1
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Khisamutdinov EF, Sweeney BA, Leontis NB. Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs. Nucleic Acids Res 2021; 49:9574-9593. [PMID: 34403481 PMCID: PMC8450098 DOI: 10.1093/nar/gkab703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/29/2021] [Indexed: 02/01/2023] Open
Abstract
Sequence variation in a widespread, recurrent, structured RNA 3D motif, the Sarcin/Ricin (S/R), was studied to address three related questions: First, how do the stabilities of structured RNA 3D motifs, composed of non-Watson–Crick (non-WC) basepairs, compare to WC-paired helices of similar length and sequence? Second, what are the effects on the stabilities of such motifs of isosteric and non-isosteric base substitutions in the non-WC pairs? And third, is there selection for particular base combinations in non-WC basepairs, depending on the temperature regime to which an organism adapts? A survey of large and small subunit rRNAs from organisms adapted to different temperatures revealed the presence of systematic sequence variations at many non-WC paired sites of S/R motifs. UV melting analysis and enzymatic digestion assays of oligonucleotides containing the motif suggest that more stable motifs tend to be more rigid. We further found that the base substitutions at non-Watson–Crick pairing sites can significantly affect the thermodynamic stabilities of S/R motifs and these effects are highly context specific indicating the importance of base-stacking and base-phosphate interactions on motif stability. This study highlights the significance of non-canonical base pairs and their contributions to modulating the stability and flexibility of RNA molecules.
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Affiliation(s)
- Emil F Khisamutdinov
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403, USA.,Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Blake A Sweeney
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Neocles B Leontis
- Department of Chemistry and Center for Photochemical Science, Bowling Green State University, Bowling Green, OH 43403, USA
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2
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Blanchet MF, St-Onge K, Lisi V, Robitaille J, Hamel S, Major F. Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships. Nucleic Acids Res 2014; 42:11261-71. [PMID: 25200082 PMCID: PMC4176186 DOI: 10.1093/nar/gku816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Anti-infection drugs target vital functions of infectious agents, including their ribosome and other essential non-coding RNAs. One of the reasons infectious agents become resistant to drugs is due to mutations that eliminate drug-binding affinity while maintaining vital elements. Identifying these elements is based on the determination of viable and lethal mutants and associated structures. However, determining the structure of enough mutants at high resolution is not always possible. Here, we introduce a new computational method, MC-3DQSAR, to determine the vital elements of target RNA structure from mutagenesis and available high-resolution data. We applied the method to further characterize the structural determinants of the bacterial 23S ribosomal RNA sarcin–ricin loop (SRL), as well as those of the lead-activated and hammerhead ribozymes. The method was accurate in confirming experimentally determined essential structural elements and predicting the viability of new SRL variants, which were either observed in bacteria or validated in bacterial growth assays. Our results indicate that MC-3DQSAR could be used systematically to evaluate the drug-target potentials of any RNA sites using current high-resolution structural data.
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Affiliation(s)
- Marc-Frédérick Blanchet
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada Department of Computer Science and Operations Research, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
| | - Karine St-Onge
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada Department of Computer Science and Operations Research, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
| | - Véronique Lisi
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
| | - Julie Robitaille
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
| | - Sylvie Hamel
- Department of Computer Science and Operations Research, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
| | - François Major
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada Department of Computer Science and Operations Research, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
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3
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Mitkevich VA, Shyp V, Petrushanko IY, Soosaar A, Atkinson GC, Tenson T, Makarov AA, Hauryliuk V. GTPases IF2 and EF-G bind GDP and the SRL RNA in a mutually exclusive manner. Sci Rep 2012; 2:843. [PMID: 23150791 PMCID: PMC3496166 DOI: 10.1038/srep00843] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/17/2012] [Indexed: 01/05/2023] Open
Abstract
Translational GTPases (trGTPases) are involved in all four stages of protein biosynthesis: initiation, elongation, termination and ribosome recycling. The trGTPases Initiation Factor 2 (IF2) and Elongation Factor G (EF-G) respectively orchestrate initiation complex formation and translocation of the peptidyl-tRNA:mRNA complex through the bacterial ribosome. The ribosome regulates the GTPase cycle and efficiently discriminates between the GDP- and GTP-bound forms of these proteins. Using Isothermal Titration Calorimetry, we have investigated interactions of IF2 and EF-G with the sarcin-ricin loop of the 23S rRNA, a crucial element of the GTPase-associated center of the ribosome. We show that binding of IF2 and EF-G to a 27 nucleotide RNA fragment mimicking the sarcin-ricin loop is mutually exclusive with that of GDP, but not of GTP, providing a mechanism for destabilization of the ribosome-bound GDP forms of translational GTPases.
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Affiliation(s)
- Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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4
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Wang L, Pulk A, Wasserman MR, Feldman MB, Altman RB, Cate JHD, Blanchard SC. Allosteric control of the ribosome by small-molecule antibiotics. Nat Struct Mol Biol 2012; 19:957-63. [PMID: 22902368 PMCID: PMC3645490 DOI: 10.1038/nsmb.2360] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/13/2012] [Indexed: 12/15/2022]
Abstract
Protein synthesis is targeted by numerous, chemically distinct antibiotics that bind and inhibit key functional centers of the ribosome. Using single-molecule imaging and X-ray crystallography, we show that the aminoglycoside neomycin blocks aminoacyl-transfer RNA (aa-tRNA) selection and translocation as well as ribosome recycling by binding to helix 69 (H69) of 23S ribosomal RNA within the large subunit of the Escherichia coli ribosome. There, neomycin prevents the remodeling of intersubunit bridges that normally accompanies the process of subunit rotation to stabilize a partially rotated ribosome configuration in which peptidyl (P)-site tRNA is constrained in a previously unidentified hybrid position. Direct measurements show that this neomycin-stabilized intermediate is incompatible with the translation factor binding that is required for distinct protein synthesis reactions. These findings reveal the functional importance of reversible intersubunit rotation to the translation mechanism and shed new light on the allosteric control of ribosome functions by small-molecule antibiotics.
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MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/pharmacology
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/drug effects
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Models, Molecular
- Neomycin/chemistry
- Neomycin/pharmacology
- Protein Biosynthesis/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acyl/metabolism
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/drug effects
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/drug effects
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Leyi Wang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
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5
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Shi X, Khade PK, Sanbonmatsu KY, Joseph S. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J Mol Biol 2012; 419:125-38. [PMID: 22459262 DOI: 10.1016/j.jmb.2012.03.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 03/10/2012] [Accepted: 03/17/2012] [Indexed: 11/19/2022]
Abstract
The sarcin-ricin loop (SRL) is one of the longest conserved sequences in the 23S ribosomal RNA. The SRL has been accepted as crucial for the activity of the ribosome because it is targeted by cytotoxins such as α-sarcin and ricin that completely abolish translation. Nevertheless, the precise functional role of the SRL in translation is not known. Recent biochemical and structural studies indicate that the SRL is critical for triggering GTP hydrolysis on elongation factor Tu (EF-Tu) and elongation factor G (EF-G). To determine the functional role of the SRL in the elongation stage of protein synthesis, we analyzed mutations in the SRL that are known to abolish protein synthesis and are lethal to cells. Here, we show that the SRL is not critical for GTP hydrolysis on EF-Tu and EF-G. The SRL also is not essential for peptide bond formation. Our results, instead, suggest that the SRL is crucial for anchoring EF-G on the ribosome during mRNA-tRNA translocation.
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MESH Headings
- Binding Sites
- Conserved Sequence
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Fungal Proteins/metabolism
- Guanosine Triphosphate/metabolism
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/genetics
- Peptide Elongation Factor Tu/metabolism
- Protein Binding
- Protein Biosynthesis
- Protein Structure, Secondary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ricin/metabolism
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Affiliation(s)
- Xinying Shi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
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6
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Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis. Nat Protoc 2011; 6:580-92. [PMID: 21527916 DOI: 10.1038/nprot.2011.306] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The protocol describes the site-specific chemical modification of 23S rRNA of Thermus aquaticus ribosomes. The centerpiece of this 'atomic mutagenesis' approach is the site-specific incorporation of non-natural nucleoside analogs into 23S rRNA in the context of the entire 70S ribosome. This technique exhaustively makes use of the available crystallographic structures of the ribosome for designing detailed biochemical experiments aiming at unraveling molecular insights of ribosomal functions. The generation of chemically engineered ribosomes carrying a particular non-natural 23S rRNA residue at the site of interest, a procedure that typically takes less than 2 d, allows the study of translation at the molecular level and goes far beyond the limits of standard mutagenesis approaches. This methodology, in combination with the presented tests for ribosomal functions adapted to chemically engineered ribosomes, allows unprecedented molecular insight into the mechanisms of protein biosynthesis.
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7
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Chirkova A, Erlacher MD, Clementi N, Zywicki M, Aigner M, Polacek N. The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res 2010; 38:4844-55. [PMID: 20375101 PMCID: PMC2919715 DOI: 10.1093/nar/gkq213] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the fact that all 23S rRNA nucleotides that build the ribosomal peptidyl transferase ribozyme are universally conserved, standard and atomic mutagenesis studies revealed the nucleobase identities being non-critical for catalysis. This indicates that these active site residues are highly conserved for functions distinct from catalysis. To gain insight into potential contributions, we have manipulated the nucleobases via an atomic mutagenesis approach and have utilized these chemically engineered ribosomes for in vitro translation reactions. We show that most of the active site nucleobases could be removed without significant effects on polypeptide production. Our data however highlight the functional importance of the universally conserved non-Watson-Crick base pair at position A2450-C2063. Modifications that disrupt this base pair markedly impair translation activities, while having little effects on peptide bond formation, tRNA drop-off and ribosome-dependent EF-G GTPase activity. Thus it seems that disruption of the A2450-C2063 pair inhibits a reaction following transpeptidation and EF-G action during the elongation cycle. Cumulatively our data are compatible with the hypothesis that the integrity of this A-C wobble base pair is essential for effective tRNA translocation through the peptidyl transferase center during protein synthesis.
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Affiliation(s)
- Anna Chirkova
- Innsbruck Biocenter, Medical University Innsbruck, Division of Genomics and RNomics, Innsbruck, Austria
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8
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García-Ortega L, Alvarez-García E, Gavilanes JG, Martínez-del-Pozo A, Joseph S. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. Nucleic Acids Res 2010; 38:4108-19. [PMID: 20215430 PMCID: PMC2896532 DOI: 10.1093/nar/gkq151] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin α-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin–ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interacts with translation factors that hydrolyze GTP, and it is important for their binding to the ribosome, but its precise role is not yet understood. We studied the effect of α-sarcin on defined steps of translation by the bacterial ribosome. α-Sarcin-treated ribosomes showed no defects in mRNA and tRNA binding, peptide-bond formation and sparsomycin-dependent translocation. Cleavage of SRL slightly affected binding of elongation factor Tu ternary complex (EF-Tu•GTP•tRNA) to the ribosome. In contrast, the activity of elongation factor G (EF-G) was strongly impaired in α-sarcin-treated ribosomes. Importantly, cleavage of SRL inhibited EF-G binding, and consequently GTP hydrolysis and mRNA–tRNA translocation. These results suggest that the SRL is more critical in EF-G than ternary complex binding to the ribosome implicating different requirements in this region of the ribosome during protein elongation.
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Affiliation(s)
- Lucía García-Ortega
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
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9
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Lancaster L, Lambert NJ, Maklan EJ, Horan LH, Noller HF. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. RNA (NEW YORK, N.Y.) 2008; 14:1999-2012. [PMID: 18755834 PMCID: PMC2553751 DOI: 10.1261/rna.1202108] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The sarcin-ricin loop (SRL) of 23S rRNA in the large ribosomal subunit is a factor-binding site that is essential for GTP-catalyzed steps in translation, but its precise functional role is thus far unknown. Here, we replaced the 15-nucleotide SRL with a GAAA tetraloop and affinity purified the mutant 50S subunits for functional and structural analysis in vitro. The SRL deletion caused defects in elongation-factor-dependent steps of translation and, unexpectedly, loss of EF-Tu-independent A-site tRNA binding. Detailed chemical probing analysis showed disruption of a network of rRNA tertiary interactions that hold together the 23S rRNA elements of the functional core of the 50S subunit, accompanied by loss of ribosomal protein L16. Our results reveal an influence of the SRL on the higher-order structure of the 50S subunit, with implications for its role in translation.
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Affiliation(s)
- Laura Lancaster
- Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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