101
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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102
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Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA. Ribosome•RelA structures reveal the mechanism of stringent response activation. eLife 2016; 5. [PMID: 27434674 PMCID: PMC4974054 DOI: 10.7554/elife.17029] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/18/2016] [Indexed: 12/18/2022] Open
Abstract
Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Eugene Bah
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Rohini Madireddy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ying Zhang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Axel F Brilot
- Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Nikolaus Grigorieff
- Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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103
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Shakiba B, Dayeri M, Mohammad-Rafiee F. Modeling of ribosome dynamics on a ds-mRNA under an external load. J Chem Phys 2016; 145:025101. [PMID: 27421425 DOI: 10.1063/1.4958321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.
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Affiliation(s)
- Bahareh Shakiba
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Maryam Dayeri
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Farshid Mohammad-Rafiee
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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104
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Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors. Proc Natl Acad Sci U S A 2016; 113:8188-93. [PMID: 27382179 DOI: 10.1073/pnas.1605127113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. The translation inhibitors negamycin and tetracycline interfere with tRNA binding to the aminoacyl-tRNA site on the small 30S ribosomal subunit. However, two negamycin resistance mutations display unexpected differential antibiotic susceptibility profiles. Mutant U1060A in 16S Escherichia coli rRNA is resistant to both antibiotics, whereas mutant U1052G is simultaneously resistant to negamycin and hypersusceptible to tetracycline. Using a combination of microbiological, biochemical, single-molecule fluorescence transfer experiments, and X-ray crystallography, we define the specific structural defects in the U1052G mutant 70S E. coli ribosome that explain its divergent negamycin and tetracycline susceptibility profiles. Unexpectedly, the U1052G mutant ribosome possesses a second tetracycline binding site that correlates with its hypersusceptibility. The creation of a previously unidentified antibiotic binding site raises the prospect of identifying similar phenomena in antibiotic-resistant pathogens in the future.
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105
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Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G. New Structural Insights into Translational Miscoding. Trends Biochem Sci 2016; 41:798-814. [PMID: 27372401 DOI: 10.1016/j.tibs.2016.06.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/23/2016] [Accepted: 06/02/2016] [Indexed: 01/16/2023]
Abstract
The fidelity of translation depends strongly on the selection of the correct aminoacyl-tRNA that is complementary to the mRNA codon present in the ribosomal decoding center. The ribosome occasionally makes mistakes by selecting the wrong substrate from the pool of aminoacyl-tRNAs. Here, we summarize recent structural advances that may help to clarify the origin of missense errors that occur during decoding. These developments suggest that discrimination between tRNAs is based primarily on steric complementarity and shape acceptance rather than on the number of hydrogen bonds between the molding of the decoding center and the codon-anticodon duplex. They strengthen the hypothesis that spatial mimicry, due either to base tautomerism or ionization, drives infidelity in ribosomal translation.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS UPR9002/University of Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France.
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106
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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107
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Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. Proc Natl Acad Sci U S A 2016; 113:7527-32. [PMID: 27330110 DOI: 10.1073/pnas.1604790113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.
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108
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Savir Y, Tlusty T. Comment on "Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity". Phys Rev E 2016; 93:056401. [PMID: 27301009 DOI: 10.1103/physreve.93.056401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
We examined [Y. Savir and T. Tlusty, Cell 153, 471 (2013)10.1016/j.cell.2013.03.032] the decoding performance of tRNA by the ribosome. For this purpose, we specified the kinetics of tRNA decoding and the corresponding energy landscape, from which we calculated the steady-state decoding rate R_{C}. Following our work, Xie reexamined [P. Xie, Phys. Rev. E 92, 022716 (2015)10.1103/PhysRevE.92.022716] the energy landscape of tRNA decoding. His analysis relies on an alternative expression for R_{C}, while claiming that the expression we use is missing some terms. In this Comment we rederive in detail our expression for the steady-state decoding rate R_{C}, show they hold, explain why the alternative expression for R_{C} is inaccurate, and discuss the underlying intuition.
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Affiliation(s)
- Yonatan Savir
- Department of Physiology, Biophysics and Systems Biology, Faculty of Medicine, Technion, Haifa, 31096, Israel
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Research, UNIST, Ulsan, Korea; Department of Physics, Ulsan National Institute for Science and Technology, Ulsan, Korea; Simons Center for Systems Biology, Institute for Advanced Study, Einstein Drive, Princeton NJ 08540, USA; and Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540, USA
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109
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Chellat MF, Raguž L, Riedl R. Targeting Antibiotic Resistance. Angew Chem Int Ed Engl 2016; 55:6600-26. [PMID: 27000559 PMCID: PMC5071768 DOI: 10.1002/anie.201506818] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/10/2015] [Indexed: 12/11/2022]
Abstract
Finding strategies against the development of antibiotic resistance is a major global challenge for the life sciences community and for public health. The past decades have seen a dramatic worldwide increase in human-pathogenic bacteria that are resistant to one or multiple antibiotics. More and more infections caused by resistant microorganisms fail to respond to conventional treatment, and in some cases, even last-resort antibiotics have lost their power. In addition, industry pipelines for the development of novel antibiotics have run dry over the past decades. A recent world health day by the World Health Organization titled "Combat drug resistance: no action today means no cure tomorrow" triggered an increase in research activity, and several promising strategies have been developed to restore treatment options against infections by resistant bacterial pathogens.
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Affiliation(s)
- Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Luka Raguž
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.
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110
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Noel JK, Chahine J, Leite VBP, Whitford PC. Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophys J 2016; 107:2881-2890. [PMID: 25517153 DOI: 10.1016/j.bpj.2014.10.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/25/2014] [Accepted: 10/16/2014] [Indexed: 11/26/2022] Open
Abstract
To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-transfer RNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. Although a commonly used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome.
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Affiliation(s)
- Jeffrey K Noel
- Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Jorge Chahine
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
| | - Vitor B P Leite
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
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111
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Frank J. Whither Ribosome Structure and Dynamics Research? (A Perspective). J Mol Biol 2016; 428:3565-9. [PMID: 27178840 DOI: 10.1016/j.jmb.2016.04.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 04/29/2016] [Indexed: 12/24/2022]
Abstract
As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we have gained through recent advances in cryo-EM. It is pointed out that single-molecule FRET and cryo-EM form natural complements in the characterization of ribosome dynamics and transitions among equilibrating states of in vitro translational systems.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Columbia University, 116th and Broadway, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, 650 W. 168th Street, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
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112
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Tinoco I, Kim HK, Yan S. Frameshifting dynamics. Biopolymers 2016; 99:1147-66. [PMID: 23722586 DOI: 10.1002/bip.22293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 01/26/2023]
Abstract
Translation of messenger RNA by a ribosome occurs three nucleotides at a time from start signal to stop. However, a frameshift means that some nucleotides are read twice or some are skipped, and the following sequence of amino acids is completely different from the sequence in the original frame. In some messenger RNAs, including viral RNAs, frameshifting is programmed with RNA signals to produce specific ratios of proteins vital to the replication of the organism. The mechanisms that cause frameshifting have been studied for many years, but there are no definitive conclusions. We review ribosome structure and dynamics in relation to frameshifting dynamics provided by classical ensemble studies, and by new single-molecule methods using optical tweezers and FRET.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460
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113
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Juette MF, Terry DS, Wasserman MR, Altman RB, Zhou Z, Zhao H, Blanchard SC. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale. Nat Methods 2016; 13:341-4. [PMID: 26878382 PMCID: PMC4814340 DOI: 10.1038/nmeth.3769] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/17/2015] [Indexed: 02/07/2023]
Abstract
Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis.
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Affiliation(s)
- Manuel F. Juette
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Daniel S. Terry
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Michael R. Wasserman
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Roger B. Altman
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Hong Zhao
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
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114
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Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Cell 2016; 163:1267-1280. [PMID: 26590426 DOI: 10.1016/j.cell.2015.10.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/07/2015] [Accepted: 10/21/2015] [Indexed: 01/13/2023]
Abstract
Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements.
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115
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Affiliation(s)
- Mathieu F. Chellat
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Luka Raguž
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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116
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Tolla DA, Kiley PJ, Lomnitz JG, Savageau MA. Design principles of a conditional futile cycle exploited for regulation. MOLECULAR BIOSYSTEMS 2016; 11:1841-9. [PMID: 25851148 DOI: 10.1039/c5mb00055f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we characterize the design principles of futile cycling in providing rapid adaptation by regulatory proteins that act as environmental sensors. In contrast to the energetically wasteful futile cycles that are avoided in metabolic pathways, here we describe a conditional futile cycle exploited for a regulatory benefit. The FNR (fumarate and nitrate reduction) cycle in Escherichia coli operates under two regimes - a strictly futile cycle in the presence of O2 and as a pathway under anoxic conditions. The computational results presented here use FNR as a model system and provide evidence that cycling of this transcription factor and its labile sensory cofactor between active and inactive states affords rapid signaling and adaptation. We modify a previously developed mechanistic model to examine a family of FNR models each with different cycling speeds but mathematically constrained to be otherwise equivalent, and we identify a trade-off between energy expenditure and response time that can be tuned by evolution to optimize cycling rate of the FNR system for a particular ecological context. Simulations mimicking experiments with proposed double mutant strains offer suggestions for experimentally testing our predictions and identifying potential fitness effects. Our approach provides a computational framework for analyzing other conditional futile cycles, which when placed in their larger biological context may be found to confer advantages to the organism.
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Affiliation(s)
- Dean A Tolla
- Biomedical Engineering Department, University of California, One Shields Ave, Davis, CA 95616, USA
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117
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Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD. N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat Struct Mol Biol 2016; 23:110-5. [PMID: 26751643 PMCID: PMC4826618 DOI: 10.1038/nsmb.3148] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022]
Abstract
N(6)-methylation of adenosine (forming m(6)A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)A in mRNA decoding. Although m(6)A base-pairs with uridine during decoding, as shown by X-ray crystallographic analyses of Thermus thermophilus ribosomal complexes, our measurements in an Escherichia coli translation system revealed that m(6)A modification of mRNA acts as a barrier to tRNA accommodation and translation elongation. The interaction between an m(6)A-modified codon and cognate tRNA echoes the interaction between a near-cognate codon and tRNA, because delay in tRNA accommodation depends on the position and context of m(6)A within codons and on the accuracy level of translation. Overall, our results demonstrate that chemical modification of mRNA can change translational dynamics.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Ka-Weng Ieong
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Hasan Demirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jin Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Alexey Petrov
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.,Program in Biophysics, Stanford University, Stanford, California, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Dan Dominissini
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Gideon Rechavi
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Israel &Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
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118
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Zheng Q, Jockusch S, Rodríguez-Calero GG, Zhou Z, Zhao H, Altman RB, Abruña HD, Blanchard SC. Intra-molecular triplet energy transfer is a general approach to improve organic fluorophore photostability. Photochem Photobiol Sci 2015; 15:196-203. [PMID: 26700693 DOI: 10.1039/c5pp00400d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability.
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Affiliation(s)
- Qinsi Zheng
- Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, New York, NY, USA
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119
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Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun 2015; 6:10209. [PMID: 26681117 PMCID: PMC4703863 DOI: 10.1038/ncomms10209] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/13/2015] [Indexed: 12/20/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer. Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.
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Affiliation(s)
- Gayan Senavirathne
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Kathy R Chaurasiya
- Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Center for Applied Mathematical Science, University of Southern California, Los Angeles, California 90089, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA.,Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
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120
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Zimmermann MT, Jia K, Jernigan RL. Ribosome Mechanics Informs about Mechanism. J Mol Biol 2015; 428:802-810. [PMID: 26687034 DOI: 10.1016/j.jmb.2015.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/27/2022]
Abstract
The essential aspects of the ribosome's mechanism can be extracted from coarse-grained simulations, including the ratchet motion, the movement together of critical bases at the decoding center, and movements of the peptide tunnel lining that assist in the expulsion of the synthesized peptide. Because of its large size, coarse graining helps to simplify and to aid in the understanding of its mechanism. Results presented here utilize coarse-grained elastic network modeling to extract the dynamics, and both RNAs and proteins are coarse grained. We review our previous results, showing the well-known ratchet motions and the motions in the peptide tunnel and in the mRNA tunnel. The motions of the lining of the peptide tunnel appear to assist in the expulsion of the growing peptide chain, and clamps at the ends of the mRNA tunnel with three proteins ensure that the mRNA is held tightly during decoding and essential for the helicase activity at the entrance. The entry clamp may also assist in base recognition to ensure proper selection of the incoming tRNA. The overall precision of the ribosome machine-like motions is remarkable.
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Affiliation(s)
| | - Kejue Jia
- Jernigan Laboratory, Iowa State University, Ames, IA 50011, USA.
| | - Robert L Jernigan
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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121
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Liu J, Hanne J, Britton BM, Shoffner M, Albers AE, Bennett J, Zatezalo R, Barfield R, Rabuka D, Lee JB, Fishel R. An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore. Sci Rep 2015; 5:16883. [PMID: 26582263 PMCID: PMC4652282 DOI: 10.1038/srep16883] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/07/2015] [Indexed: 11/09/2022] Open
Abstract
Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.
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Affiliation(s)
- Jiaquan Liu
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Jeungphill Hanne
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Brooke M Britton
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Matthew Shoffner
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | - Jared Bennett
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Rachel Zatezalo
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | | | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210.,Physics Department, The Ohio State University, Columbus, OH 43210
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122
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Probing the Translation Dynamics of Ribosomes Using Zero-Mode Waveguides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 139:1-43. [PMID: 26970189 DOI: 10.1016/bs.pmbts.2015.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In order to coordinate the complex biochemical and structural feat of converting triple-nucleotide codons into their corresponding amino acids, the ribosome must physically manipulate numerous macromolecules including the mRNA, tRNAs, and numerous translation factors. The ribosome choreographs binding, dissociation, physical movements, and structural rearrangements so that they synergistically harness the energy from biochemical processes, including numerous GTP hydrolysis steps and peptide bond formation. Due to the dynamic and complex nature of translation, the large cast of ligands involved, and the large number of possible configurations, tracking the global time evolution or dynamics of the ribosome complex in translation has proven to be challenging for bulk methods. Conventional single-molecule fluorescence experiments on the other hand require low concentrations of fluorescent ligands to reduce background noise. The significantly reduced bimolecular association rates under those conditions limit the number of steps that can be observed within the time window available to a fluorophore. The advent of zero-mode waveguide (ZMW) technology has allowed the study of translation at near-physiological concentrations of labeled ligands, moving single-molecule fluorescence microscopy beyond focused model systems into studying the global dynamics of translation in realistic setups. This chapter reviews the recent works using the ZMW technology to dissect the mechanism of translation initiation and elongation in prokaryotes, including complex processes such as translational stalling and frameshifting. Given the success of the technology, similarly complex biological processes could be studied in near-physiological conditions with the controllability of conventional in vitro experiments.
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123
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Reilly DT, Kim SH, Katzenellenbogen JA, Schroeder CM. Fluorescent Nanoconjugate Derivatives with Enhanced Photostability for Single Molecule Imaging. Anal Chem 2015; 87:11048-57. [DOI: 10.1021/acs.analchem.5b03059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Daniel T. Reilly
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sung Hoon Kim
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John A. Katzenellenbogen
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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124
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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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125
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Xie P. Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022716. [PMID: 26382441 DOI: 10.1103/physreve.92.022716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Indexed: 06/05/2023]
Abstract
The performance of ribosome translation can be characterized by two factors, the translation rate and fidelity. Here, we provide analytical studies of the effect of the near-cognate tRNAs on the two factors. It is shown that the increase of the concentration of the near-cognate tRNAs relative to that of the cognate tRNA has negative effects on the ribosome translation by reducing both the translation rate and the translation fidelity. The effect of the near-cognate ternary complexes on the translation rate results mainly from the initial selection phase, whereas the proofreading phase has a minor effect. By contrast, the effect of the near-cognate ternary complexes on the fidelity results almost equally from the two phases. By using two successive phases, the initial selection and the proofreading, the ribosome can achieve higher translation fidelity than the product of the fidelity when only the initial selection is included and when only the proofreading is included, especially at the large ratio of the concentration of the near-cognate tRNAs compared to that of the cognate tRNA. Moreover, we study the changes of the free energy landscape in the tRNA decoding step. It is found that the rate constants of the tRNA decoding step measured experimentally give the minimum energy changes for the ribosomal complex to attain the optimal performance with both the highest decoding rate and fidelity and/or with the maximum value of the decoding fitness function. This suggests that the ribosome has evolved to utilize the minimum free energy changes gained from the conformational changes of the ribosome, EF-Tu, and tRNA to achieve the optimal performance in the tRNA decoding.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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126
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Structural insights into the translational infidelity mechanism. Nat Commun 2015; 6:7251. [PMID: 26037619 PMCID: PMC4468848 DOI: 10.1038/ncomms8251] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022] Open
Abstract
The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-binding site. These structures show that in the codon-anticodon duplex, a G·U mismatch adopts the Watson-Crick geometry, indicating a shift in the tautomeric equilibrium or ionization of the nucleobase. Additional structures with mismatches in the 70S decoding centre show that the binding of any tRNA induces identical rearrangements in the centre, which favours either isosteric or close to the Watson-Crick geometry codon-anticodon pairs. Overall, the results suggest that a mismatch escapes discrimination by preserving the shape of a Watson-Crick pair and indicate that geometric selection via tautomerism or ionization dominates the translational infidelity mechanism.
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127
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Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA, Blanchard SC, Steitz TA, Wilson DN. Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A. Mol Cell 2015; 58:832-44. [PMID: 26028538 DOI: 10.1016/j.molcel.2015.04.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/23/2015] [Accepted: 04/07/2015] [Indexed: 01/12/2023]
Abstract
The increase in multi-drug-resistant bacteria is limiting the effectiveness of currently approved antibiotics, leading to a renewed interest in antibiotics with distinct chemical scaffolds. We have solved the structures of the Thermus thermophilus 70S ribosome with A-, P-, and E-site tRNAs bound and in complex with either the aminocyclitol-containing antibiotic hygromycin A (HygA) or the nucleoside antibiotic A201A. Both antibiotics bind at the peptidyl transferase center and sterically occlude the CCA-end of the A-tRNA from entering the A site of the peptidyl transferase center. Single-molecule Förster resonance energy transfer (smFRET) experiments reveal that HygA and A201A specifically interfere with full accommodation of the A-tRNA, leading to the presence of tRNA accommodation intermediates and thereby inhibiting peptide bond formation. Thus, our results provide not only insight into the mechanism of action of HygA and A201A, but also into the fundamental process of tRNA accommodation during protein synthesis.
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Affiliation(s)
- Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Agata L Starosta
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Manuel F Juette
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Wanli Lu
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
| | - Benjamin J Burnett
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - George Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
| | - Kevin A Reynolds
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, New York, NY 10065, USA.
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Daniel N Wilson
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.
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128
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Chen B, Kaledhonkar S, Sun M, Shen B, Lu Z, Barnard D, Lu TM, Gonzalez RL, Frank J. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. Structure 2015; 23:1097-105. [PMID: 26004440 DOI: 10.1016/j.str.2015.04.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 03/16/2015] [Accepted: 04/05/2015] [Indexed: 11/25/2022]
Abstract
Ribosomal subunit association is a key checkpoint in translation initiation but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding, and ribosome recycling, are amenable to study with this method.
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Affiliation(s)
- Bo Chen
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sandip Kaledhonkar
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Bingxin Shen
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Zonghuan Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - David Barnard
- Wadsworth Center, Albany, New York State Department of Health, Albany, NY 12201, USA
| | - Toh-Ming Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Joachim Frank
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.
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129
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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130
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Caban K, Gonzalez RL. The emerging role of rectified thermal fluctuations in initiator aa-tRNA- and start codon selection during translation initiation. Biochimie 2015; 114:30-8. [PMID: 25882682 DOI: 10.1016/j.biochi.2015.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
Abstract
Decades of genetic, biochemical, biophysical, and structural studies suggest that the conformational dynamics of the translation machinery (TM), of which the ribosome is the central component, play a fundamental role in the mechanism and regulation of translation. More recently, single-molecule fluorescence resonance energy transfer (smFRET) studies have provided a unique and powerful approach for directly monitoring the real-time dynamics of the TM. Indeed, smFRET studies of the elongation stage of translation have significantly enriched our understanding of the mechanisms through which stochastic, thermally driven conformational fluctuations of the TM are exploited to drive and regulate the individual steps of translation elongation [1]. Beyond translation elongation, smFRET studies of the conformational dynamics of the initiation stage of translation offer great potential for providing mechanistic information that has thus far remained difficult or impossible to obtain using traditional methods. This is particularly true of the mechanisms through which the accuracy of initiator tRNA- and start codon selection is established during translation initiation. Given that translation initiation is a major checkpoint for regulating the translation of mRNAs, obtaining such mechanistic information holds great promise for our understanding of the translational regulation of gene expression. Here, we provide an overview of the bacterial translation initiation pathway, summarize what is known regarding the biochemical functions of the IFs, and discuss various new and exciting mechanistic insights that have emerged from several recently published smFRET studies of the mechanisms that guide initiator tRNA- and start codon selection during translation initiation. These studies provide a springboard for future investigations of the conformational dynamics of the more complex eukaryotic translation initiation pathway and mechanistic studies of the role of translational regulation of gene expression in human health and disease.
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Affiliation(s)
- Kelvin Caban
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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131
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Abstract
Although the basic facts about the ribosome were already known 40 years ago, elucidating its atomic structure and molecular mechanisms required sheer persistence and the innovative use of new technology and methods. These advances have transformed our understanding of translation in the cell.
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Affiliation(s)
- V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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132
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High-resolution structure of the Escherichia coli ribosome. Nat Struct Mol Biol 2015; 22:336-41. [PMID: 25775265 PMCID: PMC4429131 DOI: 10.1038/nsmb.2994] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 02/19/2015] [Indexed: 01/21/2023]
Abstract
Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation remain poorly understood. Moreover, the function of modifications to ribosomal RNA and ribosomal proteins are unclear. Here we present the structure of the Escherichia coli 70S ribosome to 2.4 Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and suggest how solvation contributes to ribosome integrity and function. The structure also suggests how the conformation of ribosomal protein uS12 likely impacts its contribution to messenger RNA decoding. This structure helps to explain the phylogenetic conservation of key elements of the ribosome, including posttranscriptional and posttranslational modifications and should serve as a basis for future antibiotic development.
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133
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Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods Enzymol 2015; 558:539-570. [PMID: 26068753 PMCID: PMC4886477 DOI: 10.1016/bs.mie.2015.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Spliceosomes are multimegadalton RNA-protein complexes responsible for the faithful removal of noncoding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition, and versatile structural dynamics. Single-molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues toward studying the mechanisms of biomolecular machines isolated directly from complex biological specimens, such as cell extracts. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy in exemplary single-molecule pull-down FRET studies of the yeast spliceosome and discuss the broad application potential of this technique.
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Affiliation(s)
- Matthew L Kahlscheuer
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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134
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Abstract
Non-equilibrium processes are vital features of biological systems. Despite this universally accepted fact, gene regulation is typically formalized into models that assume thermodynamic equilibrium. As experimental evidence expands the repertoire of non-equilibrium genome regulatory mechanisms, theoreticians are challenged to devise general approaches to accommodate and suggest functions for non-equilibrium processes. Ahsendorf et al. provide one such framework, which is discussed in the context of the growing complexity of eukaryotic gene regulation.
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135
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Wang J, Caban K, Gonzalez RL. Ribosomal initiation complex-driven changes in the stability and dynamics of initiation factor 2 regulate the fidelity of translation initiation. J Mol Biol 2015; 427:1819-34. [PMID: 25596426 DOI: 10.1016/j.jmb.2014.12.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/12/2014] [Accepted: 12/29/2014] [Indexed: 12/23/2022]
Abstract
Joining of the large, 50S, ribosomal subunit to the small, 30S, ribosomal subunit initiation complex (IC) during bacterial translation initiation is catalyzed by the initiation factor (IF) IF2. Because the rate of subunit joining is coupled to the IF, transfer RNA (tRNA), and mRNA codon compositions of the 30S IC, the subunit joining reaction functions as a kinetic checkpoint that regulates the fidelity of translation initiation. Recent structural studies suggest that the conformational dynamics of the IF2·tRNA sub-complex forming on the intersubunit surface of the 30S IC may play a significant role in the mechanisms that couple the rate of subunit joining to the IF, tRNA, and codon compositions of the 30S IC. To test this hypothesis, we have developed a single-molecule fluorescence resonance energy transfer signal between IF2 and tRNA that has enabled us to monitor the conformational dynamics of the IF2·tRNA sub-complex across a series of 30S ICs. Our results demonstrate that 30S ICs undergoing rapid subunit joining display a high affinity for IF2 and an IF2·tRNA sub-complex that primarily samples a single conformation. In contrast, 30S ICs that undergo slower subunit joining exhibit a decreased affinity for IF2 and/or a change in the conformational dynamics of the IF2·tRNA sub-complex. These results strongly suggest that 30S IC-driven changes in the stability of IF2 and the conformational dynamics of the IF2·tRNA sub-complex regulate the efficiency and fidelity of subunit joining during translation initiation.
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Affiliation(s)
- Jiangning Wang
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA
| | - Kelvin Caban
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA.
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136
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Nguyen F, Starosta AL, Arenz S, Sohmen D, Dönhöfer A, Wilson DN. Tetracycline antibiotics and resistance mechanisms. Biol Chem 2014; 395:559-75. [PMID: 24497223 DOI: 10.1515/hsz-2013-0292] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/30/2014] [Indexed: 11/15/2022]
Abstract
The ribosome and protein synthesis are major targets within the cell for inhibition by antibiotics, such as the tetracyclines. The tetracycline family of antibiotics represent a large and diverse group of compounds, ranging from the naturally produced chlortetracycline, introduced into medical usage in the 1940s, to second and third generation semi-synthetic derivatives of tetracycline, such as doxycycline, minocycline and more recently the glycylcycline tigecycline. Here we describe the mode of interaction of tetracyclines with the ribosome and mechanism of action of this class of antibiotics to inhibit translation. Additionally, we provide an overview of the diverse mechanisms by which bacteria obtain resistance to tetracyclines, ranging from efflux, drug modification, target mutation and the employment of specialized ribosome protection proteins.
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137
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van de Meent JW, Bronson JE, Wiggins CH, Gonzalez RL. Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments. Biophys J 2014; 106:1327-37. [PMID: 24655508 DOI: 10.1016/j.bpj.2013.12.055] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 12/12/2013] [Accepted: 12/31/2013] [Indexed: 10/25/2022] Open
Abstract
Many single-molecule experiments aim to characterize biomolecular processes in terms of kinetic models that specify the rates of transition between conformational states of the biomolecule. Estimation of these rates often requires analysis of a population of molecules, in which the conformational trajectory of each molecule is represented by a noisy, time-dependent signal trajectory. Although hidden Markov models (HMMs) may be used to infer the conformational trajectories of individual molecules, estimating a consensus kinetic model from the population of inferred conformational trajectories remains a statistically difficult task, as inferred parameters vary widely within a population. Here, we demonstrate how a recently developed empirical Bayesian method for HMMs can be extended to enable a more automated and statistically principled approach to two widely occurring tasks in the analysis of single-molecule fluorescence resonance energy transfer (smFRET) experiments: 1), the characterization of changes in rates across a series of experiments performed under variable conditions; and 2), the detection of degenerate states that exhibit the same FRET efficiency but differ in their rates of transition. We apply this newly developed methodology to two studies of the bacterial ribosome, each exemplary of one of these two analysis tasks. We conclude with a discussion of model-selection techniques for determination of the appropriate number of conformational states. The code used to perform this analysis and a basic graphical user interface front end are available as open source software.
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Affiliation(s)
| | | | - Chris H Wiggins
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York.
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138
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Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. Proc Natl Acad Sci U S A 2014; 111:16274-9. [PMID: 25368144 DOI: 10.1073/pnas.1414401111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 Å resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.
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139
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MacDougall DD, Gonzalez RL. Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. J Mol Biol 2014; 427:1801-18. [PMID: 25308340 DOI: 10.1016/j.jmb.2014.09.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 11/30/2022]
Abstract
Ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (IFs) regulate association of the 30S initiation complex (IC) with the 50S subunit to control formation of a 70S IC that can enter into the elongation stage of protein synthesis. The GTP-bound form of IF2 accelerates subunit joining, whereas IF3 antagonizes subunit joining and plays a prominent role in maintaining translation initiation fidelity. The molecular mechanisms through which IF2 and IF3 collaborate to regulate the efficiency of 70S IC formation, including how they affect the dynamics of subunit joining, remain poorly defined. Here, we use single-molecule fluorescence resonance energy transfer to monitor the interactions between IF2 and the GTPase-associated center (GAC) of the 50S subunit during real-time subunit joining reactions in the absence and presence of IF3. In the presence of IF3, IF2-mediated subunit joining becomes reversible, and subunit joining events cluster into two distinct classes corresponding to formation of shorter- and longer-lifetime 70S ICs. Inclusion of IF3 within the 30S IC was also found to alter the conformation of IF2 relative to the GAC, suggesting that IF3's regulatory effects may stem in part from allosteric modulation of IF2-GAC interactions. The results are consistent with a model in which IF3 can exert control over the efficiency of subunit joining by modulating the conformation of the 30S IC, which in turn influences the formation of stabilizing intersubunit contacts and thus the reaction's degree of reversibility.
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Affiliation(s)
- Daniel D MacDougall
- Columbia University Department of Chemistry, 3000 Broadway, New York, NY 10027, USA
| | - Ruben L Gonzalez
- Columbia University Department of Chemistry, 3000 Broadway, New York, NY 10027, USA.
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140
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Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA. Mol Cell 2014; 56:541-50. [PMID: 25306922 DOI: 10.1016/j.molcel.2014.09.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/18/2014] [Accepted: 09/18/2014] [Indexed: 11/23/2022]
Abstract
Negamycin (NEG) is a ribosome-targeting antibiotic that exhibits clinically promising activity. Its binding site and mode of action have remained unknown. We solved the structure of the Thermus thermophilus ribosome bound to mRNA and three tRNAs, in complex with NEG. The drug binds to both small and large ribosomal subunits at nine independent sites. Resistance mutations in the 16S rRNA unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit as the primary site of antibiotic action in the bacterial and, possibly, eukaryotic ribosome. At this site, NEG contacts 16S rRNA as well as the anticodon loop of the A-site tRNA. Although the NEG site of action overlaps with that of tetracycline (TET), the two antibiotics exhibit different activities: while TET sterically hinders binding of aminoacyl-tRNA to the ribosome, NEG stabilizes its binding, thereby inhibiting translocation and stimulating miscoding.
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141
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Kinz-Thompson CD, Gonzalez RL. smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding. FEBS Lett 2014; 588:3526-38. [PMID: 25066296 PMCID: PMC4779314 DOI: 10.1016/j.febslet.2014.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
Abstract
The selectivity with which a biomolecule can bind its cognate ligand when confronted by the vast array of structurally similar, competing ligands that are present in the cell underlies the fidelity of some of the most fundamental processes in biology. Because they collectively comprise one of only a few methods that can sensitively detect the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding, single-molecule fluorescence, and particularly single-molecule fluorescence resonance energy transfer (smFRET), approaches have revolutionized studies of ligand-binding reactions. Here, we describe a widely used smFRET strategy that enables investigations of a large variety of ligand-binding reactions, and discuss two such reactions, aminoacyl-tRNA selection during translation elongation and splice site selection during spliceosome assembly, that highlight both the successes and challenges of smFRET studies of ligand-binding reactions. We conclude by reviewing a number of emerging experimental and computational approaches that are expanding the capabilities of smFRET approaches for studies of ligand-binding reactions and that promise to reveal the mechanisms that control the selectivity of ligand binding with unprecedented resolution.
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Affiliation(s)
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, United States.
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142
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Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U. Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS J 2014; 281:3701-18. [PMID: 24966114 DOI: 10.1111/febs.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/10/2014] [Accepted: 06/23/2014] [Indexed: 01/26/2023]
Abstract
Genes that are laterally acquired by a new host species often contain codons that are non-optimal to the tRNA repertoire of the new host, which may lead to insufficient translational levels. Inefficient translation can be overcome by different mechanisms, such as incremental amelioration of the coding sequence, compensatory mutations in the regulatory sequences leading to increased transcription or increase in gene copy number. However, there is also a possibility that ribosomal mutations can improve the expression of such genes. To test this hypothesis, we examined the effects of point mutations in the endogenous ribosomal proteins S12 and S5 in Escherichia coli, which are known to be involved in the decoding of the mRNA, on the efficiency of translation of exogenous genes that use non-optimal codons, in vivo. We show that an S12 mutant in E. coli is able to express exogenous genes, with non-optimal codons, to higher levels than the wild-type, and explore the mechanisms underlying this phenomenon in this mutant. Our results suggest that the transient emergence of mutants that allow efficient expression of exogenous genes with non-optimal codons could also increase the chances of fixation of laterally transferred genes.
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Affiliation(s)
- Gidi Pelchovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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143
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Noel JK, Whitford PC. How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function. Isr J Chem 2014. [DOI: 10.1002/ijch.201400018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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144
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Burnett BJ, Altman RB, Ferguson A, Wasserman MR, Zhou Z, Blanchard SC. Direct evidence of an elongation factor-Tu/Ts·GTP·Aminoacyl-tRNA quaternary complex. J Biol Chem 2014; 289:23917-27. [PMID: 24990941 DOI: 10.1074/jbc.m114.583385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During protein synthesis, elongation factor-Tu (EF-Tu) bound to GTP chaperones the entry of aminoacyl-tRNA (aa-tRNA) into actively translating ribosomes. In so doing, EF-Tu increases the rate and fidelity of the translation mechanism. Recent evidence suggests that EF-Ts, the guanosine nucleotide exchange factor for EF-Tu, directly accelerates both the formation and dissociation of the EF-Tu-GTP-Phe-tRNA(Phe) ternary complex (Burnett, B. J., Altman, R. B., Ferrao, R., Alejo, J. L., Kaur, N., Kanji, J., and Blanchard, S. C. (2013) J. Biol. Chem. 288, 13917-13928). A central feature of this model is the existence of a quaternary complex of EF-Tu/Ts·GTP·aa-tRNA(aa). Here, through comparative investigations of phenylalanyl, methionyl, and arginyl ternary complexes, and the development of a strategy to monitor their formation and decay using fluorescence resonance energy transfer, we reveal the generality of this newly described EF-Ts function and the first direct evidence of the transient quaternary complex species. These findings suggest that EF-Ts may regulate ternary complex abundance in the cell through mechanisms that are distinct from its guanosine nucleotide exchange factor functions.
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Affiliation(s)
| | | | - Angelica Ferguson
- Tri-Institutional Program in Chemical Biology, Weill Cornell Medical College, New York, New York 10065
| | | | - Zhou Zhou
- From the Department of Physiology and Biophysics and
| | - Scott C Blanchard
- From the Department of Physiology and Biophysics and Tri-Institutional Program in Chemical Biology, Weill Cornell Medical College, New York, New York 10065
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145
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Tan LH, Xing H, Lu Y. DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles. Acc Chem Res 2014; 47:1881-90. [PMID: 24871359 PMCID: PMC4066914 DOI: 10.1021/ar500081k] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Several properties of nanomaterials, such as
morphologies (e.g.,
shapes and surface structures) and distance dependent properties (e.g.,
plasmonic and quantum confinement effects), make nanomaterials uniquely
qualified as potential choices for future applications from catalysis
to biomedicine. To realize the full potential of these nanomaterials,
it is important to demonstrate fine control of the morphology of individual
nanoparticles, as well as precise spatial control of the position,
orientation, and distances between multiple nanoparticles. In addition,
dynamic control of nanomaterial assembly in response to multiple stimuli,
with minimal or no error, and the reversibility of the assemblies
are also required. In this Account, we summarize recent progress of
using DNA as a powerful programmable tool to realize the above goals.
First, inspired by the discovery of genetic codes in biology, we have
discovered DNA sequence combinations to control different morphologies
of nanoparticles during their growth process and have shown that these
effects are synergistic or competitive, depending on the sequence
combination. The DNA, which guides the growth of the nanomaterial,
is stable and retains its biorecognition ability. Second, by taking
advantage of different reactivities of phosphorothioate and phosphodiester
backbone, we have placed phosphorothioate at selective positions on
different DNA nanostructures including DNA tetrahedrons. Bifunctional
linkers have been used to conjugate phosphorothioate on one end and
bind nanoparticles or proteins on the other end. In doing so, precise
control of distances between two or more nanoparticles or proteins
with nanometer resolution can be achieved. Furthermore, by developing
facile methods to functionalize two hemispheres of Janus nanoparticles
with two different DNA sequences regioselectively, we have demonstrated
directional control of nanomaterial assembly, where DNA strands with
specific hybridization serve as orthogonal linkers. Third, by using
functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic
control of assemblies of gold nanoparticles, quantum dots, carbon
nanotubes, and iron oxide nanoparticles in response to one or more
stimuli cooperatively have been achieved, resulting in colorimetric,
fluorescent, electrochemical, and magnetic resonance signals for a
wide range of targets, such as metal ions, small molecules, proteins,
and intact cells. Fourth, by mimicking biology, we have employed DNAzymes
as proofreading units to remove errors in nanoparticle assembly and
further used DNAzyme cascade reactions to modify or repair DNA sequences
involved in the assembly. Finally, by taking advantage of different
affinities of biotin and desthiobiotin toward streptavidin, we have
demonstrated reversible assembly of proteins on DNA origami.
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Affiliation(s)
- Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Hang Xing
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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146
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Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Dynamic pathways of -1 translational frameshifting. Nature 2014; 512:328-32. [PMID: 24919156 PMCID: PMC4472451 DOI: 10.1038/nature13428] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/01/2014] [Indexed: 12/16/2022]
Abstract
Spontaneous changes in the reading frame of translation are rare (frequency of 10−3 – 10−4 per codon)1, but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide “slippery sequence” usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3′ end of the 16S ribosomal rRNA (internal Shine-Dalgarno (SD) sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (−1 frame) and continues by translating a new sequence of amino acids2,3. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here, we apply single-molecule fluorescence to track the compositional and conformational dynamics of the individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the −1 frame are characterized by a 10-fold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalyzed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNALys sampling and accommodation to the empty A site either lead to the slippage of the tRNAs into the −1 frame or maintain the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for −1 frameshifting, highlighting multiple kinetic branchpoints during elongation.
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Affiliation(s)
- Jin Chen
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Alexey Petrov
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Magnus Johansson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Albert Tsai
- 1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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147
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Zhang X, Walker RC, Phizicky EM, Mathews DH. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput 2014; 10:3473-3483. [PMID: 25136272 PMCID: PMC4132867 DOI: 10.1021/ct500107y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Indexed: 12/25/2022]
Abstract
![]()
Modified nucleotides are prevalent
in tRNA. Experimental studies
reveal that these covalent modifications play an important role in
tuning tRNA function. In this study, molecular dynamics (MD) simulations
were used to investigate how modifications alter tRNA dynamics. The
X-ray crystal structures of tRNA(Asp), tRNA(Phe), and tRNA(iMet),
both with and without modifications, were used as initial structures
for 333 ns explicit solvent MD simulations with AMBER. For each tRNA
molecule, three independent trajectory calculations were performed,
giving an aggregate of 6 μs of total MD across six molecules.
The global root-mean-square deviations (RMSD) of atomic positions
show that modifications only introduce significant rigidity to the
global structure of tRNA(Phe). Interestingly, RMSDs of the anticodon
stem-loop (ASL) suggest that modified tRNA has a more rigid structure
compared to the unmodified tRNA in this domain. The anticodon RMSDs
of the modified tRNAs, however, are higher than those of corresponding
unmodified tRNAs. These findings suggest that the rigidity of the
anticodon stem-loop is finely tuned by modifications, where rigidity
in the anticodon arm is essential for tRNA translocation in the ribosome,
and flexibility of the anticodon is important for codon recognition.
Sugar pucker and water residence time of pseudouridines in modified
tRNAs and corresponding uridines in unmodified tRNAs were assessed,
and the results reinforce that pseudouridine favors the 3′-endo
conformation and has a higher tendency to interact with water. Principal
component analysis (PCA) was used to examine correlated motions in
tRNA. Additionally, covariance overlaps of PCAs were compared for
trajectories of the same molecule and between trajectories of modified
and unmodified tRNAs. The comparison suggests that modifications alter
the correlated motions. For the anticodon bases, the extent of stacking
was compared between modified and unmodified molecules, and only unmodified
tRNA(Asp) has significantly higher percentage of stacking time. Overall,
the simulations reveal that the effect of covalent modification on
tRNA dynamics is not simple, with modifications increasing flexibility
in some regions of the structure and increasing rigidity in other
regions.
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Affiliation(s)
- Xiaoju Zhang
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego , La Jolla, California 92093, United States ; Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
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148
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Whitford PC, Sanbonmatsu KY. Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys 2014; 139:121919. [PMID: 24089731 DOI: 10.1063/1.4817212] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function. A large biomolecular complex for which atomic models are available is the ribosome. In the cell, the ribosome reads messenger RNA (mRNA) in order to synthesize proteins. During this essential process, the ribosome undergoes a wide range of conformational rearrangements. One of the most poorly understood transitions is translocation: the process by which transfer RNA (tRNA) molecules move between binding sites inside of the ribosome. The first step of translocation is the adoption of a "hybrid" configuration by the tRNAs, which is accompanied by large-scale rotations in the ribosomal subunits. To illuminate the relationship between these rearrangements, we apply MD simulations using a multi-basin structure-based (SMOG) model, together with targeted molecular dynamics protocols. From 120 simulated transitions, we demonstrate the viability of a particular route during P/E hybrid-state formation, where there is asynchronous movement along rotation and tRNA coordinates. These simulations not only suggest an ordering of events, but they highlight atomic interactions that may influence the kinetics of hybrid-state formation. From these simulations, we also identify steric features (H74 and surrounding residues) encountered during the hybrid transition, and observe that flexibility of the single-stranded 3'-CCA tail is essential for it to reach the endpoint. Together, these simulations provide a set of structural and energetic signatures that suggest strategies for modulating the physical-chemical properties of protein synthesis by the ribosome.
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Affiliation(s)
- Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
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149
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Shimizu Y. Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Front Microbiol 2014; 5:170. [PMID: 24782856 PMCID: PMC3989591 DOI: 10.3389/fmicb.2014.00170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/28/2014] [Indexed: 11/13/2022] Open
Abstract
During protein synthesis in cells, translating ribosomes may encounter abnormal situations that lead to retention of immature peptidyl-tRNA on the ribosome due to failure of suitable termination processes. Bacterial cells handle such situations by employing three systems that rescue the stalled translation machinery. The transfer messenger RNA/small protein B (tmRNA/SmpB) system, also called the trans-translation system, rescues stalled ribosomes by initiating template switching from the incomplete mRNA to the short open reading frame of tmRNA, leading to the production of a protein containing a C-terminal tag that renders it susceptible to proteolysis. The ArfA/RF2 and ArfB systems rescue stalled ribosomes directly by hydrolyzing the immature peptidyl-tRNA remaining on the ribosome. Here, the biochemical aspects of these systems, as clarified by recent studies, are reviewed.
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Affiliation(s)
- Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, Quantitative Biology Center - RIKEN Kobe, Hyogo, Japan
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150
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Satpati P, Sund J, Aqvist J. Structure-based energetics of mRNA decoding on the ribosome. Biochemistry 2014; 53:1714-22. [PMID: 24564511 DOI: 10.1021/bi5000355] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The origin of high fidelity in bacterial protein synthesis on the ribosome remains a fundamental unsolved problem despite available three-dimensional structures of different stages of the translation process. However, these structures open up the possibility of directly computing the energetics of tRNA selection that is required for an authentic understanding of fidelity in decoding. Here, we report extensive computer simulations that allow us to quantitatively calculate tRNA discrimination and uncover the energetics underlying accuracy in code translation. We show that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond formation. While the selection process is obviously controlled by kinetics, the underlying thermodynamics explains the origin of the high degree of accuracy. The existence of both low- and high-selectivity states provides an efficient mechanism for initial selection and proofreading that does not require codon-dependent long-range structural signaling within the ribosome. It is instead the distinctly unequal population of the high-selectivity states for cognate and noncognate substrates that is the key discriminatory factor. The simulations reveal the essential roles played both by the 30S subunit conformational switch and by the common tRNA modification at position 37 in amplifying the accuracy.
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Affiliation(s)
- Priyadarshi Satpati
- Department of Cell and Molecular Biology, Uppsala University , Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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