1
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Imamoto JM, Zauhar RJ, Bruist MF. Sarcin/Ricin Domain RNA Retains Its Structure Better Than A-RNA in Adaptively Biased Molecular Dynamics Simulations. J Phys Chem B 2022; 126:10018-10033. [PMID: 36417896 DOI: 10.1021/acs.jpcb.2c05859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Less than one in thirty of the RNA sequences transcribed in humans are translated into protein. The noncoding RNA (ncRNA) functions in catalysis, structure, regulation, and more. However, for the most part, these functions are poorly characterized. RNA is modular and described by motifs that include helical A-RNA with canonical Watson-Crick base-pairing as well as structures with only noncanonical base pairs. Understanding the structure and dynamics of motifs will aid in deciphering functions of specific ncRNAs. We present computational studies on a standard sarcin/ricin domain (SRD), citrus bark cracking viroid SRD, as well as A-RNA. We have applied enhanced molecular dynamics techniques that construct an inverse free-energy surface (iFES) determined by collective variables that monitor base-pairing and backbone conformation. Each SRD RNA is flanked on each side by A-RNA, allowing comparison of the behavior of these motifs in the same molecule. The RNA iFESs have single peaks, indicating that the combined motifs should denature as a single cohesive unit, rather than by regional melting. Local root-mean-square deviation (RMSD) analysis and communication propensity (CProp, variance in distances between residue pairs) reveal distinct motif properties. Our analysis indicates that the standard SRD is more stable than the viroid SRD, which is more stable than A-RNA. Base pairs at SRD to A-RNA transitions have limited flexibility. Application of CProp reveals extraordinary stiffness of the SRD, allowing residues on opposite sides of the motif to sense each other's motions.
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Affiliation(s)
- Jason M Imamoto
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Randy J Zauhar
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
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2
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Streit D, Schleiff E. The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:684626. [PMID: 34381476 PMCID: PMC8351944 DOI: 10.3389/fpls.2021.684626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2'-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
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3
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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4
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Abstract
The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
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5
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Osborn MF, White JD, Haley MM, DeRose VJ. Platinum-RNA modifications following drug treatment in S. cerevisiae identified by click chemistry and enzymatic mapping. ACS Chem Biol 2014; 9:2404-11. [PMID: 25055168 PMCID: PMC4201330 DOI: 10.1021/cb500395z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
With
the importance of RNA-based regulatory pathways, the potential
for targeting noncoding and coding RNAs by small molecule therapeutics
is of great interest. Platinum(II) complexes including cisplatin (cis-diamminedichloroplatinum(II)) are widely prescribed
anticancer compounds that form stable adducts on nucleic acids. In
tumors, DNA damage from Pt(II) initiates apoptotic signaling, but
this activity is not necessary for cytotoxicity (e.g., Yu et al., 2008), suggesting accumulation and consequences
of Pt(II) lesions on non-DNA targets. We previously reported an azide-functionalized
compound, picazoplatin, designed for post-treatment click labeling
that enables detection of Pt complexes (White et al., 2013). Here, we report in-gel fluorescent detection of Pt-bound
rRNA and tRNA extracted from picazoplatin-treated S. cerevisiae and labeled using Cu-free click chemistry. These data provide the
first evidence that cellular tRNA is a platinum drug substrate. We
assess Pt(II) binding sites within rRNA from cisplatin-treated S. cerevisiae, in regions where damage is linked to significant
downstream consequences including the sarcin-ricin loop (SRL) Helix
95. Pt-RNA adducts occur on the nucleotide substrates of ribosome-inactivating
proteins, as well as on the bulged-G motif critical for elongation
factor recognition of the loop. At therapeutically relevant concentrations,
Pt(II) also binds robustly within conserved cation-binding pockets
in Domains V and VI rRNA at the peptidyl transferase center. Taken
together, these results demonstrate a convenient click chemistry methodology
that can be applied to identify other metal or covalent modification-based
drug targets and suggest a ribotoxic mechanism for cisplatin cytotoxicity.
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Affiliation(s)
- Maire F. Osborn
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Jonathan D. White
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Michael M. Haley
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
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6
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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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7
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Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. J Phys Chem B 2013; 117:14302-19. [PMID: 24144333 PMCID: PMC3946555 DOI: 10.1021/jp408530w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Nonisosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. The MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that the inability to form stable cWW geometry is an important factor in the case of the first base pair of the flexible region of the SR motif. A comparison of structural, bioinformatics, SHAPE probing, and MD simulation data reveals that explicit solvent MD simulations neatly reflect the viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Craig L. Zirbel
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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8
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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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9
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Clementi N, Chirkova A, Puffer B, Micura R, Polacek N. Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation. Nat Chem Biol 2010; 6:344-51. [PMID: 20348921 DOI: 10.1038/nchembio.341] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 01/21/2010] [Indexed: 11/09/2022]
Abstract
Following ribosomal peptide bond formation, the reaction products, peptidyl-tRNA and deacylated tRNA, need to be translocated from the A- and P-sites to the P- and E-sites, respectively. This process is facilitated by the GTPase elongation factor G (EF-G). The mechanism describing how the ribosome activates GTP hydrolysis is poorly understood in molecular terms. By using an 'atomic mutagenesis' approach, which allows the manipulation of specific functional groups on 23S rRNA nucleotides in the context of the entire ribosome, we disclose the adenine exocyclic N6 amino group at A2660 of the sarcin-ricin loop as a key determinant for triggering GTP hydrolysis on EF-G. We show that the purine pi system-expanding characteristics of the exocyclic functional group at the C6 position of A2660 are essential. We propose that stacking interactions of A2660 with EF-G may act as a molecular trigger to induce repositioning of suspected functional amino acids in EF-G that in turn promote GTP hydrolysis.
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Affiliation(s)
- Nina Clementi
- Innsbruck Biocenter, Medical University Innsbruck, Division of Genomics and RNomics, Innsbruck, Austria
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10
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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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11
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Chan YL, Wool IG. The integrity of the sarcin/ricin domain of 23 S ribosomal RNA is not required for elongation factor-independent peptide synthesis. J Mol Biol 2008; 378:12-9. [PMID: 18342885 DOI: 10.1016/j.jmb.2008.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/30/2008] [Accepted: 02/09/2008] [Indexed: 10/22/2022]
Abstract
The elongation stage of protein synthesis consists of repeated cycles of the binding of aminoacyl-tRNA, peptide bond formation, and translocation. The process is normally catalyzed by the elongation factors Tu and G; however, the reactions can proceed, at least in prescribed and limited circumstance, in the absence of the elongation factors, a finding that strongly implies that the chemistry of protein synthesis is inherent in the ribosome. The sarcin/ricin domain in 23 S rRNA, the site of inactivation of ribosomes by ribotoxins, is where the elongation factors bind. The question that arises is whether the sarcin/ricin domain is necessary for factor-independent peptide synthesis. The answer is that it is not. The disruption of the sarcin/ricin domain by covalent modification with either sarcin or pokeweed antiviral protein did not affect factor-independent peptide synthesis; nor did lethal mutations of nucleotides that abolish the binding of elongation factors. The results imply that the sole function of the sarcin/ricin domain is to provide a binding site for the elongation factors and, hence, to facilitate the elongation reactions. The results also raise the possibility of the co-evolution of the sarcin/ricin domain and the elongation factors.
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Affiliation(s)
- Yuen-Ling Chan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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12
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Goto N, Kurokawa K, Yasunaga T. Analysis of invariant sequences in 266 complete genomes. Gene 2007; 401:172-80. [PMID: 17728079 DOI: 10.1016/j.gene.2007.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 07/13/2007] [Accepted: 07/16/2007] [Indexed: 11/29/2022]
Abstract
To date, the complete genome sequences of more than 250 organisms have been determined. This information can now be used to determine whether there exist any invariant sequences that are conserved among all organisms, from bacteria to plants, animals, and humans. The existence of invariant sequences would strongly suggest that these sequences have been inherited unchanged from the last common ancestor of all life, and that they have essential functions. We have developed a new software program to identify invariant sequences conserved among the currently sequenced genomes and applied this analysis to the complete genome sequences of 266 organisms. We have identified 3 invariant DNA sequences longer than or equal to 11 bp and 6 invariant amino acid sequences longer than or equal to 6 aa. The longest invariant DNA sequence, AAGTCGTACAAGGT (15 bp), was found in the 16S/18S rRNA gene. Two 8 aa sequences, GHVDHGKT in IF2 and EF-Tu and DTPGHVDF in EF-G, were the longest invariant amino acid sequences detected. These sequences could be essential elements from the genome of the last common ancestor and may have remained unchanged throughout evolution.
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MESH Headings
- Amino Acid Sequence/genetics
- Animals
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Base Sequence/genetics
- Conserved Sequence/genetics
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Genome
- Genome, Archaeal
- Genome, Bacterial
- Genome, Fungal
- Genome, Human
- Genome, Plant
- Humans
- Protein Biosynthesis/genetics
- Protein Processing, Post-Translational/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Software
- Transcription, Genetic
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Affiliation(s)
- Naohisa Goto
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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13
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Yassin A, Mankin AS. Potential New Antibiotic Sites in the Ribosome Revealed by Deleterious Mutations in RNA of the Large Ribosomal Subunit. J Biol Chem 2007; 282:24329-42. [PMID: 17591769 DOI: 10.1074/jbc.m703106200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosome is the main target for antibiotics that inhibit protein biosynthesis. Despite the chemical diversity of the known antibiotics that affect functions of the large ribosomal subunit, these drugs act on only a few sites corresponding to some of the known functional centers. We have used a genetic approach for identifying structurally and functionally critical sites in the ribosome that can be used as new antibiotic targets. By using randomly mutagenized rRNA genes, we mapped rRNA sites where nucleotide alterations impair the ribosome function or assembly and lead to a deleterious phenotype. A total of 77 single-point deleterious mutations were mapped in 23 S rRNA and ranked according to the severity of their deleterious phenotypes. Many of the mutations mapped to familiar functional sites that are targeted by known antibiotics. However, a number of mutations were located in previously unexplored regions. The distribution of the mutations in the spatial structure of the ribosome showed a strong bias, with the strongly deleterious mutations being mainly localized at the interface of the large subunit and the mild ones on the solvent side. Five sites where deleterious mutations tend to cluster within discrete rRNA elements were identified as potential new antibiotic targets. One of the sites, the conserved segment of helix 38, was studied in more detail. Although the ability of the mutant 50 S subunits to associate with 30 S subunits was impaired, the lethal effect of mutations in this rRNA element was unrelated to its function as an intersubunit bridge. Instead, mutations in this region had a profound deleterious effect on the ribosome assembly.
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Affiliation(s)
- Aymen Yassin
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, USA
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14
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Nagano K, Nagano N. Mechanism of translation based on intersubunit complementarities of ribosomal RNAs and tRNAs. J Theor Biol 2006; 245:644-68. [PMID: 17196221 DOI: 10.1016/j.jtbi.2006.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 11/06/2006] [Accepted: 11/06/2006] [Indexed: 11/16/2022]
Abstract
A universal rule is found about nucleotide sequence complementarities between the regions 2653-2666 in the GTPase-binding site of 23S rRNA and 1064-1077 of 16S rRNA as well as between the region 1103-1107 of 16S rRNA and GUUCG (or GUUCA) of tRNAs. This rule holds for all species in the living kingdoms except for two protista mitochondrial rRNAs of Trypanosoma brucei and Plasmodium falciparum. We found that quite similar relationships for the two species hold under the assumption presented in the present paper. The complementarity between T-loop of tRNA and the region 1103-1107 of 16S rRNA suggests that the first interaction of a ribosome with aminoacyl-tRNAEF-TuGTP ternary complex or EF-GGDP complex could occur at the region 1103-1107 of 16S rRNA with the T-loop-D-loop contact region of the ternary complex or the domain IV-V bridge region of the EF-GGDP complex. The second interaction should occur between the A-site codon and the anticodon loop or between the anticodon stem/loop of A-site tRNA and the tip of domain IV of EF-G. The above stepwise interactions would facilitate the collision of the region 1064-1077 of 16S rRNA with the region around A2660 at the alpha-sarcin/ricin loop of 23S rRNA. In this way, the universal rule is capable of explaining how spectinomycin-binding region of 16S rRNA takes part in translocation, how GTPases such as EF-Tu and EF-G can be introduced into their binding site on the large subunit ribosome in proper orientation efficiently and also how driving forces for tRNA movement are produced in translocation and codon recognition. The analysis of T-loops of all tRNAs also presents an evolutionary trend from a random and seemingly primitive sequence, as defined to be Y type, to the most developed structure, such as either 5G7 or 5A7 types in the present definition.
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MESH Headings
- Animals
- Base Pairing/genetics
- Base Sequence
- Codon/genetics
- Guanosine Triphosphate/metabolism
- Hydrolysis
- Mitochondria/genetics
- Models, Genetic
- Mutation
- Nucleic Acid Conformation
- Plasmodium falciparum/genetics
- Protein Biosynthesis/genetics
- RNA/genetics
- RNA, Mitochondrial
- RNA, Protozoan/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer/genetics
- Sequence Homology, Nucleic Acid
- Translocation, Genetic/genetics
- Trypanosoma brucei brucei/genetics
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Affiliation(s)
- Kozo Nagano
- Nagano Research Institute of Molecular Biology, 4-8-24 Higiriyama, Kohnan-ku, Yokohama 233-0015, Japan.
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15
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Chan YL, Dresios J, Wool IG. A pathway for the transmission of allosteric signals in the ribosome through a network of RNA tertiary interactions. J Mol Biol 2005; 355:1014-25. [PMID: 16359709 DOI: 10.1016/j.jmb.2005.11.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Revised: 11/10/2005] [Accepted: 11/11/2005] [Indexed: 10/25/2022]
Abstract
There are a large number of tertiary contacts between nucleotides in 23S rRNA, but which are of functional importance is not known. Disruption of one between A2662 in the sarcin/ricin loop (SRL) and A2531 in the peptidyl-transferase center (PTC) has adverse effects on cell growth and on the ability of ribosomes to catalyze some but not other partial reactions of elongation. A lethal A2662C mutation is suppressed by a concomitant lethal A2531 mutation. Ribosomes with non-lethal A2531 mutations, treated with base-specific reagents, have alterations of nucleotides in the PTC (home of A2531) and, more significantly, in nucleotides in the SRL and in the GTPase center. The results suggest that the function of ribosomal centers is coordinated by a set of sequential conformational changes in rRNA that are a response to signals transmitted through a network of tertiary interactions.
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Affiliation(s)
- Yuen-Ling Chan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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16
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Sergiev PV, Kiparisov SV, Burakovsky DE, Lesnyak DV, Leonov AA, Bogdanov AA, Dontsova OA. The Conserved A-site Finger of the 23S rRNA: Just One of the Intersubunit Bridges or a Part of the Allosteric Communication Pathway? J Mol Biol 2005; 353:116-23. [PMID: 16165153 DOI: 10.1016/j.jmb.2005.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/12/2005] [Accepted: 08/01/2005] [Indexed: 11/17/2022]
Abstract
During the translocation of tRNAs and mRNA relative to the ribosome, the B1a, B1b and B1c bridges undergo the most extensive conformational changes among the bridges between the large and the small ribosomal subunits. The B1a bridge, also called the "A-site finger" (ASF), is formed by the 23S rRNA helix 38, which is located right above the ribosomal A-site. Here, we deleted part of the ASF so that the B1a intersubunit bridge could not be formed (DeltaB1a). The mutation led to a less efficient subunit association. A number of functional activities of the DeltaB1a ribosomes, such as tRNA binding to the P and A-sites, translocation and EF-G-related GTPase reaction were preserved. A moderate decrease in EF-G-related GTPase stimulation by the P-site occupation by deacylated tRNA was observed. This suggests that the B1a bridge is not involved in the most basic steps of the elongation cycle, but rather in the fine-tuning of the ribosomal activity. Chemical probing of ribosomes carrying the ASF truncation revealed structural differences in the 5S rRNA and in the 23S rRNA helices located between the peptidyltransferase center and the binding site of the elongation factors. Interestingly, reactivity changes were found in the P-loop, an important functional region of the 23S rRNA. It is likely that the A-site finger, in addition to its role in subunit association, forms part of the system of allosteric signal exchanges between the small subunit decoding center and the functional centers on the large subunit.
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Affiliation(s)
- Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation
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17
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Chan YL, Correll CC, Wool IG. The location and the significance of a cross-link between the sarcin/ricin domain of ribosomal RNA and the elongation factor-G. J Mol Biol 2004; 337:263-72. [PMID: 15003445 DOI: 10.1016/j.jmb.2004.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 01/13/2004] [Accepted: 01/14/2004] [Indexed: 11/20/2022]
Abstract
During translocation peptidyl-tRNA moves from the A-site to the P-site and mRNA is displaced by three nucleotides in the 3' direction. This reaction is catalyzed by elongation factor-G (EF-G) and is associated with ribosome-dependent hydrolysis of GTP. The molecular basis of translocation is the most important unsolved problem with respect to ribosome function. A critical question, one that might provide a clue to the mechanism of translocation, is the precise identity of the contacts between EF-G and ribosome components. To make the identification, a covalent bond was formed, by ultraviolet irradiation, between EF-G and a sarcin/ricin domain (SRD) oligoribonucleotide containing 5-iodouridine. The cross-link was established, by mass spectroscopy and by Edman degradation, to be between a tryptophan at position 127 in the G domain in EF-G and either one of two 5-iodouridine nucleotides in the sequence UAG2655U in the SRD. G2655 is a critical identity element for the recognition of the factor's ribosomal binding site. The site of the cross-link provides the first direct evidence that the SRD is in close proximity to the EF-G catalytic center. The proximity suggests that the SRD RNA has a role in the activation of GTP hydrolysis that leads to a transition in the conformation of the factor and to its release from the ribosome.
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Affiliation(s)
- Yuen-Ling Chan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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18
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Leonov AA, Sergiev PV, Bogdanov AA, Brimacombe R, Dontsova OA. Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation. J Biol Chem 2003; 278:25664-70. [PMID: 12730236 DOI: 10.1074/jbc.m302873200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A method for preparation of Escherichia coli ribosomes carrying lethal mutations in 23 S rRNA was developed. The method is based on the site-directed incorporation of a streptavidin binding tag into functionally neutral sites of the 23 S rRNA and subsequent affinity chromatography. It was tested with ribosomes mutated at the 23 S rRNA position 2655 (the elongation factor (EF)-G binding site). Ribosomes carrying the lethal G2655C mutation were purified and studied in vitro. It was found in particular that this mutation confers strong inhibition of the translocation process but only moderately affects GTPase activity and binding of EF-G.
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Affiliation(s)
- Andrei A Leonov
- Department of Chemistry, Moscow State University, 119899 Moscow, Russia
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19
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King TH, Liu B, McCully RR, Fournier MJ. Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol Cell 2003; 11:425-35. [PMID: 12620230 DOI: 10.1016/s1097-2765(03)00040-6] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
One of the oldest questions in RNA science is the role of nucleotide modification. Here, the importance of pseudouridine formation (Psi) in the peptidyl transferase center of rRNA was examined by depleting yeast cells of 1-5 snoRNAs that guide a total of six Psi modifications. Translation was impaired substantially with loss of a conserved Psi in the A site of tRNA binding. Depletion of other Psis had subtle or no apparent effect on activity; however, synergistic effects were observed in some combinations. Pseudouridines are proposed to enhance ribosome activity by altering rRNA folding and interactions, with some Psis having greater effects than others. The possibility that modifying snoRNPs might affect ribosome structure in other ways is also discussed.
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MESH Headings
- Base Sequence
- Cell Division
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptidyl Transferases/chemistry
- Peptidyl Transferases/metabolism
- Protein Biosynthesis
- Protein Structure, Secondary
- Pseudouridine/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- RNA, Small Untranslated
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Affiliation(s)
- Thomas H King
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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20
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Glück A, Wool IG. Analysis by systematic deletion of amino acids of the action of the ribotoxin restrictocin. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1594:115-26. [PMID: 11825614 DOI: 10.1016/s0167-4838(01)00290-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of contiguous deletions were made in a cDNA encoding the ribonuclease restrictocin with the purpose of identifying the amino acids that are essential for the cleavage of the phosphodiester bond on the 3' side of G4325 in the alpha-sarcin/ricin domain of mammalian (rat) 28S rRNA. In all 93 of 149 amino acids, 62% of the residues in restrictocin, were not essential for the action of the toxin. Of the five residues that have been proposed to constitute the active site, three could be deleted without loss of activity if they were part of a deletion of three or five amino acids but not if they were removed singly. It is likely that the loss of these three residues is compensated for by a neighboring residue that occupies the structural space created by the larger amino acid deletions. This was demonstrated to be the case for the active site residue Glu95 which in the deletion mutant Delta91-95 is replaced by Asp90. Systematic deletion of amino acids is a rapid, cost effective method for identifying the residues in a protein likely to contribute directly to function and, hence, deserving of closer scrutiny. Moreover, a semiquantitative estimate of the contribution of the residue to function can be made. For this reason the method may be useful for functional proteomics.
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Affiliation(s)
- Anton Glück
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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21
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Smith MW, Meskauskas A, Wang P, Sergiev PV, Dinman JD. Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 2001; 21:8264-75. [PMID: 11713264 PMCID: PMC99992 DOI: 10.1128/mcb.21.24.8264-8275.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
rRNAs are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs are actively involved in different ribosome functions. Our previous demonstration that yeast 5S rRNA mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. At the time, however, the highly repetitive nature of the genes encoding rRNAs precluded more detailed genetic and molecular analyses. A new genetic system allows all 5S rRNAs in the cell to be transcribed from a small, easily manipulated plasmid. The system is also amenable for the study of the other rRNAs, and provides an ideal genetic platform for detailed structural and functional studies. Saturation mutagenesis reveals regions of 5S rRNA that are required for cell viability, translational accuracy, and virus propagation. Unexpectedly, very few lethal alleles were identified, demonstrating the resilience of this molecule. Superimposition of genetic phenotypes on a physical map of 5S rRNA reveals the existence of phenotypic clusters of mutants, suggesting that specific regions of 5S rRNA are important for specific functions. Mapping these mutants onto the Haloarcula marismortui large subunit reveals that these clusters occur at important points of physical interaction between 5S rRNA and the different functional centers of the ribosome. Our analyses lead us to propose that one of the major functions of 5S rRNA may be to enhance translational fidelity by acting as a physical transducer of information between all of the different functional centers of the ribosome.
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Affiliation(s)
- M W Smith
- Department of Molecular Genetics and Microbiology, Rutgers University and University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
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22
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Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Chan YL, Sitikov AS, Wool IG. The phenotype of mutations of the base-pair C2658.G2663 that closes the tetraloop in the sarcin/ricin domain of Escherichia coli 23 S ribosomal RNA. J Mol Biol 2000; 298:795-805. [PMID: 10801349 DOI: 10.1006/jmbi.2000.3720] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA is a part of the site for the association of elongation factors with ribosomes and for that reason is critical for the binding of aminoacyl-tRNA and for translocation during the reiterative elongation reactions of protein synthesis. The SRD has a GAGA tetraloop that is shut off by a Watson-Crick C2658 x G2663 pair. The contribution of this pair to the function of the ribosome has been evaluated by constructing mutations in the nucleotides and determining their phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a G2663C transversion mutation that disrupts the Watson-Crick pair was lethal. Double transversion mutations, C2658G x G2663C and C2658A x G2663U, that reverse the polarity of the pyrimidine and the purine but restore the potential to form a canonical pair, were also lethal. Induction of transcription of 23 S rRNA with the same mutations, but encoded in a plasmid with a lambdaP(L) promoter and expressed at a lower level, retarded growth. The sedimentation profiles of ribosomes with transversion mutations in C2658 and/or G2663 are altered; the ratio of 50 S subunits to 30 S particles is changed and polysomes are reduced. Ribosomes with a G2663C, a C2658G x G2663C, or a C2658A x G2663U mutation in 23 S rRNA were not active in protein synthesis, indeed, they appeared to inhibit the activity of ribosomes with wild-type 23 S rRNA. Transversion mutations in the analogs of C2658 and G2663 decreased binding of EF-G to SRD oligoribonucleotides; the same mutations in 23 S rRNA decreased binding of the factor to intact ribosomes. The most severe phenotype, in growth, in protein synthesis, and in the binding of EF-G, was associated with a C2658G x G2663C mutation; it is surprising that this was more severe than an analogous C2658A x G2663U mutation. A double transition mutation, C2658U x G2663A, which is not known to have occurred in nature, had no effect on the growth of cells or on the function of ribosomes. The lethal phenotype of transversion mutations in C2658 and G2663 appears to derive from a loss of the capacity of ribosomes to bind EF-G and by indirection the EF-Tu ternary complex.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/metabolism
- Base Pairing/genetics
- Base Sequence
- Binding Sites
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Fungal Proteins
- Genes, Lethal/genetics
- Guanosine Triphosphate/metabolism
- Mutation/genetics
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Peptide Elongation Factor G/metabolism
- Peptides/metabolism
- Phenotype
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- Protein Binding
- Protein Biosynthesis/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ricin/metabolism
- Thermodynamics
- rRNA Operon/genetics
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Affiliation(s)
- Y L Chan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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Correll CC, Wool IG, Munishkin A. The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution. J Mol Biol 1999; 292:275-87. [PMID: 10493875 DOI: 10.1006/jmbi.1999.3072] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia coli 23 S rRNA was determined at 1.11 A resolution. The domain folds into a hairpin distorted by four non-canonical base-pairs and one base triple. The fold is stabilized by cross-strand and intra-stand stacking; no intramolecular stabilizing metal ions are observed. This is the first structure to reveal in great detail the geometry and the hydration of two common motifs that are conserved in this rRNA domain, a GAGA tetraloop and a G-bulged cross-strand A stack. Differences in the region connecting these motifs to the stem in the E. coli and in the rat sarcin/ricin domains may contribute to the species-specific binding of elongation factors. Correlation of nucleotide protection data with the structure indicates that the domain has two surfaces. One surface is accessible, lies primarily in the major groove, and is likely to bind the elongation factors. The second lies primarily in the minor groove, and is likely to be buried in the ribosome. This minor groove surface includes the Watson-Crick faces of the cytosine bases in the unusual A2654.C2666 and U2653.C2667 water-mediated base-pairs.
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Affiliation(s)
- C C Correll
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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