1
|
Patrick EM, Yadav R, Senanayake K, Cotter K, Putnam AA, Jankowsky E, Comstock MJ. High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582829. [PMID: 38496418 PMCID: PMC10942383 DOI: 10.1101/2024.02.29.582829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
DEAD-box RNA helicases are ubiquitous in all domains of life where they bind and remodel RNA and RNA-protein complexes. DEAD-box helicases unwind RNA duplexes by local opening of helical regions without directional movement through the duplexes and some of these enzymes, including Ded1p from Saccharomyces cerevisiae, oligomerize to effectively unwind RNA duplexes. Whether and how DEAD-box helicases coordinate oligomerization and unwinding is not known and it is unclear how many base pairs are actively opened. Using high-resolution optical tweezers and fluorescence, we reveal a highly dynamic and stochastic process of multiple Ded1p protomers assembling on and unwinding an RNA duplex. One Ded1p protomer binds to a duplex-adjacent ssRNA tail and promotes binding and subsequent unwinding of the duplex by additional Ded1p protomers in 4-6 bp steps. The data also reveal rapid duplex unwinding and rezipping linked with binding and dissociation of individual protomers and coordinated with the ATP hydrolysis cycle.
Collapse
|
2
|
Jarmoskaite I, Helmers AE, Russell R. Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins. Methods Enzymol 2022; 673:53-76. [PMID: 35965018 PMCID: PMC10040262 DOI: 10.1016/bs.mie.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA helicase proteins perform coupled reactions in which cycles of ATP binding and hydrolysis are used to drive local unwinding of double-stranded RNA (dsRNA). For some helicases in the ubiquitous DEAD-box family, these local unwinding events are integral to folding transitions in structured RNAs, and thus these helicases function as RNA chaperones. An important measure of the efficiency of the helicase-catalyzed reaction is the ATP utilization value, which represents the average number of ATP molecules hydrolyzed during RNA unwinding or a chaperone-assisted RNA structural rearrangement. Here we outline procedures that can be used to measure the ATP utilization value in RNA unwinding or folding transitions. As an example of an RNA folding transition, we focus on the refolding of the Tetrahymena thermophila group I intron ribozyme from a long-lived misfolded structure to its native structure, and we outline strategies for adapting this assay to other RNA folding transitions. For a simple dsRNA unwinding event, the ATP utilization value provides a measure of the coupling between the ATPase and RNA unwinding activities, and for a complex RNA structural transition it can give insight into the scope of the rearrangement and the efficiency with which the helicase uses the energy from ATPase cycles to promote the rearrangement.
Collapse
Affiliation(s)
- Inga Jarmoskaite
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Anna E Helmers
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States.
| |
Collapse
|
3
|
Jarmoskaite I, Tijerina P, Russell R. ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme. J Biol Chem 2020; 296:100132. [PMID: 33262215 PMCID: PMC7948464 DOI: 10.1074/jbc.ra120.015029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/17/2020] [Accepted: 12/01/2020] [Indexed: 12/31/2022] Open
Abstract
DEAD-box helicase proteins perform ATP-dependent rearrangements of structured RNAs throughout RNA biology. Short RNA helices are unwound in a single ATPase cycle, but the ATP requirement for more complex RNA structural rearrangements is unknown. Here we measure the amount of ATP used for native refolding of a misfolded group I intron ribozyme by CYT-19, a Neurospora crassa DEAD-box protein that functions as a general chaperone for mitochondrial group I introns. By comparing the rates of ATP hydrolysis and ribozyme refolding, we find that several hundred ATP molecules are hydrolyzed during refolding of each ribozyme molecule. After subtracting nonproductive ATP hydrolysis that occurs in the absence of ribozyme refolding, we find that approximately 100 ATPs are hydrolyzed per refolded RNA as a consequence of interactions specific to the misfolded ribozyme. This value is insensitive to changes in ATP and CYT-19 concentration and decreases with decreasing ribozyme stability. Because of earlier findings that ∼90% of global ribozyme unfolding cycles lead back to the kinetically preferred misfolded conformation and are not observed, we estimate that each global unfolding cycle consumes ∼10 ATPs. Our results indicate that CYT-19 functions as a general RNA chaperone by using a stochastic, energy-intensive mechanism to promote RNA unfolding and refolding, suggesting an evolutionary convergence with protein chaperones.
Collapse
Affiliation(s)
- Inga Jarmoskaite
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Pilar Tijerina
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
| |
Collapse
|
4
|
Licatalosi DD, Ye X, Jankowsky E. Approaches for measuring the dynamics of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1565. [PMID: 31429211 PMCID: PMC7006490 DOI: 10.1002/wrna.1565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 12/17/2022]
Abstract
RNA-protein interactions are pivotal for the regulation of gene expression from bacteria to human. RNA-protein interactions are dynamic; they change over biologically relevant timescales. Understanding the regulation of gene expression at the RNA level therefore requires knowledge of the dynamics of RNA-protein interactions. Here, we discuss the main experimental approaches to measure dynamic aspects of RNA-protein interactions. We cover techniques that assess dynamics of cellular RNA-protein interactions that accompany biological processes over timescales of hours or longer and techniques measuring the kinetic dynamics of RNA-protein interactions in vitro. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Evolution and Genomics > Ribonomics.
Collapse
Affiliation(s)
- Donny D Licatalosi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
5
|
Jalihal AP, Lund PE, Walter NG. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032441. [PMID: 30936188 DOI: 10.1101/cshperspect.a032441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNAs, across their numerous classes, often work in concert with proteins in RNA-protein complexes (RNPs) to execute critical cellular functions. Ensemble-averaging methods have been instrumental in revealing many important aspects of these RNA-protein interactions, yet are insufficiently sensitive to much of the dynamics at the heart of RNP function. Single-molecule fluorescence microscopy (SMFM) offers complementary, versatile tools to probe RNP conformational and compositional changes in detail. In this review, we first outline the basic principles of SMFM as applied to RNPs, describing key considerations for labeling, imaging, and quantitative analysis. We then sample applications of in vitro and in vivo single-molecule visualization using the case studies of pre-messenger RNA (mRNA) splicing and RNA silencing, respectively. After discussing specific insights single-molecule fluorescence methods have yielded, we briefly review recent developments in the field and highlight areas of anticipated growth.
Collapse
Affiliation(s)
- Ameya P Jalihal
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109.,Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
6
|
Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs. Biochem Soc Trans 2017; 45:1313-1321. [PMID: 29150525 DOI: 10.1042/bst20170095] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/03/2023]
Abstract
Structured RNAs and RNA-protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how their distinct mechanisms enable DEAD-box proteins to disrupt RNA base pairs on the surfaces of structured RNAs and RNPs, while some DEAH-box proteins are adept at disrupting base pairs in the interior of RNPs. Proteins from these families use these mechanisms to chaperone folding and promote rearrangements of structured RNAs and RNPs, including the spliceosome, and may use related mechanisms to maintain cellular messenger RNAs in unfolded or partially unfolded conformations.
Collapse
|
7
|
Robert-Paganin J, Halladjian M, Blaud M, Lebaron S, Delbos L, Chardon F, Capeyrou R, Humbert O, Henry Y, Henras AK, Réty S, Leulliot N. Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding. Nucleic Acids Res 2017; 45:1539-1552. [PMID: 28180308 PMCID: PMC5388414 DOI: 10.1093/nar/gkw1233] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023] Open
Abstract
The DEAH box helicase Prp43 is a bifunctional enzyme from the DEAH/RHA helicase family required both for the maturation of ribosomes and for lariat intron release during splicing. It interacts with G-patch domain containing proteins which activate the enzymatic activity of Prp43 in vitro by an unknown mechanism. In this work, we show that the activation by G-patch domains is linked to the unique nucleotide binding mode of this helicase family. The base of the ATP molecule is stacked between two residues, R159 of the RecA1 domain (R-motif) and F357 of the RecA2 domain (F-motif). Using Prp43 F357A mutants or pyrimidine nucleotides, we show that the lack of stacking of the nucleotide base to the F-motif decouples the NTPase and helicase activities of Prp43. In contrast the R159A mutant (R-motif) showed reduced ATPase and helicase activities. We show that the Prp43 R-motif mutant induces the same phenotype as the absence of the G-patch protein Gno1, strongly suggesting that the processing defects observed in the absence of Gno1 result from a failure to activate the Prp43 helicase. Overall we propose that the stacking between the R- and F-motifs and the nucleotide base is important for the activity and regulation of this helicase family.
Collapse
Affiliation(s)
- Julien Robert-Paganin
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Maral Halladjian
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Magali Blaud
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Simon Lebaron
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Lila Delbos
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Florian Chardon
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Régine Capeyrou
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, France
| | - Stéphane Réty
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| |
Collapse
|
8
|
Busa VF, Rector MJ, Russell R. The DEAD-Box Protein CYT-19 Uses Arginine Residues in Its C-Tail To Tether RNA Substrates. Biochemistry 2017. [PMID: 28650145 DOI: 10.1021/acs.biochem.7b00362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich "C-tail" that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the 11 arginines reduced RNA unwinding activity (kcat/KM) to a degree equivalent to that seen upon removal of the C-tail, suggesting that a minimum or "threshold" number of arginines is required. In addition, a mutant with 16 arginines displayed RNA unwinding activity greater than that of wild-type CYT-19. The C-tail modifications impacted unwinding only of RNA helices within constructs that included an adjacent helix or structured RNA element that would allow C-tail binding, indicating that the helicase core remained active in the mutants. In addition, changes in RNA unwinding efficiency of the mutants were mirrored by changes in functional RNA affinity, as determined from the RNA concentration dependence of ATPase activity, suggesting that the C-tail functions primarily to increase RNA affinity. Interestingly, the salt concentration dependence of RNA unwinding activity is unaffected by C-tail composition, suggesting that the C-tail uses primarily hydrogen bonding, not electrostatic interactions, to bind double-stranded RNA. Our results provide insights into how an unstructured C-tail contributes to DEAD-box protein activity and suggest parallels with other families of RNA- and DNA-binding proteins.
Collapse
Affiliation(s)
- Veronica F Busa
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
| | - Maxwell J Rector
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
| | - Rick Russell
- Department of Molecular Biosciences and Institute for Cellular & Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
9
|
Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
Collapse
|
10
|
Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Díez J. A novel translational control mechanism involving RNA structures within coding sequences. Genome Res 2016; 27:95-106. [PMID: 27821408 PMCID: PMC5204348 DOI: 10.1101/gr.209015.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022]
Abstract
The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses, we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site; second, they are directly bound by Dhh1 with a specific binding distribution; and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.
Collapse
Affiliation(s)
- Jennifer Jungfleisch
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Danny D Nedialkova
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - Ivan Dotu
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Katherine E Sloan
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany
| | - Neus Martinez-Bosch
- Program of Cancer Research, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Lukas Brüning
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany
| | - Emanuele Raineri
- Statistical Genomics, Centro Nacional de Analisis Genomica, 08028 Barcelona, Spain
| | - Pilar Navarro
- Program of Cancer Research, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Markus T Bohnsack
- Institute for Molecular Biology, Göttingen University Medical Department, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, 37073 Göttingen, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany.,Faculty of Medicine, University of Münster, 48149 Münster, Germany
| | - Juana Díez
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| |
Collapse
|
11
|
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
|
12
|
Liu SR, Hu CG, Zhang JZ. Regulatory effects of cotranscriptional RNA structure formation and transitions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:562-74. [PMID: 27028291 DOI: 10.1002/wrna.1350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Sheng-Rui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
13
|
Ruminski DJ, Watson PY, Mahen EM, Fedor MJ. A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo. RNA (NEW YORK, N.Y.) 2016; 22:416-27. [PMID: 26759451 PMCID: PMC4748819 DOI: 10.1261/rna.055178.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/05/2015] [Indexed: 05/24/2023]
Abstract
RNAs must assemble into specific structures in order to carry out their biological functions, but in vitro RNA folding reactions produce multiple misfolded structures that fail to exchange with functional structures on biological time scales. We used carefully designed self-cleaving mRNAs that assemble through well-defined folding pathways to identify factors that differentiate intracellular and in vitro folding reactions. Our previous work showed that simple base-paired RNA helices form and dissociate with the same rate and equilibrium constants in vivo and in vitro. However, exchange between adjacent secondary structures occurs much faster in vivo, enabling RNAs to quickly adopt structures with the lowest free energy. We have now used this approach to probe the effects of an extensively characterized DEAD-box RNA helicase, Mss116p, on a series of well-defined RNA folding steps in yeast. Mss116p overexpression had no detectable effect on helix formation or dissociation kinetics or on the stability of interdomain tertiary interactions, consistent with previous evidence that intracellular factors do not affect these folding parameters. However, Mss116p overexpression did accelerate exchange between adjacent helices. The nonprocessive nature of RNA duplex unwinding by DEAD-box RNA helicases is consistent with a branch migration mechanism in which Mss116p lowers barriers to exchange between otherwise stable helices by the melting and annealing of one or two base pairs at interhelical junctions. These results suggest that the helicase activity of DEAD-box proteins like Mss116p distinguish intracellular RNA folding pathways from nonproductive RNA folding reactions in vitro and allow RNA structures to overcome kinetic barriers to thermodynamic equilibration in vivo.
Collapse
Affiliation(s)
- Dana J Ruminski
- Department of Chemical Physiology, Department of Cell and Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Peter Y Watson
- Department of Chemical Physiology, Department of Cell and Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Elisabeth M Mahen
- Department of Chemical Physiology, Department of Cell and Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Martha J Fedor
- Department of Chemical Physiology, Department of Cell and Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| |
Collapse
|
14
|
Zhao L, Mao Y, Zhou J, Zhao Y, Cao Y, Chen X. Multifunctional DDX3: dual roles in various cancer development and its related signaling pathways. Am J Cancer Res 2016; 6:387-402. [PMID: 27186411 PMCID: PMC4859668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023] Open
Abstract
DEAD-box RNA helicase 3 (DDX3) is a highly conserved family member of DEAD-box protein, which is a cluster of ATP-dependent and the largest family of RNA helicase. DEAD-box family is characterized by the regulation of ATPase and helicase activities, the modulation of RNA metabolism, and the actors of RNA binding proteins or molecular chaperones to interact with other proteins or RNA. For DDX3, it exerts its multifaceted roles in viral manipulation, stress response, hypoxia, radiation response and apoptosis, and is closely related to cancer development and progression. DDX3 has dual roles in different cancer types and can act as either an oncogene or tumor suppressor gene during cancer progression. In the present review, we mainly provide an overview of current knowledge on dual roles of DDX3 in various types of cancer, including breast cancer, lung cancer, colorectal cancer, hepatocellular carcinoma, oral squamous cell carcinoma, Ewing sarcoma, glioblastoma multiforme and gallbladder carcinoma, and illustrate the regulatory mechanisms for leading these two controversial biological effects. Furthermore, we summarize the essential signaling pathways that DDX3 participated, especially the Wnt/β-catenin signaling and EMT related signaling (TGF-β, Notch, Hedgehog pathways), which are crucial to DDX3 mediated cancer metastasis process. Thoroughly exploring the dual roles of DDX3 in cancer development and the essential signaling pathways it involved, it will help us open new perspectives to develop novel promising targets to elevate therapeutic effects and facilitate the "Personalized medicine" or "Precision medicine" to come into clinic.
Collapse
Affiliation(s)
- Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Yuelong Zhao
- School of Computer Science and Engineering, South China University of TechnologyGuangzhou 510640, Guangdong, China
| | - Ya Cao
- Cancer Research Institute, School of Basic Medical Science, Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, China
| |
Collapse
|
15
|
Putnam AA, Gao Z, Liu F, Jia H, Yang Q, Jankowsky E. Division of Labor in an Oligomer of the DEAD-Box RNA Helicase Ded1p. Mol Cell 2015. [PMID: 26212457 DOI: 10.1016/j.molcel.2015.06.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Most aspects of RNA metabolism involve DEAD-box RNA helicases, enzymes that bind and remodel RNA and RNA-protein complexes in an ATP-dependent manner. Here we show that the DEAD-box helicase Ded1p oligomerizes in the cell and in vitro, and unwinds RNA as a trimer. Two protomers bind the single-stranded region of RNA substrates and load a third protomer to the duplex, which then separates the strands. ATP utilization differs between the strand-separating protomer and those bound to the single-stranded region. Binding of the eukaryotic initiation factor 4G to Ded1p interferes with oligomerization and thereby modulates unwinding activity and RNA affinity of the helicase. Our data reveal a strict division of labor between the Ded1p protomers in the oligomer. This mode of oligomerization fundamentally differs from other helicases. Oligomerization represents a previously unappreciated level of regulation for DEAD-box helicase activities.
Collapse
Affiliation(s)
- Andrea A Putnam
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Zhaofeng Gao
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Fei Liu
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; College of Veterinary Medicine, Nanjing Agricultural University, Number 1 Weigang, Nanjing 210095, P.R. China
| | - Huijue Jia
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; BGI Shenzen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, P.R. China
| | - Quansheng Yang
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; McArdle Laboratory of Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology and Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| |
Collapse
|
16
|
Bhartiya D, Chandramouli B, Kumar N. Co-evolutionary analysis implies auxiliary functions of HSP110 in Plasmodium falciparum. Proteins 2015; 83:1513-25. [DOI: 10.1002/prot.24842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/21/2015] [Accepted: 05/27/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Deeksha Bhartiya
- Institute of Cytology and Preventive Oncology (ICMR); Noida 201301 Uttar Pradesh India
| | | | - Niti Kumar
- CSIR-Central Drug Research Institute; Lucknow 226031 Uttar Pradesh India
| |
Collapse
|
17
|
Affiliation(s)
- Rick Russell
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
18
|
Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases. Int J Mol Sci 2015; 16:2269-93. [PMID: 25622248 PMCID: PMC4346836 DOI: 10.3390/ijms16022269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.
Collapse
|