, Maundrell K, Rozanska A, Pierredon S, Powell CA, Jourdain AA, Hulo N, Lightowlers RN, Chrzanowska‐Lightowlers ZM et al (2017) The pseudouridine synthase RPUSD4 is an essential component of mitochondrial RNA granules. J Biol Chem 292: 4519–4532 PubMed PMC
Zeng R, Smith E, Barrientos A (2018) Yeast mitoribosome large subunit assembly proceeds by hierarchical incorporation of protein clusters and modules on the inner membrane. Cell Metab 27: 645–656 PubMed PMC
Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y et al (2014) Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Nucleic Acids Res 42: 13430–13439 PubMed PMC
Zhu J, King MS, Yu M, Klipcan L, Leslie AG, Hirst J (2015) Structure of subcomplex Iβ of mammalian respiratory complex I leads to new supernumerary subunit assignments. Proc Natl Acad Sci USA 112: 12087–12092 PubMed PMC
Zikova A, Panigrahi AK, Dalley RA, Acestor N, Anupama A, Ogata Y, Myler PJ, Stuart K (2008) Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry. Mol Cell Proteomics 7: 1286–1296 PubMed PMC
Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH (2018) New tools for automated high‐resolution cryo‐EM structure determination in RELION‐3. Elife 7: e42166 PubMed PMC
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PDB
7AOI