1
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Mukhopadhyay J, Hausner G. Interconnected roles of fungal nuclear- and intron-encoded maturases: at the crossroads of mitochondrial intron splicing. Biochem Cell Biol 2024. [PMID: 38833723 DOI: 10.1139/bcb-2024-0046] [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: 06/06/2024] Open
Abstract
Group I and II introns are large catalytic RNAs (ribozymes) that are frequently encountered in fungal mitochondrial genomes. The discovery of respiratory mutants linked to intron splicing defects demonstrated that for the efficient removal of organellar introns there appears to be a requirement of protein splicing factors. These splicing factors can be intron-encoded proteins with maturase activities that usually promote the splicing of the introns that encode them (cis-acting) and/or nuclear-encoded factors that can promote the splicing of a range of different introns (trans-acting). Compared to plants organellar introns, fungal mitochondrial intron splicing is still poorly explored, especially in terms of the synergy of nuclear factors with intron-encoded maturases that has direct impact on splicing through their association with intron RNA. In addition, nuclear-encoded accessory factors might drive the splicing impetus through translational activation, mitoribosome assembly, and phosphorylation-mediated RNA turnover. This review explores protein-assisted splicing of introns by nuclear and mitochondrial-encoded maturases as a means of mitonuclear interplay that could respond to environmental and developmental factors promoting phenotypic adaptation and potentially speciation. It also highlights key evolutionary events that have led to changes in structure and ATP-dependence to accommodate the dual functionality of nuclear and organellar splicing factors.
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Affiliation(s)
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Zheng M, Song Y, Wang L, Yang D, Yan J, Sun Y, Hsu YF. CaRH57, a RNA helicase, contributes pepper tolerance to heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108202. [PMID: 37995575 DOI: 10.1016/j.plaphy.2023.108202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
RNA helicases (RHs) are required for most aspects of RNA metabolism and play an important role in plant stress tolerance. Heat stress (HS) causes the deleterious effects on plant cells, such as membrane disruption and protein misfolding, which results in the inhibition of plant growth and development. In this study, CaRH57 was identified from pepper (Capsicum annuum) and encodes a DEAD-box RH. CaRH57 was induced by HS, and overexpression of CaRH57 in Atrh57-1 rescued the glucose-sensitive phenotype of Atrh57-1, suggesting the functional replacement of CaRH57 to AtRH57. The nucleolus-localized CaRH57 possessed a RH activity in vitro. CaRH57 knockdown impaired pepper heat tolerance, showing severe necrosis and enhanced ROS accumulation in the region of the shoot tip. Additionally, accumulation of aberrant-spliced CaHSFA1d and CaHSFA9d was enhanced, and the corresponding mature mRNA levels were reduced in the TRV2 (Tobacco rattle virus)-CaRH57-infected plants compared with the control plants under HS. Overall, these results suggested that CaRH57 acted as a RH to confer pepper heat tolerance and was required for the proper pre-mRNA splicing of some HS-related genes.
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Affiliation(s)
- Min Zheng
- School of Life Sciences, Southwest University, Chongqing, China.
| | - Yu Song
- School of Life Sciences, Southwest University, Chongqing, China
| | - Lingyu Wang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Dandan Yang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Jiawen Yan
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yutao Sun
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yi-Feng Hsu
- School of Life Sciences, Southwest University, Chongqing, China.
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3
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Potratz JP, Russell R. Tracking Native Tetrahymena Ribozyme Folding with Fluorescence. Biochemistry 2023; 62:3173-3180. [PMID: 37910627 PMCID: PMC10666665 DOI: 10.1021/acs.biochem.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/07/2023] [Indexed: 11/03/2023]
Abstract
Folding of the Tetrahymena group I intron ribozyme and other structured RNAs has been measured using a catalytic activity assay to monitor the native state formation by cleavage of a radiolabeled oligonucleotide substrate. While highly effective, the assay has inherent limitations present in any radioactivity- and gel-based assay. Administrative and safety considerations arise from the radioisotope, and data collection is laborious due to the use of polyacrylamide gels. Here we describe a fluorescence-based, solution assay that allows for more efficient data acquisition. The substrate is labeled with 6-carboxyfluorescein (6FAM) fluorophore and black hole quencher (BHQ1) at the 5' and 3' ends, respectively. Substrate cleavage results in release of the quencher, increasing the fluorescence signal by an average of 30-fold. A side-by-side comparison with the radioactivity-based assay shows good agreement in monitoring Tetrahymena ribozyme folding from a misfolded conformation to the native state, albeit with increased uncertainty. The lower precision of the fluorescence assay is compensated for by the relative ease and efficiency of the workflow. In addition, this assay will allow institutions that do not use radioactive materials to monitor native folding of the Tetrahymena ribozyme, and the same strategy should be amenable to native folding of other ribozymes.
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Affiliation(s)
- Jeffrey P. Potratz
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
- Department
of Physical Sciences, Concordia University
Wisconsin, 12800 North
Lake Shore Drive, Mequon, Wisconsin 53097, United States
| | - Rick Russell
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
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4
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Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
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5
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Weis K, Hondele M. The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. Annu Rev Biochem 2022; 91:197-219. [PMID: 35303788 DOI: 10.1146/annurev-biochem-032620-105429] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DEAD-box ATPases constitute a very large protein family present in all cells, often in great abundance. From bacteria to humans, they play critical roles in many aspects of RNA metabolism, and due to their widespread importance in RNA biology, they have been characterized in great detail at both the structural and biochemical levels. DEAD-box proteins function as RNA-dependent ATPases that can unwind short duplexes of RNA, remodel ribonucleoprotein (RNP) complexes, or act as clamps to promote RNP assembly. Yet, it often remains enigmatic how individual DEAD-box proteins mechanistically contribute to specific RNA-processing steps. Here, we review the role of DEAD-box ATPases in the regulation of gene expression and propose that one common function of these enzymes is in the regulation of liquid-liquid phase separation of RNP condensates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | - Maria Hondele
- Biozentrum, University of Basel, Basel, Switzerland;
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6
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Zaharias S, Zhang Z, Davis K, Fargason T, Cashman D, Yu T, Zhang J. Intrinsically disordered electronegative clusters improve stability and binding specificity of RNA-binding proteins. J Biol Chem 2021; 297:100945. [PMID: 34246632 PMCID: PMC8348266 DOI: 10.1016/j.jbc.2021.100945] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022] Open
Abstract
RNA-binding proteins play crucial roles in various cellular functions and contain abundant disordered protein regions. The disordered regions in RNA-binding proteins are rich in repetitive sequences, such as poly-K/R, poly-N/Q, poly-A, and poly-G residues. Our bioinformatic analysis identified a largely neglected repetitive sequence family we define as electronegative clusters (ENCs) that contain acidic residues and/or phosphorylation sites. The abundance and length of ENCs exceed other known repetitive sequences. Despite their abundance, the functions of ENCs in RNA-binding proteins are still elusive. To investigate the impacts of ENCs on protein stability, RNA-binding affinity, and specificity, we selected one RNA-binding protein, the ribosomal biogenesis factor 15 (Nop15), as a model. We found that the Nop15 ENC increases protein stability and inhibits nonspecific RNA binding, but minimally interferes with specific RNA binding. To investigate the effect of ENCs on sequence specificity of RNA binding, we grafted an ENC to another RNA-binding protein, Ser/Arg-rich splicing factor 3. Using RNA Bind-n-Seq, we found that the engineered ENC inhibits disparate RNA motifs differently, instead of weakening all RNA motifs to the same extent. The motif site directly involved in electrostatic interaction is more susceptible to the ENC inhibition. These results suggest that one of functions of ENCs is to regulate RNA binding via electrostatic interaction. This is consistent with our finding that ENCs are also overrepresented in DNA-binding proteins, whereas underrepresented in halophiles, in which nonspecific nucleic acid binding is inhibited by high concentrations of salts.
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Affiliation(s)
- Steve Zaharias
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kenneth Davis
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Derek Cashman
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee, USA
| | - Tao Yu
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota, USA
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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7
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Donsbach P, Klostermeier D. Regulation of RNA helicase activity: principles and examples. Biol Chem 2021; 402:529-559. [PMID: 33583161 DOI: 10.1515/hsz-2020-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for non-sequence-specific interaction with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.
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Affiliation(s)
- Pascal Donsbach
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
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8
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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.
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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.
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9
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Donsbach P, Yee BA, Sanchez-Hevia D, Berenguer J, Aigner S, Yeo GW, Klostermeier D. The Thermus thermophilus DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism. RNA (NEW YORK, N.Y.) 2020; 26:1557-1574. [PMID: 32669294 PMCID: PMC7566566 DOI: 10.1261/rna.075580.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate specificity and guide the helicase to a specific RNA. However, the in vivo RNA substrates of most helicases are currently not defined. The DEAD-box helicase Hera from Thermus thermophilus contains a helicase core, followed by a dimerization domain and an RNA binding domain that folds into an RNA recognition motif (RRM). The RRM mediates high affinity binding to an RNA hairpin, and an adjacent duplex is then unwound by the helicase core. Hera is a cold-shock protein, and has been suggested to act as an RNA chaperone under cold-shock conditions. Using crosslinking immunoprecipitation of Hera/RNA complexes and sequencing, we show that Hera binds to a large fraction of T. thermophilus RNAs under normal-growth and cold-shock conditions without a strong sequence preference, in agreement with a structure-specific recognition of RNAs and a general function in RNA metabolism. Under cold-shock conditions, Hera is recruited to RNAs with high propensities to form stable secondary structures. We show that selected RNAs identified, including a set of tRNAs, bind to Hera in vitro, and activate the Hera helicase core. Gene ontology analysis reveals an enrichment of genes related to translation, including mRNAs of ribosomal proteins, tRNAs, tRNA ligases, and tRNA-modifying enzymes, consistent with a key role of Hera in ribosome and tRNA metabolism.
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Affiliation(s)
- Pascal Donsbach
- University of Muenster, Institute for Physical Chemistry, 48149 Muenster, Germany
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Dione Sanchez-Hevia
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, 48149 Muenster, Germany
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10
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Tauber D, Tauber G, Parker R. Mechanisms and Regulation of RNA Condensation in RNP Granule Formation. Trends Biochem Sci 2020; 45:764-778. [PMID: 32475683 PMCID: PMC7211619 DOI: 10.1016/j.tibs.2020.05.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 01/01/2023]
Abstract
Ribonucleoprotein (RNP) granules are RNA-protein assemblies that are involved in multiple aspects of RNA metabolism and are linked to memory, development, and disease. Some RNP granules form, in part, through the formation of intermolecular RNA-RNA interactions. In vitro, such trans RNA condensation occurs readily, suggesting that cells require mechanisms to modulate RNA-based condensation. We assess the mechanisms of RNA condensation and how cells modulate this phenomenon. We propose that cells control RNA condensation through ATP-dependent processes, static RNA buffering, and dynamic post-translational mechanisms. Moreover, perturbations in these mechanisms can be involved in disease. This reveals multiple cellular mechanisms of kinetic and thermodynamic control that maintain the proper distribution of RNA molecules between dispersed and condensed forms.
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Affiliation(s)
- Devin Tauber
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80308, USA
| | - Gabriel Tauber
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80308, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80308, USA.
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11
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Abstract
RNA-binding proteins chaperone the biological functions of noncoding RNA by reducing RNA misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality control over RNP biogenesis. Recent studies of Escherichia coli CspA, HIV NCp, and E. coli Hfq are beginning to show how RNA-binding proteins remodel RNA structures. These different protein families use common strategies for disrupting or annealing RNA double helices, which can be used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in bacteria.
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12
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González-Gutiérrez JA, Díaz-Jiménez DF, Vargas-Pérez I, Guillén-Solís G, Stülke J, Olmedo-Álvarez G. The DEAD-Box RNA Helicases of Bacillus subtilis as a Model to Evaluate Genetic Compensation Among Duplicate Genes. Front Microbiol 2018; 9:2261. [PMID: 30337909 PMCID: PMC6178137 DOI: 10.3389/fmicb.2018.02261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/05/2018] [Indexed: 11/29/2022] Open
Abstract
The presence of duplicated genes in organisms is well documented. There is increasing interest in understanding how these genes subfunctionalize and whether functional overlap can explain the fact that some of these genes are dispensable. Bacillus subtilis possesses four DEAD-box RNA helicases (DBRH) genes, cshA, cshB, deaD/yxiN, and yfmL that make a good case to study to what extent they can complement each other despite their subfunctionalization. They possess the highly conserved N-terminal catalytic domain core common to RNA helicases, but different carboxy-terminal ends. All four genes have been shown to have independent functions although all participate in rRNA assembly. None of the B. subtilis DBRH is essential for growth at 37°C, and all single deletion mutants exhibit defective growth at 18°C except for ΔdeaD/yxiN. Evaluation of double mutants did not reveal negative epistasis, suggesting that they do not have overlapping functions. The absence of any one gene distorts the expression pattern of the others, but not in a specific pattern suggestive of compensation. Overexpression of these paralogous genes in the different mutant backgrounds did not result in cross-complementation, further confirming their lack of buffering capability. Since no complementation could be observed among full sized proteins, we evaluated to what extent the superfamily 2 (SF2) helicase core of the smallest DBRH, YfmL, could be functional when hooked to each of the C-terminal end of CshA, CshB, and DeaD/YxiN. None of the different chimeras complemented the different mutants, and instead, all chimeras inhibited the growth of the ΔyfmL mutant, and other combinations were also deleterious. Our findings suggest that the long time divergence between DEAD-box RNA helicase genes has resulted in specialized activities in RNA metabolism and shows that these duplicated genes cannot buffer one another.
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Affiliation(s)
- José Antonio González-Gutiérrez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Guanajuato, Mexico
| | - Diana Fabiola Díaz-Jiménez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Guanajuato, Mexico
| | - Itzel Vargas-Pérez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Guanajuato, Mexico
| | - Gabriel Guillén-Solís
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Guanajuato, Mexico
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13
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Lee K, Shiva Kumar P, McQuade S, Lee JY, Park S, An Z, Piccoli B. Experimental and Mathematical Analyses Relating Circadian Period and Phase of Entrainment in Neurospora crassa. J Biol Rhythms 2017; 32:550-559. [PMID: 29183256 DOI: 10.1177/0748730417738611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian rhythms are observed in most organisms on earth and are known to play a major role in successful adaptation to the 24-h cycling environment. Circadian phenotypes are characterized by a free-running period that is observed in constant conditions and an entrained phase that is observed in cyclic conditions. Thus, the relationship between the free-running period and phase of entrainment is of interest. A popular simple rule has been that the entrained phase is the expression of the period in a cycling environment (i.e., that a short period causes an advanced phase and a long period causes a delayed phase). However, there are experimental data that are not explained by this simple relationship, and no systematic study has been done to explore all possible period-phase relationships. Here, we show the existence of stable period-phase relationships that are exceptions to this rule. First, we analyzed period-phase relationships using populations with different degrees of genome complexity. Second, we generated isogenic F1 populations by crossing 14 classical period mutants to the same female and analyzed 2 populations with a short period/delayed phase and a long period/advanced phase. Third, we generated a mathematical model to account for such variable relationships between period and phase. Our analyses support the view that the circadian period of an organism is not the only predictor of the entrained phase.
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Affiliation(s)
- Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, New Jersey.,Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Prithvi Shiva Kumar
- Department of Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Sean McQuade
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Joshua Y Lee
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Sohyun Park
- Department of Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Zheming An
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Benedetto Piccoli
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, New Jersey
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14
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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.
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