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Steitz TA. From the structure and function of the ribosome to new antibiotics (Nobel Lecture). Angew Chem Int Ed Engl 2010; 49:4381-98. [PMID: 20509130 DOI: 10.1002/anie.201000708] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University and the Howard Hughes Medical Institute, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
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52
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53
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Steitz T. Von der Struktur und Funktion des Ribosoms zu neuen Antibiotika (Nobel-Aufsatz). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000708] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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54
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Giegé R, Sauter C. Biocrystallography: past, present, future. HFSP JOURNAL 2010; 4:109-21. [PMID: 21119764 PMCID: PMC2929629 DOI: 10.2976/1.3369281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/02/2010] [Indexed: 02/02/2023]
Abstract
The evolution of biocrystallography from the pioneers' time to the present era of global biology is presented in relation to the development of methodological and instrumental advances for molecular sample preparation and structure elucidation over the last 6 decades. The interdisciplinarity of the field that generated cross-fertilization between physics- and biology-focused themes is emphasized. In particular, strategies to circumvent the main bottlenecks of biocrystallography are discussed. They concern (i) the way macromolecular targets are selected, designed, and characterized, (ii) crystallogenesis and how to deal with physical and biological parameters that impact crystallization for growing and optimizing crystals, and (iii) the methods for crystal analysis and 3D structure determination. Milestones that have marked the history of biocrystallography illustrate the discussion. Finally, the future of the field is envisaged. Wide gaps of the structural space need to be filed and membrane proteins as well as intrinsically unstructured proteins still constitute challenging targets. Solving supramolecular assemblies of increasing complexity, developing a "4D biology" for decrypting the kinematic changes in macromolecular structures in action, integrating these structural data in the whole cell organization, and deciphering biomedical implications will represent the new frontiers.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
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55
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Granneman S, Petfalski E, Swiatkowska A, Tollervey D. Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking. EMBO J 2010; 29:2026-36. [PMID: 20453830 PMCID: PMC2892368 DOI: 10.1038/emboj.2010.86] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 04/14/2010] [Indexed: 12/21/2022] Open
Abstract
Understanding of eukaryotic ribosome synthesis has been slowed by a lack of structural data for the pre-ribosomal particles. We report rRNA-binding sites for six late-acting 40S ribosome synthesis factors, three of which cluster around the 3' end of the 18S rRNA in model 3D structures. Enp1 and Ltv1 were previously implicated in 'beak' structure formation during 40S maturation--and their binding sites indicate direct functions. The kinase Rio2, putative GTPase Tsr1 and dimethylase Dim1 bind sequences involved in tRNA interactions and mRNA decoding, indicating that their presence is incompatible with translation. The Dim1- and Tsr1-binding sites overlap with those of homologous Escherichia coli proteins, revealing conservation in assembly pathways. The primary binding sites for the 18S 3'-endonuclease Nob1 are distinct from its cleavage site and were unaltered by mutation of the catalytic PIN domain. Structure probing indicated that at steady state the cleavage site is likely unbound by Nob1 and flexible in the pre-rRNA. Nob1 binds before pre-rRNA cleavage, and we conclude that structural reorganization is needed to bring together the catalytic PIN domain and its target.
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Affiliation(s)
- Sander Granneman
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
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56
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Abstract
This year's Nobel Prize in Chemistry rewards Ada Yonath, Tom Steitz, and Venki Ramakrishnan for their groundbreaking structural studies on the ribosome.
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57
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Wei Y, Daunert S. Enabling technologies in discovery: the 2009 Nobel Prize and its implications in antibiotic design. Anal Bioanal Chem 2010; 396:1623-6. [PMID: 20127083 DOI: 10.1007/s00216-009-3427-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
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58
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Nierhaus KH. Nobel Prize for the elucidation of ribosome structure and insight into the translation mechanism. Angew Chem Int Ed Engl 2010; 48:9225-8. [PMID: 19899182 DOI: 10.1002/anie.200905795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Knud H Nierhaus
- Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestrasse 73, 14195 Berlin, Germany.
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59
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HU YL. Studies on Structure and Function of Ribosome: a Brief Introduction to 2009 Nobel Prize in Chemistry. PROG BIOCHEM BIOPHYS 2009. [DOI: 10.3724/sp.j.1206.2009.00607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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60
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Sprinzl M, Erdmann VA. Protein biosynthesis on ribosomes in molecular resolution: Nobel Prize for chemistry 2009 goes to three chemical biologists. Chembiochem 2009; 10:2851-3. [PMID: 19938030 DOI: 10.1002/cbic.200900652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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61
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Oubridge C, Krummel DAP, Leung AKW, Li J, Nagai K. Interpreting a low resolution map of human U1 snRNP using anomalous scatterers. Structure 2009; 17:930-8. [PMID: 19604473 PMCID: PMC2712673 DOI: 10.1016/j.str.2009.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 04/21/2009] [Accepted: 05/07/2009] [Indexed: 12/03/2022]
Abstract
We recently determined the crystal structure of the functional core of human U1 snRNP, consisting of nine proteins and one RNA, based on a 5.5 Å resolution electron density map. At 5–7 Å resolution, α helices and β sheets appear as rods and slabs, respectively, hence it is not possible to determine protein fold de novo. Using inverse beam geometry, accurate anomalous signals were obtained from weakly diffracting and radiation sensitive P1 crystals. We were able to locate anomalous scatterers with positional errors below 2 Å. This enabled us not only to place protein domains of known structure accurately into the map but also to trace an extended polypeptide chain, of previously undetermined structure, using selenomethionine derivatives of single methionine mutants spaced along the sequence. This method of Se-Met scanning, in combination with structure prediction, is a powerful tool for building a protein of unknown fold into a low resolution electron density map.
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Affiliation(s)
- Chris Oubridge
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England, UK
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62
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Nierhaus K. Nobelpreiswürdig: Aufklärung der Ribosomenstruktur und Einblicke in den Mechanismus der Translation. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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63
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Romby P, Marzi et Eric Westhof S. La structure atomique du ribosome en pleine lumière. Med Sci (Paris) 2009; 25:977-81. [DOI: 10.1051/medsci/20092511977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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64
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Simonović M, Steitz TA. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:612-23. [PMID: 19595805 DOI: 10.1016/j.bbagrm.2009.06.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/23/2009] [Accepted: 06/25/2009] [Indexed: 10/20/2022]
Abstract
The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.
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Affiliation(s)
- Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1170, 900 S Ashland Ave., Chicago, IL 60607, USA
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65
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Pomeranz Krummel DA, Oubridge C, Leung AKW, Li J, Nagai K. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature 2009; 458:475-80. [PMID: 19325628 PMCID: PMC2673513 DOI: 10.1038/nature07851] [Citation(s) in RCA: 263] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 02/04/2009] [Indexed: 12/03/2022]
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66
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Dalal K, Nguyen N, Alami M, Tan J, Moraes TF, Lee WC, Maurus R, Sligar SS, Brayer GD, Duong F. Structure, binding, and activity of Syd, a SecY-interacting protein. J Biol Chem 2009; 284:7897-902. [PMID: 19139097 PMCID: PMC2658082 DOI: 10.1074/jbc.m808305200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/19/2008] [Indexed: 01/20/2023] Open
Abstract
The Syd protein has been implicated in the Sec-dependent transport of polypeptides across the bacterial inner membrane. Using Nanodiscs, we here provide direct evidence that Syd binds the SecY complex, and we demonstrate that interaction involves the two electropositive and cytosolic loops of the SecY subunit. We solve the crystal structure of Syd and together with cysteine cross-link analysis, we show that a conserved concave and electronegative groove constitutes the SecY-binding site. At the membrane, Syd decreases the activity of the translocon containing loosely associated SecY-SecE subunits, whereas in detergent solution Syd disrupts the SecYEG heterotrimeric associations. These results support the role of Syd in proofreading the SecY complex biogenesis and point to the electrostatic nature of the Sec channel interaction with its cytosolic partners.
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Affiliation(s)
- Kush Dalal
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
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67
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Abstract
Since the mid-1990s, insights obtained from electron microscopy and X-ray crystallography have transformed our understanding of how the most important ribozyme in the cell, the ribosome, catalyzes protein synthesis. This review provides a brief account of how this structural revolution came to pass, and the impact it has had on our understanding of how the ribosome decodes messenger RNAs.
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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68
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Genetic analysis of the invariant residue G791 in Escherichia coli 16S rRNA implicates RelA in ribosome function. J Bacteriol 2009; 191:2042-50. [PMID: 19168615 DOI: 10.1128/jb.00904-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies identified G791 in Escherichia coli 16S rRNA as an invariant residue for ribosome function. In order to establish the functional role of this residue in protein synthesis, we searched for multicopy suppressors of the mutant ribosomes that bear a G-to-U substitution at position 791. We identified relA, a gene whose product has been known to interact with ribosomes and trigger a stringent response. Overexpression of RelA resulted in the synthesis of approximately 1.5 times more chloramphenicol acetyltransferase (CAT) protein than could be synthesized by the mutant ribosomes in the absence of RelA overexpression. The ratio of mutant rRNA to the total ribosome pool was not changed, and the steady-state level of CAT mRNA was decreased by RelA overexpression. These data confirmed that the phenotype of RelA as a multicopy suppressor of the mutant ribosome did not result from the enhanced synthesis of mutant rRNA or CAT mRNA from the plasmid. To test whether the phenotype of RelA was related to the stringent response induced by the increased cellular level of (p)ppGpp, we screened for mutant RelA proteins whose overexpression enhances CAT protein synthesis by the mutant ribosomes as effectively as wild-type RelA overexpression and then screened for those whose overexpression does not produce sufficiently high levels of (p)ppGpp to trigger the stringent response under the condition of amino acid starvation. Overexpression of the isolated mutant RelA proteins resulted in the accumulation of (p)ppGpp in cells, which was amounted to approximately 18.2 to 38.9% of the level of (p)ppGpp found in cells that overexpress the wild-type RelA. These findings suggest that the function of RelA as a multicopy suppressor of the mutant ribosome does not result from its (p)ppGpp synthetic activity. We conclude that RelA has a previously unrecognized role in ribosome function.
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69
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Karmali AM, Blundell TL, Furnham N. Model-building strategies for low-resolution X-ray crystallographic data. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:121-7. [PMID: 19171966 PMCID: PMC2631632 DOI: 10.1107/s0907444908040006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 11/27/2008] [Indexed: 11/24/2022]
Abstract
Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.
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Affiliation(s)
- Anjum M Karmali
- Department of Biochemistry, University of Cambridge, Cambridge, England
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70
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Edwards KA, Baeumner AJ. Liposome-enhanced lateral-flow assays for the sandwich-hybridization detection of RNA. Methods Mol Biol 2009; 504:185-215. [PMID: 19159099 DOI: 10.1007/978-1-60327-569-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Clinical and environmental analyses frequently necessitate rapid, simple, and inexpensive point-of-care or field tests. These semiquantitative tests may be later followed up by confirmatory laboratory-based assays, but can provide an initial scenario assessment important for resource mobilization and threat confinement. Lateral-flow assays (LFAs) and dip-stick assays, which are typically antibody-based and yield a visually detectable signal, provide an assay format suiting these applications extremely well. Signal generation is commonly obtained through the use of colloidal gold or latex beads, which yield a colored band either directly proportional or inversely proportional to the concentration of the analyte of interest. Here, dye-encapsulating liposomes as an alternative are discussed. The LFA biosensors described in this chapter rely on the sandwich-hybridization of a nucleic acid sequence-based amplified (NASBA) mRNA target between a membrane immobilized capture probe and a visible dye (sulforhodamine B)-encapsulating liposome conjugated reporter probe. Although the methodology of this chapter is focused on LFAs for the detection of RNA through sandwich hybridization, the information within can be readily adapted for sandwich and competitive immunoassays. Included are an introduction and application notes toward this end. These include notes ranging from the detection of nonamplified RNA and single-stranded DNA, conjugation protocols for antibodies and other proteins to liposomes, and universal assay formats.
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Affiliation(s)
- Katie A Edwards
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
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71
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Bashan A, Yonath A. The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility. J Mol Struct 2008; 890:289-294. [PMID: 19915655 PMCID: PMC2757297 DOI: 10.1016/j.molstruc.2008.03.043] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by "gluing" symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment.
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Affiliation(s)
- Anat Bashan
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
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72
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Powell ML, Napthine S, Jackson RJ, Brierley I, Brown TDK. Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein. RNA (NEW YORK, N.Y.) 2008; 14:2394-2406. [PMID: 18824510 PMCID: PMC2578862 DOI: 10.1261/rna.1231008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/18/2008] [Indexed: 05/26/2023]
Abstract
Coupled expression of the M1 and BM2 open-reading frames (ORFs) of influenza B from the dicistronic segment 7 mRNA occurs by a process of termination-dependent reinitiation. The AUG start codon of the BM2 ORF overlaps the stop codon of the upstream M1 ORF in the pentanucleotide UAAUG, and BM2 synthesis is dependent upon translation of the M1 ORF and termination at the stop codon. Here, we have investigated the mRNA sequence requirements for BM2 expression. Termination-reinitiation is dependent upon 45 nucleotide (nt) of RNA immediately upstream of the UAAUG pentanucleotide, which includes an essential stretch complementary to 18S rRNA helix 26. Thus, similar to the caliciviruses, base-pairing between mRNA and rRNA is likely to play a role in tethering the 40S subunit to the mRNA following termination at the M1 stop codon. Consistent with this, repositioning of the M1 stop codon more than 24 nt downstream from the BM2 start codon inhibited BM2 expression. RNA structure probing revealed that the RNA upstream of the UAAUG overlap is not highly structured, but upon encountering the M1 stop codon by the ribosome, a stem-loop may form immediately 5' of the ribosome, with the 18S rRNA complementary region in the apical loop and in close proximity to helix 26. Mutational analysis reveals that the normal requirements for start site selection in BM2 expression are suspended, with little effect of initiation codon context and efficient use of noncanonical initiation codons. This suggests that the full complement of initiation factors is not required for the reinitiation process.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Codon, Terminator/genetics
- Codon, Terminator/metabolism
- Influenza B virus/genetics
- Influenza B virus/metabolism
- Models, Biological
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational/genetics
- Peptide Chain Termination, Translational/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Viral Proteins/biosynthesis
- Viral Proteins/genetics
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Affiliation(s)
- Michael L Powell
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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73
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Abstract
The determination of the high-resolution structures of ribosomal subunits in the year 2000 and of the entire ribosome a few years later are revolutionizing our understanding of the role of the ribosome in translation. In the present article, I summarize the main contributions from our laboratory to this worldwide effort. These include the determination of the structure of the 30S ribosomal subunit and its complexes with antibiotics, the role of the 30S subunit in decoding, and the high-resolution structure of the entire 70S ribosome complexed with mRNA and tRNA.
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74
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Heredia-Moya J, Kirk KL. Synthesis of beta-(S-methyl)thioaspartic acid and derivatives. Bioorg Med Chem 2008; 16:5908-13. [PMID: 18468905 PMCID: PMC2587367 DOI: 10.1016/j.bmc.2008.04.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/24/2008] [Accepted: 04/24/2008] [Indexed: 11/17/2022]
Abstract
Beta-(S-Methyl)thioaspartic acid occurs as a posttranslational modification at position 88 in Escherichia coli ribosomal protein S12, a position that is a mutational hotspot resulting in both antibiotic-resistant and antibiotic-sensitive phenotypes. Critical to research designed to determine the biological function of beta-(S-methyl)thioaspartic acid will be the availability of synthetic beta-(S-methyl)thioaspartic acid as well as derivatives designed for peptide incorporation. We report here the synthesis of beta-(S-methyl)thioaspartic acid and derivatives. The installation of the beta-methylthio moiety into the aspartic acid structure was accomplished by electrophilic sulfenylation of N-protected-l-aspartic acid derivatives with 2,4-dinitrophenyl methyl disulfide. Following this key transformation, we were able to prepare protected beta-(S-methyl)thioaspartic acid derivative suitable for peptide coupling.
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Affiliation(s)
- Jorge Heredia-Moya
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892. USA
| | - Kenneth L. Kirk
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892. USA
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75
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Pisarev AV, Kolupaeva VG, Yusupov MM, Hellen CUT, Pestova TV. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J 2008; 27:1609-21. [PMID: 18464793 DOI: 10.1038/emboj.2008.90] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 04/10/2008] [Indexed: 02/05/2023] Open
Abstract
The position of mRNA on 40S ribosomal subunits in eukaryotic initiation complexes was determined by UV crosslinking using mRNAs containing uniquely positioned 4-thiouridines. Crosslinking of mRNA positions (+)11 to ribosomal protein (rp) rpS2(S5p) and rpS3(S3p), and (+)9-(+)11 and (+)8-(+)9 to h18 and h34 of 18S rRNA, respectively, indicated that mRNA enters the mRNA-binding channel through the same layers of rRNA and proteins as in prokaryotes. Upstream of the P-site, the proximity of positions (-)3/(-)4 to rpS5(S7p) and h23b, (-)6/(-)7 to rpS14(S11p), and (-)8-(-)11 to the 3'-terminus of 18S rRNA (mRNA/rRNA elements forming the bacterial Shine-Dalgarno duplex) also resembles elements of the bacterial mRNA path. In addition to these striking parallels, differences between mRNA paths included the proximity in eukaryotic initiation complexes of positions (+)7/(+)8 to the central region of h28, (+)4/(+)5 to rpS15(S19p), and (-)6 and (-)7/(-)10 to eukaryote-specific rpS26 and rpS28, respectively. Moreover, we previously determined that eukaryotic initiation factor2alpha (eIF2alpha) contacts position (-)3, and now report that eIF3 interacts with positions (-)8-(-)17, forming an extension of the mRNA-binding channel that likely contributes to unique aspects of eukaryotic initiation.
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Affiliation(s)
- Andrey V Pisarev
- Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
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76
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Rakauskaitė R, Dinman JD. rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance. Nucleic Acids Res 2008; 36:1497-507. [PMID: 18203742 PMCID: PMC2275155 DOI: 10.1093/nar/gkm1179] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 12/24/2007] [Accepted: 12/26/2007] [Indexed: 11/29/2022] Open
Abstract
To ensure accurate and rapid protein synthesis, nearby and distantly located functional regions of the ribosome must dynamically communicate and coordinate with one another through a series of information exchange networks. The ribosome is approximately 2/3 rRNA and information should pass mostly through this medium. Here, two viable mutants located in the peptidyltransferase center (PTC) of yeast ribosomes were created using a yeast genetic system that enables stable production of ribosomes containing only mutant rRNAs. The specific mutants were C2820U (Escherichia coli C2452) and Psi2922C (E. coli U2554). Biochemical and genetic analyses of these mutants suggest that they may trap the PTC in the 'open' or aa-tRNA bound conformation, decreasing peptidyl-tRNA binding. We suggest that these structural changes are manifested at the biological level by affecting large ribosomal subunit biogenesis, ribosomal subunit joining during initiation, susceptibility/resistance to peptidyltransferase inhibitors, and the ability of ribosomes to properly decode termination codons. These studies also add to our understanding of how information is transmitted both locally and over long distances through allosteric networks of rRNA-rRNA and rRNA-protein interactions.
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Affiliation(s)
| | - Jonathan D. Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, 2135 Microbiology Building, College Park, MD 20742, USA
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77
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Xie Q, Tian Y, Zheng L, Bu W. 18S rRNA hyper-elongation and the phylogeny of Euhemiptera (Insecta: Hemiptera). Mol Phylogenet Evol 2008; 47:463-71. [PMID: 18358745 DOI: 10.1016/j.ympev.2008.01.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2006] [Revised: 10/27/2007] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
The small subunit of nuclear ribosomal RNA (SSU nrRNA), whose sedimentation is mostly 18S in eukaryotes, is considered a relatively conservative marker for resolving phylogenetic relationship at the order level or higher. Length variation in SSU nrDNA is common, and can be rather large in some groups. In studies of Hexapoda phylogeny, the SSU nrDNA has been repeatedly used as a marker. Sternorrhyncha has been rarely included. The lengths of SSU nrDNAs of sternorrhynchids, the basal group of Hemiptera identified in the previous study are 0.3-0.6 kb longer than the usual ones in Hexapoda (1.8-1.9 kb). To use the entire SSU nrDNA sequences or the length-variable parts could cause alignment trouble and therefore affect phylogenetic results, as shown in this study of Euhemiptera phylogeny. Two problems are particularly noticeable. One is that two hyper-variable regions flanking a short length-conservative region could become overlapped in the alignment. This will destroy the positional homology over a larger range. The other is that, when a base pair in a stem of the secondary structure is located near the length-variable regions (LVRs), the simultaneous positional homology of these two bases in the pair is always lost in the alignment results. In this study, the secondary structure model of Hexapoda SSU nrRNA was slightly adjusted and the LVR distributions in it were finely positioned. The noise caused by the hyper LVRs was eliminated and the simultaneous homology for the paired bases was recovered based on the secondary structure model. These corrections improved the quality of the data matrix and hence improved the resolving behavior of the algorithm used. This study provided more convincing evidence for resolving the Euhemiptera suborders phylogeny as (Archaeorrhyncha+(Clypeorrhyncha+(Coleorrhyncha+Heteroptera))). This result provided a more solid background for outgroup determination according to the phylogenetic studies inside each suborder. The problems caused by LVRs have seldom been well addressed. As phylogenetic reconstruction depends more on the data matrix itself than on the algorithm, and length variation of SSU/LSU rRNA exists more or less in any group, it is necessary to closely investigate the effect of rRNA length variation on alignment and phylogenetic reconstruction in more groups.
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Affiliation(s)
- Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Department of Zoology, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
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78
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Abstract
Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.
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Affiliation(s)
| | | | - R. Knight
- *To whom correspondence should be addressed. Tel: 303-492-1984; Fax: 303-492-7744;
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79
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Abstract
All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base–base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson–Crick as well as non-Watson–Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis.
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Affiliation(s)
| | - E. Westhof
- To whom correspondence should be addressed. Tel/Fax: +33 388 41 70 46; Email :
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80
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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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81
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Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry 2006; 45:11776-89. [PMID: 17002278 PMCID: PMC4070884 DOI: 10.1021/bi0605787] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Internal loops play an important role in structure and folding of RNA and in recognition of RNA by other molecules such as proteins and ligands. An understanding of internal loops with propensities to form a particular structure will help predict RNA structure, recognition, and function. The structures of internal loops 5' 1009CUAAG1013 3'/3' 1168GAAGC1164 5' and 5' 998CUAAG1002 3'/3' 1157GAAGC1153 5' from helix 40 of the large subunit rRNA in Deinococcus radiodurans and Escherichia coli, respectively, are phylogenetically conserved, suggesting functional relevance. The energetics and NMR solution structure of the loop were determined in the duplex 5' 1GGCUAAGAC9 3'/3' 18CCGAAGCUG10 5'. The internal loop forms a different structure in solution and in the crystal structures of the ribosomal subunits. In particular, the crystal structures have a bulged out adenine at the equivalent of position A15 and a reverse Hoogsteen UA pair (trans Watson-Crick/Hoogsteen UA) at the equivalent of U4 and A14, whereas the solution structure has a single hydrogen bond UA pair (cis Watson-Crick/sugar edge A15U4) between U4 and A15 and a sheared AA pair (trans Hoogsteen/sugar edge A14A5) between A5 and A14. There is cross-strand stacking between A6 and A14 (A6/A14/A15 stacking pattern) in the NMR structure. All three structures have a sheared GA pair (trans Hoogsteen/sugar edge A6G13) at the equivalent of A6 and G13. The internal loop has contacts with ribosomal protein L20 and other parts of the RNA in the crystal structures. These contacts presumably provide the free energy to rearrange the base pairing in the loop. Evidently, molecular recognition of this internal loop involves induced fit binding, which could confer several advantages. The predicted thermodynamic stability of the loop agrees with the experimental value, even though the thermodynamic model assumes a Watson-Crick UA pair.
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Affiliation(s)
- Neelaabh Shankar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Gang Chen
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Thomas R. Krugh
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
- Center for Pediatric Biomedical Research and Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642
- To whom correspondence should be addressed. Phone: (585) 275-3207. Fax: (585) 276-0205.
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82
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Réblová K, Lankas F, Rázga F, Krasovska MV, Koca J, Sponer J. Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 2006; 82:504-20. [PMID: 16538608 DOI: 10.1002/bip.20503] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Molecular dynamics (MD) simulations were employed to investigate the structure, dynamics, and local base-pair step deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopic studies. Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulge bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing. In agreement with nuclear magnetic resonance (NMR) and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area. Molecular dynamics (MD) simulations reveal a number of reversible alpha-gamma backbone flips that correspond to transitions between two known A-RNA backbone families. The flipped substates do not cumulate along the trajectory and lead to a modest transient reduction of helical twist with no significant influence on the overall geometry of the duplexes. Despite their considerable flexibility, the simulated structures are very stable with no indication of substantial force field inaccuracies.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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83
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Sveshnikov NN, Dickman MH, Pope MT. Dicarboxylatodirhodium derivatives of polyoxotungstates. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2005.10.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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84
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Mengel-Jørgensen J, Jensen SS, Rasmussen A, Poehlsgaard J, Iversen JJL, Kirpekar F. Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact. J Biol Chem 2006; 281:22108-22117. [PMID: 16731530 DOI: 10.1074/jbc.m600377200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the post-transcriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.
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Affiliation(s)
- Jonas Mengel-Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Søren Skov Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Anette Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jacob Poehlsgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jens Jørgen Lønsmann Iversen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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85
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Inagaki S, Numata K, Kondo T, Tomita M, Yasuda K, Kanai A, Kageyama Y. Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells 2006; 10:1163-73. [PMID: 16324153 DOI: 10.1111/j.1365-2443.2005.00910.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
One of the most surprising results to emerge from mammalian cDNA sequencing projects is that thousands of mRNA-like non-coding RNAs (ncRNAs) are expressed and constitute at least 10% of poly(A)(+) RNAs. In most cases, however, the functions of these RNA molecules remain unclear. To clarify the biological significance of mRNA-like ncRNAs, we computationally screened 11,691 Drosophila melanogaster full-length cDNAs. After eliminating presumable protein-coding transcripts, 136 were identified as strong candidates for mRNA-like ncRNAs. Although most of these putative ncRNAs are found throughout the Drosophila genus, predicted amino acid sequences are not conserved even in related species, suggesting that these transcripts are actually non-coding RNAs. In situ hybridization analyses revealed that 35 of the transcripts are expressed during embryogenesis, of which 27 were detected only in specific tissues including the tracheal system, midgut primordial cells, visceral mesoderm, germ cells and the central and peripheral nervous system. These highly regulated expression patterns suggest that many mRNA-like ncRNAs play important roles in multiple steps of organogenesis and cell differentiation in Drosophila. This is the first report that the majority of mRNA-like ncRNAs in a model organism are expressed in specific tissues and cell types.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Differentiation/genetics
- Conserved Sequence
- DNA, Complementary/analysis
- DNA, Complementary/genetics
- Drosophila/embryology
- Drosophila/genetics
- Embryonic Development/genetics
- Evolution, Molecular
- Gene Expression Regulation, Developmental
- Models, Genetic
- Open Reading Frames/genetics
- Organogenesis/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Sachi Inagaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Japan
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86
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Yatime L, Mechulam Y, Blanquet S, Schmitt E. Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer. Structure 2006; 14:119-28. [PMID: 16407071 DOI: 10.1016/j.str.2005.09.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 09/23/2005] [Accepted: 09/23/2005] [Indexed: 11/25/2022]
Abstract
Eukaryotic and archaeal initiation factors 2 (e/aIF2) are heterotrimeric proteins (alphabetagamma) supplying the small subunit of the ribosome with methionylated initiator tRNA. This study reports the crystallographic structure of an aIF2alphagamma heterodimer from Sulfolobus solfataricus bound to Gpp(NH)p-Mg(2+). aIF2gamma is in a closed conformation with the G domain packed on domains II and III. The C-terminal domain of aIF2alpha interacts with domain II of aIF2gamma. Conformations of the two switch regions involved in GTP binding are similar to those encountered in an EF1A:GTP:Phe-tRNA(Phe) complex. Comparison with the EF1A structure suggests that only the gamma subunit of the aIF2alphagamma heterodimer contacts tRNA. Because the alpha subunit markedly reinforces the affinity of tRNA for the gamma subunit, a contribution of the alpha subunit to the switch movements observed in the gamma structure is considered.
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Affiliation(s)
- Laure Yatime
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France
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87
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Sakamoto T, Mahara A, Yamagata K, Iwase R, Yamaoka T, Murakami A. Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution. Biophys J 2006; 89:4122-8. [PMID: 16319080 PMCID: PMC1366977 DOI: 10.1529/biophysj.105.062455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is no methodology for the estimation of the dynamic features of large-molecular-weight RNAs in homogeneous physiological media. In this report, a luminescence anisotropy-based method using a long-lifetime luminescent oligonucleotide probe for the estimation of the dynamic features of large-molecular-weight RNA is described. As a luminescent probe, Ru(II) complex-labeled oligonucleotides, which have a complementary sequence to the single-stranded regions of Escherichia coli 16S rRNA, were synthesized. After the hybridization of the probe to single-stranded regions of 16S rRNA, the segmental motions of the regions were evaluated by time-resolved luminescence anisotropy analysis. In 16S rRNA, the L2 site (323-332 nt) was found to be the most flexible among the seven sites chosen. From a comparison between the hybridization kinetics of oligonucleotides to these single-stranded regions and the rotational correlation times, it was suggested that the flexibility of the single-stranded region was closely correlated with the hybridization kinetics. Furthermore, results of the luminescence lifetime measurement and luminescence quenching experiments suggested that the highly flexible region was located on the surface of the 16S rRNA and that the less flexible region was located in the depths of 16S rRNA.
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Affiliation(s)
- Takashi Sakamoto
- Department of Polymer Science and Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
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88
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Bhargava K, Spremulli LL. Role of the N- and C-terminal extensions on the activity of mammalian mitochondrial translational initiation factor 3. Nucleic Acids Res 2005; 33:7011-8. [PMID: 16340009 PMCID: PMC1310894 DOI: 10.1093/nar/gki1007] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Mammalian mitochondrial translational initiation factor 3 (IF3mt) promotes initiation complex formation on mitochondrial 55S ribosomes in the presence of IF2mt, fMet-tRNA and poly(A,U,G). The mature form of IF3mt is predicted to be 247 residues. Alignment of IF3mt with bacterial IF3 indicates that it has a central region with 20–30% identity to the bacterial factors. Both the N- and C-termini of IF3mt have extensions of ∼30 residues compared with bacterial IF3. To examine the role of the extensions on IF3mt, deletion constructs were prepared in which the N-terminal extension, the C-terminal extension or both extensions were deleted. These truncated derivatives were slightly more active in promoting initiation complex formation than the mature form of IF3mt. Mitochondrial 28S subunits have the ability to bind fMet-tRNA in the absence of mRNA. IF3mt promotes the dissociation of the fMet-tRNA bound in the absence of mRNA. This activity of IF3mt requires the C-terminal extension of this factor. Mitochondrial 28S subunits also bind mRNA independently of fMet-tRNA or added initiation factors. IF3mt has no effect on the formation of these complexes and cannot dissociate them once formed. These observations have lead to a new model for the function of IF3mt in mitochondrial translational initiation.
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Affiliation(s)
| | - Linda L. Spremulli
- To whom correspondence should be addressed. Tel: +1 919 966 1567; Fax: +1 919 966 3675;
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89
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Bonicontro A, Risuleo G. Structural studies of E. coli ribosomes by spectroscopic techniques: a specialized review. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 62:1070-80. [PMID: 15950526 DOI: 10.1016/j.saa.2005.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 04/15/2005] [Indexed: 05/02/2023]
Abstract
We present a review on our interdisciplinary line of research based on strategies of molecular biology and biophysics. These have been applied to the study of the prokaryotic ribosome of the bacterium Escherichia coli. Our investigations on this organelle have continued for more than a decade and we have adopted different spectroscopic biophysical techniques such as: dielectric and fluorescence spectroscopy as well as light scattering (photon correlation spectroscopy). Here we report studies on the whole 70S ribosomes and on the separated subunits 30S and 50S. Our results evidence intrinsic structural features of the subunits: the small shows a more "floppy" structure, while the large one appears to be more rigid. Also, an inner "kernel" formed by the RNA/protein association is found within the ribosome. This kernel is surrounded by a ribonucleoprotein complex more exposed to the solvent. Initial analyses were done on the so called Kaldtschmit-Wittmann ribosome: more recently we have extended the studies to the "tight couple" ribosome known for its better functional performance in vitro. Data evidence a phenomenological correlation between the differential biological activity and the intrinsic structural properties of the two-ribosome species. Finally, investigations were also conducted on particles treated at sub-denaturing temperatures and on ribosomes partially deproteinized by salt treatment (ribosomal cores). Results suggest that the thermal treatment and the selective removal of proteins cause analogous structural alterations.
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Affiliation(s)
- Adalberto Bonicontro
- INFM-CRS SOFT, Dipartimento di Fisica, Università di Roma La Sapienza, P.le A. Moro 2, I-00185 Roma, Italy
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90
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Nagiec EE, Wu L, Swaney SM, Chosay JG, Ross DE, Brieland JK, Leach KL. Oxazolidinones inhibit cellular proliferation via inhibition of mitochondrial protein synthesis. Antimicrob Agents Chemother 2005; 49:3896-902. [PMID: 16127068 PMCID: PMC1195406 DOI: 10.1128/aac.49.9.3896-3902.2005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The oxazolidinones are a relatively new structural class of antibacterial agents that act by inhibiting bacterial protein synthesis. The oxazolidinones inhibit mitochondrial protein synthesis, as shown by [35S]methionine incorporation into intact rat heart mitochondria. Treatment of K562 human erythroleukemia cells with the oxazolidinone eperezolid resulted in a time- and concentration-dependent inhibition of cell proliferation. The cells remained viable, but an increase in doubling time was observed with eperezolid treatment. Inhibition was reversible, since washing and refeeding of cells in the absence of compound resulted in a resumption of growth. The growth-inhibitory effect of the oxazolidinones did not appear to be cell type specific, and inhibition of CHO and HEK cells also was demonstrated. Treatment of cells resulted in a decrease in mitochondrial cytochrome oxidase subunit I levels, consistent with an inhibition of mitochondrial protein synthesis. Eperezolid caused no growth inhibition of rho zero (rho0) cells, which contain no mitochondrial DNA; however, the growth of the parent 143B cells was inhibited. These results provide a direct demonstration that the inhibitory effect of eperezolid in mammalian cells is the result of mitochondrial protein synthesis inhibition.
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Affiliation(s)
- Eva E Nagiec
- Department of Antibacterial Pharmacology, Pfizer, Ann Arbor, MI 48105, USA
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91
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92
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Abstract
Ribosomal proteins hold a unique position in biology because their function is so closely tied to the large rRNAs of the ribosomes in all kingdoms of life. Following the determination of the complete crystal structures of both the large and small ribosomal subunits from bacteria, the functional role of the proteins has often been overlooked when focusing on rRNAs as the catalysts of translation. In this review we highlight some of the many known and important functions of ribosomal proteins, both during translation on the ribosome and in a wider context.
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Affiliation(s)
- Ditlev E Brodersen
- Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Denmark.
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93
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Abstract
The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.
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Affiliation(s)
- James M Ogle
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.
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94
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Abelian A, Walsh A, Lentzen G, Aboul-Ela F, Gait M. Targeting the A site RNA of the Escherichia coli ribosomal 30 S subunit by 2'-O-methyl oligoribonucleotides: a quantitative equilibrium dialysis binding assay and differential effects of aminoglycoside antibiotics. Biochem J 2005; 383:201-8. [PMID: 15294017 PMCID: PMC1134060 DOI: 10.1042/bj20040246] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The bacterial ribosome comprises 30 S and 50 S ribonucleoprotein subunits, contains a number of binding sites for known antibiotics and is an attractive target for selection of novel antibacterial agents. On the 30 S subunit, for example, the A site (aminoacyl site) close to the 3'-end of 16 S rRNA is highly important in the decoding process. Binding by some aminoglycoside antibiotics to the A site leads to erroneous protein synthesis and is lethal for bacteria. We targeted the A site on purified 30 S ribosomal subunits from Escherichia coli with a set of overlapping, complementary OMe (2'-O-methyl) 10-mer oligoribonucleotides. An equilibrium dialysis technique was applied to measure dissociation constants of these oligonucleotides. We show that there is a single high-affinity region, spanning from A1493 to C1510 (Kd, 29-130 nM), flanked by two lower-affinity regions, within a span from U1485 to G1516 (Kd, 310-4300 nM). Unexpectedly, addition of the aminoglycoside antibiotic paromomycin (but not hygromycin B) caused a dose-dependent increase of up to 7.5-fold in the binding of the highest affinity 10-mer 1493 to 30 S subunits. Oligonucleotides containing residues complementary to A1492 and/or A1493 showed particularly marked stimulation of binding by paromomycin. The results are consistent with high-resolution structures of antibiotic binding to the A site and with greater accessibility of residues of A1492 and A1493 upon paromomycin binding. 10-mer 1493 binding is thus a probe of the conformational switch to the 'closed' conformation triggered by paromomycin that is implicated in the discrimination by 30 S subunits of cognate from non-cognate tRNA and the translational misreading caused by paromomycin. Finally, we show that OMe oligonucleotides targeted to the A site are moderately good inhibitors of in vitro translation and that there is a limited correlation of inhibition activity with binding strength to the A site.
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Affiliation(s)
- Arthur Abelian
- *Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K
| | - Andrew P. Walsh
- *Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K
| | - Georg Lentzen
- †Vernalis, Granta Park, Abington, Cambridge CB1 6GB, U.K
| | | | - Michael J. Gait
- *Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K
- To whom correspondence should be addressed (email )
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95
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Steitz TA. On the structural basis of peptide-bond formation and antibiotic resistance from atomic structures of the large ribosomal subunit. FEBS Lett 2004; 579:955-8. [PMID: 15680981 DOI: 10.1016/j.febslet.2004.11.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 11/16/2004] [Accepted: 11/22/2004] [Indexed: 10/26/2022]
Abstract
The atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with substrates and antibiotics have provided insights into the way the 3000 nucleotide 23S rRNA folds into a compact, specific structure and interacts with 27 ribosomal proteins as well as the structural basis of the peptidyl transferase reaction and its inhibition by antibiotics. The structure shows that the ribosome is indeed a ribozyme.
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Affiliation(s)
- Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, and Howard Hughes Medical Institute, P.O. Box 208114, New Haven, CT 06520-8114, USA.
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96
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Abstract
It was first suggested that the ribosome is associated with protein synthesis in the 1950s. Initially, its components were revealed as surface-accessible proteins and as molecules of RNA apparently providing a scaffold for subunit shape. Attributing function to the proteins proved difficult, although bacterial protein L11 proved essential for binding one of the decoding protein release factors (RFs). With the discovery that RNA could be a catalyst, interest focussed on the rRNA that, in partnership with mRNA and tRNAs, could potentially mediate the chemical reaction underlying protein synthesis. rRNA interactions and conformational changes were invoked as key elements that facilitated function. The decoding RFs, which are proteins, are exceptions to this rule because they usurp a tRNA function in mediating stop signal recognition. Cryoelectron microscopy and associated image reconstruction technology have now given dramatic snapshots of almost every step of protein synthesis, and X-ray crystallography has revealed, at last, the subunits and monomeric ribosome in exquisite atomic detail.
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Affiliation(s)
- Warren P Tate
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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97
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Zhao Q, Ofverstedt LG, Skoglund U, Isaksson LA. Morphological variation of individual Escherichia coli 30S ribosomal subunits in vitro and in situ, as revealed by cryo-electron tomography. Exp Cell Res 2004; 297:495-507. [PMID: 15212951 DOI: 10.1016/j.yexcr.2004.03.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 03/18/2004] [Indexed: 11/23/2022]
Abstract
Cryo-electron tomography has been used to reconstruct the structures of individual ribosomal 30S subunits in Escherichia coli cells treated with rifampicin. Rifampicin inhibits transcription initiation, thus giving depletion of mRNA and accumulation of free 30S and 50S subunits in the cell. Here, we present the 3D morphologies of reconstructed individual 30S ribosomal subunits both in vitro and in situ from E. coli. The head, the platform, and the body of the structures show large conformational movements relative to each other. The particles were grouped into three conformational groups according to the ratio between width and height in the subunit solvent side view. Also, an S15 fusion protein derivative has been used as a physical reporter to localize S15 in the 30S subunit. The results demonstrate a considerable morphological heterogeneity and structural variability among 30S ribosomal subunits.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/ultrastructure
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/ultrastructure
- Genetic Variation
- Image Processing, Computer-Assisted
- Imaging, Three-Dimensional
- In Vitro Techniques
- Mutation
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/ultrastructure
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/ultrastructure
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/ultrastructure
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/ultrastructure
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/physiology
- Rifampin/pharmacology
- Tomography
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Affiliation(s)
- Qing Zhao
- Department of Microbiology, Stockholm University, S-106 91 Stockholm, Sweden
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98
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Abstract
The ribosome crystal structures published in the past two years have revolutionized our understanding of ribonucleoprotein structure, and more specifically, the structural basis of the peptide bonding forming activity of the ribosome. This review concentrates on the crystallographic developments that made it possible to solve these structures. It also discusses the information obtained from these structures about the three-dimensional architecture of the large ribosomal subunit, the mechanism by which it facilitates peptide bond formation, and the way antibiotics inhibit large subunit function. The work reviewed, taken as a whole, proves beyond doubt that the ribosome is an RNA enzyme, as had long been surmised on the basis of less conclusive evidence.
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Affiliation(s)
- Peter B Moore
- Departments of Molecular Biophysics and Biochemistry, Chemistry, Yale University, New Haven, Connecticut 06520, USA.
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99
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Abstract
Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."
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Affiliation(s)
- Li-June Ming
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, Tampa, Florida 33620-5250, USA.
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100
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Abstract
Recently, the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with substrates have been determined. These have provided exciting new insights into the principles of RNA structure, the mechanism of the peptidyl-transferase reaction and early events in the evolution of this RNA-protein complex assembly that is essential in all cells. The structures of the large subunit bound to a variety of antibiotics explain the effects of antibiotic resistance mutations and provide promise for the development of new antibiotics.
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Affiliation(s)
- Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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