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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:866. [PMID: 37238735 PMCID: PMC10216711 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
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2
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Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Nat Commun 2021; 12:7166. [PMID: 34887415 PMCID: PMC8660796 DOI: 10.1038/s41467-021-27400-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection. Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.
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RNA Folding and Unfolding Under Force: Single-Molecule Experiments and Their Analysis. Methods Mol Biol 2020. [PMID: 32006309 DOI: 10.1007/978-1-0716-0278-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We have previously described (Geffroy et al. Methods Mol Biol 1665:25-40, 2018) how to unfold (or fold) a single RNA molecule under force using a dual-beam optical trap setup. In this chapter, we complementarily describe how to analyze the corresponding data and how to interpret it in terms of RNA three-dimensional structure. As with all single-molecule methods, single RNA molecule force data often exhibit several discrete states where state-to-state transitions are blurred in a noisy signal. In order to cope with this limitation, we have implemented a novel strategy to analyze the data, which uses a hidden Markov modeling procedure. A representative example of such an analysis is presented.
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Chiaruttini C, Guillier M. On the role of mRNA secondary structure in bacterial translation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1579. [PMID: 31760691 DOI: 10.1002/wrna.1579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/07/2022]
Abstract
Messenger RNA (mRNA) is no longer considered as a mere informational molecule whose sole function is to convey the genetic information specified by DNA to the ribosome. Beyond this primary function, mRNA also contains additional instructions that influence the way and the extent to which this message is translated by the ribosome into protein(s). Indeed, owing to its intrinsic propensity to quickly and dynamically fold and form higher order structures, mRNA exhibits a second layer of structural information specified by the sequence itself. Besides influencing transcription and mRNA stability, this additional information also affects translation, and more precisely the frequency of translation initiation, the choice of open reading frame by recoding, the elongation speed, and the folding of the nascent protein. Many studies in bacteria have shown that mRNA secondary structure participates to the rapid adaptation of these versatile organisms to changing environmental conditions by efficiently tuning translation in response to diverse signals, such as the presence of ligands, regulatory proteins, or small RNAs. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation.
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Geffroy L, Bizebard T, Aoyama R, Ueda T, Bockelmann U. Force measurements show that uL4 and uL24 mechanically stabilize a fragment of 23S rRNA essential for ribosome assembly. RNA (NEW YORK, N.Y.) 2019; 25:472-480. [PMID: 30705137 PMCID: PMC6426284 DOI: 10.1261/rna.067504.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
In vitro reconstitution studies have shown that ribosome assembly is highly cooperative and starts with the binding of a few ribosomal (r-) proteins to rRNA. It is unknown how these early binders act. Focusing on the initial stage of the assembly of the large subunit of the Escherichia coli ribosome, we prepared a 79-nucleotide-long region of 23S rRNA encompassing the binding sites of the early binders uL4 and uL24. Force signals were measured in a DNA/RNA dumbbell configuration with a double optical tweezers setup. The rRNA fragment was stretched until unfolded, in the absence or in the presence of the r-proteins (either uL4, uL24, or both). We show that the r-proteins uL4 and uL24 individually stabilize the rRNA fragment, both acting as molecular clamps. Interestingly, this mechanical stabilization is enhanced when both proteins are bound simultaneously. Independently, we observe a cooperative binding of uL4 and uL24 to the rRNA fragment. These two aspects of r-proteins binding both contribute to the efficient stabilization of the 3D structure of the rRNA fragment under investigation. We finally consider implications of our results for large ribosomal subunit assembly.
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MESH Headings
- Base Pairing
- Base Sequence
- Biomechanical Phenomena
- Cloning, Molecular
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Optical Tweezers
- Organelle Biogenesis
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
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Affiliation(s)
| | - Thierry Bizebard
- Expression Génétique Microbienne, UMR8261 CNRS/Université Paris 7, IBPC, 75005 Paris, France
| | - Ryo Aoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, Kashiwa, Chiba 277-8562, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, Kashiwa, Chiba 277-8562, Japan
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Geffroy L, Mangeol P, Bizebard T, Bockelmann U. RNA Unzipping and Force Measurements with a Dual Optical Trap. Methods Mol Biol 2018; 1665:25-41. [PMID: 28940062 DOI: 10.1007/978-1-4939-7271-5_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In order to mechanically unfold a single RNA molecule, an RNA/DNA hybrid construction is prepared which allows specific attachment to two micrometer-sized beads. A dual-beam optical trap thus holding the construct in solution captures the beads separately. Unfolding of a molecule is obtained by increasing the distance between the traps, one trap being slowly moved while the other is held fixed. Force is measured to sub-piconewton precision by back focal plane interferometry of the bead in the fixed trap. The experiment allows us to measure structure and base-sequence-dependent force signals. In this chapter, important technical aspects of this type of single-molecule force measurements are considered.
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Affiliation(s)
- Laurent Geffroy
- Nanobiophysics, ESPCI Paris, 10 rue Vauquelin, 75005, Paris, France
| | - Pierre Mangeol
- Nanobiophysics, ESPCI Paris, 10 rue Vauquelin, 75005, Paris, France
- UMR7288 CNRS/Université Aix-Marseille, Developmental Biology Institute of Marseille (IBDM), 13288, Marseille Cedex 09, France
| | - Thierry Bizebard
- Expression Génétique Microbienne, UMR8261 CNRS/Université Paris 7, IBPC, 13 rue Pierre-et-Marie-Curie, 75005, Paris, France
| | - Ulrich Bockelmann
- Nanobiophysics, ESPCI Paris, 10 rue Vauquelin, 75005, Paris, France.
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Stem-Loop Structures within mRNA Coding Sequences Activate Translation Initiation and Mediate Control by Small Regulatory RNAs. Mol Cell 2017; 68:158-170.e3. [DOI: 10.1016/j.molcel.2017.08.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/08/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022]
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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Bercy M, Bockelmann U. Hairpins under tension: RNA versus DNA. Nucleic Acids Res 2015; 43:9928-36. [PMID: 26323319 PMCID: PMC4787782 DOI: 10.1093/nar/gkv860] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/15/2015] [Indexed: 11/21/2022] Open
Abstract
We use optical tweezers to control the folding and unfolding of individual DNA and RNA hairpins by force. Four hairpin molecules are studied in comparison: two DNA and two RNA ones. We observe that the conformational dynamics is slower for the RNA hairpins than for their DNA counterparts. Our results indicate that structures made of RNA are dynamically more stable. This difference might contribute to the fact that DNA and RNA play fundamentally different biological roles in spite of chemical similarity.
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Affiliation(s)
- Mathilde Bercy
- Laboratoire de Nanobiophysique, ESPCI ParisTech, 10 rue Vauquelin, Paris 75005, France
| | - Ulrich Bockelmann
- Laboratoire de Nanobiophysique, ESPCI ParisTech, 10 rue Vauquelin, Paris 75005, France
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Lin S, Zhang J, Strano MS, Blankschtein D. Understanding selective molecular recognition in integrated carbon nanotube-polymer sensors by simulating physical analyte binding on carbon nanotube-polymer scaffolds. SOFT MATTER 2014; 10:5991-6004. [PMID: 24992310 DOI: 10.1039/c4sm00974f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Macromolecular scaffolds made of polymer-wrapped single-walled carbon nanotubes (SWCNTs) have been explored recently (Zhang et al., Nature Nanotechnology, 2013) as a new class of molecular-recognition motifs. However, selective analyte recognition is still challenging and lacks the underlying fundamental understanding needed for its practical implementation in biological sensors. In this report, we combine coarse-grained molecular dynamics (CGMD) simulations, physical adsorption/binding theories, and photoluminescence (PL) experiments to provide molecular insight into the selectivity of such sensors towards a large set of biologically important analytes. We find that the physical binding affinities of the analytes on a bare SWCNT partially correlate with their distribution coefficients in a bulk water/octanol system, suggesting that the analyte hydrophobicity plays a key role in determining the binding affinities of the analytes considered, along with the various specific interactions between the analytes and the polymer anchor groups. Two distinct categories of analytes are identified to demonstrate a complex picture for the correlation between optical sensor signals and the simulated binding affinities. Specifically, a good correlation was found between the sensor signals and the physical binding affinities of the three hormones (estradiol, melatonin, and thyroxine), the neurotransmitter (dopamine), and the vitamin (riboflavin) to the SWCNT-polymer scaffold. The four amino acids (aspartate, glycine, histidine, and tryptophan) and the two monosaccharides (fructose and glucose) considered were identified as blank analytes which are unable to induce sensor signals. The results indicate great success of our physical adsorption-based model in explaining the ranking in sensor selectivities. The combined framework presented here can be used to screen and select polymers that can potentially be used for creating synthetic molecular recognition motifs.
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Affiliation(s)
- Shangchao Lin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Stephenson W, Keller S, Santiago R, Albrecht JE, Asare-Okai PN, Tenenbaum SA, Zuker M, Li PTX. Combining temperature and force to study folding of an RNA hairpin. Phys Chem Chem Phys 2014; 16:906-17. [DOI: 10.1039/c3cp52042k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Marsà F, Farré A, Martín-Badosa E, Montes-Usategui M. Holographic optical tweezers combined with back-focal-plane displacement detection. OPTICS EXPRESS 2013; 21:30282-94. [PMID: 24514607 DOI: 10.1364/oe.21.030282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A major problem with holographic optical tweezers (HOTs) is their incompatibility with laser-based position detection methods, such as back-focal-plane interferometry (BFPI). The alternatives generally used with HOTs, like high-speed video tracking, do not offer the same spatial and temporal bandwidths. This has limited the use of this technique in precise quantitative experiments. In this paper, we present an optical trap design that combines digital holography and back-focal-plane displacement detection. We show that, with a particularly simple setup, it is possible to generate a set of multiple holographic traps and an additional static non-holographic trap with orthogonal polarizations and that they can be, therefore, easily separated for measuring positions and forces with the high positional and temporal resolutions of laser-based detection. We prove that measurements from both polarizations contain less than 1% crosstalk and that traps in our setup are harmonic within the typical range. We further tested the instrument in a DNA stretching experiment and we discuss an interesting property of this configuration: the small drift of the differential signal between traps.
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13
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Li PTX. Analysis of diffuse K+ and Mg2+ ion binding to a two-base-pair kissing complex by single-molecule mechanical unfolding. Biochemistry 2013; 52:4991-5001. [PMID: 23842027 DOI: 10.1021/bi400646x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The folding and stability of RNA tertiary interactions depend critically on cationic conditions. It is usually difficult, however, to isolate such effects on tertiary interactions from those on the entire RNA. By manipulating conformations of single RNA molecules using optical tweezers, we distinguished individual steps of breaking and forming of a two-base-pair kissing interaction from those of secondary folding. The binding of metal ions to the small tertiary structure appeared to be saturable with an apparent Kd of 160 mM for K(+) and 1.5 mM for Mg(2+). The kissing formation was estimated to be associated with binding of ~2-3 diffuse K(+) or Mg(2+) ions. At their saturated binding, Mg(2+) provided ~3 kcal/mol more stabilizing energy to the structure than K(+). Furthermore, the cations change the unkissing forces significantly more than the kissing ones. For example, the presence of Mg(2+) ions increased the average unkissing force from 21 pN to 44 pN, surprisingly high for breaking merely two base pairs; in contrast, the mean kissing force was changed by only 4.5 pN. Interestingly, the differential salt effects on the transition forces were not caused by different changes in the height of the kinetic barriers but were instead attributed to how different molecular structures respond to the applied force. Our results showed the importance of diffuse cation binding to the stability of tertiary interaction and demonstrated the utility of mechanical unfolding in studying tertiary interactions.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences and The RNA Institute, University at Albany, SUNY , Albany, New York 12222, United States
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Revealing -1 programmed ribosomal frameshifting mechanisms by single-molecule techniques and computational methods. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012; 2012:569870. [PMID: 22545064 PMCID: PMC3321566 DOI: 10.1155/2012/569870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/16/2012] [Indexed: 01/17/2023]
Abstract
Programmed ribosomal frameshifting (PRF) serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.
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Yoshizawa S. Micro and nanotechnological tools for study of RNA. Biochimie 2012; 94:1588-94. [PMID: 22484393 DOI: 10.1016/j.biochi.2012.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 03/22/2012] [Indexed: 11/16/2022]
Abstract
Micro and nanotechnologies have originally contributed to engineering, especially in electronics. These technologies enable fabrication and assembly of materials at micrometer and nanometer scales and the manipulation of nano-objects. The power of these technologies has now been exploited in analyzes of biologically relevant molecules. In this review, the use of micro and nanotechnological tools in RNA research is described.
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Affiliation(s)
- Satoko Yoshizawa
- Centre de Génétique Moléculaire UPR 3404, CNRS, Université Paris-Sud, FRC3115 1 Ave de la Terrasse, 91190 Gif-sur-Yvette, France.
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