1
|
Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
2
|
Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
| |
Collapse
|
3
|
Jansson LI, Stone MD. Single-Molecule Analysis of Reverse Transcriptase Enzymes. Cold Spring Harb Perspect Biol 2019; 11:11/9/a032458. [PMID: 31481455 DOI: 10.1101/cshperspect.a032458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The original discovery of enzymes that synthesize DNA using an RNA template appeared to contradict the central dogma of biology, in which information is transferred, in a unidirectional way, from DNA genes into RNA molecules. The paradigm-shifting discovery of RNA-dependent DNA polymerases, also called reverse transcriptases (RTs), reshaped existing views for how cells function; however, the scope of the impact RTs impose on biology had yet to be realized. In the decades of research since the early 1970s, the biomedical and biotechnological significance of retroviral RTs, as well as the evolutionarily related telomerase enzyme, has become exceedingly clear. One common theme that has emerged in the course of RT-related research is the central role of nucleic acid binding and dynamics during enzyme function. However, directly interrogating these dynamic properties is challenging because of the stochastic properties of biological macromolecules. In this review, we describe how the development of single-molecule biophysical techniques has opened new windows through which to observe the dynamic behavior of this remarkable class of enzymes. Specifically, we focus on how the powerful single-molecule Förster resonance energy transfer (FRET) method has been exploited to study the structure and function of the human immunodeficiency virus (HIV) RT and telomerase ribonucleoprotein (RNP) enzymes. These exciting studies have refined our understanding of RT catalysis, have revealed unforeseen structural rearrangements between RTs and their nucleic acid substrates, and have helped to characterize the mode of action of RT-inhibiting drugs. We conclude with a discussion of how the ongoing development of single-molecule technologies will continue to empower researchers to probe RT mechanisms in new and exciting ways.
Collapse
Affiliation(s)
- Linnea I Jansson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| |
Collapse
|
4
|
Jia X, Sun C. Structural dynamics of the N-terminal domain and the Switch loop of Prp8 during spliceosome assembly and activation. Nucleic Acids Res 2019; 46:3833-3840. [PMID: 29635373 PMCID: PMC5934631 DOI: 10.1093/nar/gky242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
Precursor message RNA (pre-mRNA) splicing is executed by the spliceosome, a large ribonucleoprotein (RNP) machinery that is comparable to the ribosome. Driven by the rapid progress of cryo-electron microscopy (cryo-EM) technology, high resolution structures of the spliceosome in its different splicing stages have proliferated over the past three years, which has greatly facilitated the mechanistic understanding of pre-mRNA splicing. As the largest and most conserved protein in the spliceosome, Prp8 plays a pivotal role within this protein-directed ribozyme. Structure determination of different spliceosomal complexes has revealed intimate and dynamic interactions between Prp8 and catalytic RNAs as well as with other protein factors during splicing. Here we review the structural dynamics of two elements of Prp8, the N-terminal domain (N-domain) and the Switch loop, and delineate the dynamic organisation and underlying functional significance of these two elements during spliceosome assembly and activation. Further biochemical and structural dissections of idiographic splicing stages are much needed for a complete understanding of the spliceosome and pre-mRNA splicing.
Collapse
Affiliation(s)
- Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
| | - Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
| |
Collapse
|
5
|
Katranidis A, Fitter J. Single-Molecule Techniques and Cell-Free Protein Synthesis: A Perfect Marriage. Anal Chem 2019; 91:2570-2576. [PMID: 30648382 DOI: 10.1021/acs.analchem.8b03855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule techniques are currently an essential tool to study conformational changes as well as the synthesis and folding of proteins. However, the preparation of suitable protein samples is often time-consuming and demanding. The rapid development of cell-free protein synthesis over the last few years opened new perspectives for fast and easy sample preparation, but this was not fully exploited until now. Here, we take a look at the advancements in sample preparation as well as in the development of technical approaches and analytical tools, which unavoidably lead to the combination of single-molecule techniques and cell-free protein synthesis. It is an ideal combination that can unlock the full potential of studying complex biological processes in the near future.
Collapse
Affiliation(s)
| | - Jörg Fitter
- Forschungszentrum Jülich , Institute of Complex Systems ICS-5, Jülich , Germany.,RWTH Aachen , I. Physikalisches Institut (IA) , Aachen , Germany
| |
Collapse
|
6
|
Prabhakar A, Puglisi EV, Puglisi JD. Single-Molecule Fluorescence Applied to Translation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032714. [PMID: 29891562 DOI: 10.1101/cshperspect.a032714] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule fluorescence methods have illuminated the dynamics of the translational machinery. Structural and bulk biochemical experiments have provided detailed atomic and global mechanistic views of translation, respectively. Single-molecule studies of translation have bridged these views by temporally connecting the conformational and compositional states defined from structural data within the mechanistic framework of translation produced from biochemical studies. Here, we discuss the context for applying different single-molecule fluorescence experiments, and present recent applications to studying prokaryotic and eukaryotic translation. We underscore the power of observing single translating ribosomes to delineate and sort complex mechanistic pathways during initiation and elongation, and discuss future applications of current and improved technologies.
Collapse
Affiliation(s)
- Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Program in Biophysics, Stanford University, Stanford, California 94305
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| |
Collapse
|
7
|
Morisaki T, Stasevich TJ. Quantifying Single mRNA Translation Kinetics in Living Cells. Cold Spring Harb Perspect Biol 2018; 10:a032078. [PMID: 30385605 PMCID: PMC6211384 DOI: 10.1101/cshperspect.a032078] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the last hurdles to quantifying the full central dogma of molecular biology in living cells with single-molecule resolution has been the imaging of single messenger RNA (mRNA) translation. Here we describe how recent advances in protein tagging and imaging technologies are being used to precisely visualize and quantify the synthesis of nascent polypeptide chains from single mRNA in living cells. We focus on recent applications of repeat-epitope tags and describe how they enable quantification of single mRNA ribosomal densities, translation initiation and elongation rates, and translation site mobility and higher-order structure. Together with complementary live-cell assays to monitor translation using fast-maturing fluorophores and mRNA-binding protein knockoff, single-molecule studies are beginning to uncover striking and unexpected heterogeneity in gene expression at the level of translation.
Collapse
Affiliation(s)
- Tatsuya Morisaki
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J Stasevich
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys 2016; 603:118-30. [PMID: 27208427 DOI: 10.1016/j.abb.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET). The recent advances in fluorescently labeled ribosomes and translation components have resulted in success of smFRET experiments. Various methods have been employed to target fluorescent dyes to specific locations within the ribosome. Primarily, these methods have involved additional steps including subunit dissociation and/or full reconstitution, which could result in ribosomes of reduced activity and translation efficiency. In addition, substantial time and effort are required to produce limited quantities of material. To enable rapid and large-scale production of highly active, fluorescently labeled ribosomes, we have developed a procedure that combines partial reconstitution with His-tag purification. This allows for a homogeneous single-step purification of mutant ribosomes and subsequent integration of labeled proteins. Ribosomes produced with this method are shown to be as active as ribosomes purified using classical methods. While we have focused on two labeling sites in this report, the method is generalizable and can in principle be extended to any non-essential ribosomal protein.
Collapse
Affiliation(s)
- Bassem Shebl
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Drew E Menke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Min Pennella
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Raghav R Poudyal
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Peter V Cornish
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460
| | | | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, United States.
| |
Collapse
|
12
|
Affiliation(s)
- Christian M Kaiser
- QB3 Institute, and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | | |
Collapse
|
13
|
Yao L, Li Y, Tsai TW, Xu S, Wang Y. Noninvasive Measurement of the Mechanical Force Generated by Motor Protein EF-G during Ribosome Translocation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
14
|
Yao L, Li Y, Tsai TW, Xu S, Wang Y. Noninvasive Measurement of the Mechanical Force Generated by Motor Protein EF-G during Ribosome Translocation. Angew Chem Int Ed Engl 2013; 52:14041-4. [DOI: 10.1002/anie.201307419] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/23/2013] [Indexed: 01/13/2023]
|
15
|
Jahn M, Seifert J, von Bergen M, Schmid A, Bühler B, Müller S. Subpopulation-proteomics in prokaryotic populations. Curr Opin Biotechnol 2013; 24:79-87. [DOI: 10.1016/j.copbio.2012.10.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/15/2012] [Accepted: 10/24/2012] [Indexed: 10/27/2022]
|
16
|
Abstract
Elongation factor-G-catalyzed translocation of mRNA and tRNAs during protein synthesis involves large-scale conformational changes in the ribosome. Formation of hybrid-state intermediates is coupled to counterclockwise (forward) rotation of the body of the 30S subunit. Recent structural studies implicate intrasubunit rotation of the 30S head in translocation. Here, we observe rotation of the head during translocation in real time using ensemble stopped-flow FRET with ribosomes containing fluorescent probes attached to specific positions in the head and body of the 30S subunit. Our results allow ordering of the rates of movement of the 30S subunit body and head during translocation: body forward > head forward > head reverse ≥ body reverse. The rate of quenching of pyrene-labeled mRNA is consistent with coupling of mRNA translocation to head rotation.
Collapse
|