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A comparison of total RNA extraction methods for RT-PCR based differential expression of genes from Trichoderma atrobrunneum. METHODS IN MICROBIOLOGY 2022; 200:106535. [DOI: 10.1016/j.mimet.2022.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/22/2022]
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2
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Abou Elela S, Ji X. Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1521. [PMID: 30548404 DOI: 10.1002/wrna.1521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022]
Abstract
The double-stranded RNA-binding protein (dsRBP) family controls RNA editing, stability, and function in all eukaryotes. The central feature of this family is the recognition of a generic RNA duplex using highly conserved double-stranded RNA-binding domain (dsRBD) that recognizes the characteristic distance between the minor grooves created by the RNA helix. Variations on this theme that confer species and functional specificities have been reported but most dsRBPs retain their capacity to bind generic dsRNA. The ribonuclease III (RNase III) family members fall into four classes, represented by bacterial RNase III, yeast Rnt1p, human Drosha, and human Dicer, respectively. Like all dsRBPs and most members of the RNase III family, Rnt1p has a dsRBD, but unlike most of its kin, it poorly binds to generic RNA helices. Instead, Rnt1p, the only known RNase III expressed in Saccharomyces cerevisiae that lacks the RNAi (RNA interference) machinery, recognizes a specific class of stem-loop structures. To recognize the specific substrates, the dsRBD of Rnt1p is specialized, featuring a αβββααα topology and a sequence-specific RNA-binding motif at the C-terminus. Since the discovery of Rnt1p in 1996, significant progress has been made in studies of its genetics, function, structure, and mechanism of action, explaining the reasons and mechanisms for the increased specificity of this enzyme and its impact on the mechanism of RNA degradation. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sherif Abou Elela
- Microbiology and Infectiology Department, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland
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3
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Ahmad J, Baig MA, Ali AA, Al-Huqail A, Ibrahim MM, Qureshi MI. Comparative assessment of four RNA extraction methods and modification to obtain high-quality RNA from Parthenium hysterophorus leaf. 3 Biotech 2017; 7:373. [PMID: 29071170 PMCID: PMC5641483 DOI: 10.1007/s13205-017-1003-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/26/2017] [Indexed: 01/16/2023] Open
Abstract
Isolation of high-quality RNA from weed plants such as Parthenium hysterophorus is a difficult task due to the hindrance caused by numerous secondary metabolites. Such metabolites not only affect the quality and yield of RNA, but also limit the quality of downstream applications. Therefore, the present study was undertaken to design a protocol for yielding RNA with better quality and quantity from P. hysterophorus leaf which could be suitable for functional genomics. To achieve the objective, four different important RNA extraction protocols, viz. acid guanidinium thiocyanate-phenol-chloroform, phenol-LiCl precipitation, TRIzol®, and PVP-ethanol were tested. The PVP-ethanol method proved to be best among the tested protocols. This method was further modified for obtaining improved quality and yield of RNA. The modified method successfully enhanced the yield of RNA from 280 to 334 µg g-1 fresh weight. The absorbance ratio (A260/A280) was in the purity range of 1.9 that indicated the good quality of RNA. To prove the feasibility of the extracted RNA in PCR-based cDNA synthesis, actin transcripts were targeted and successfully amplified using suitable primers. The improved protocol thus not only improved the yield and quality of RNA, but also gave better results in reverse transcriptase PCR.
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Affiliation(s)
- Javed Ahmad
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110 025 India
| | - M. Affan Baig
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110 025 India
| | - Arlene A. Ali
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110 025 India
| | - Asma Al-Huqail
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, 11495 Saudi Arabia
| | - M. M. Ibrahim
- Department of Botany & Microbiology, Faculty of Science, Alexandria University, P.O. Box 21511, Alexandria, Egypt
| | - M. Irfan Qureshi
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, 110 025 India
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Comeau MA, Lafontaine DA, Abou Elela S. The catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate. Nucleic Acids Res 2016; 44:7911-21. [PMID: 27257067 PMCID: PMC5027489 DOI: 10.1093/nar/gkw507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/25/2016] [Indexed: 01/31/2023] Open
Abstract
Members of the ribonuclease III (RNase III) family regulate gene expression by triggering the degradation of double stranded RNA (dsRNA). Hundreds of RNase III cleavage targets have been identified and their impact on RNA maturation and stability is now established. However, the mechanism defining substrates’ reactivity remains unclear. In this study, we developed a real-time FRET assay for the detection of dsRNA degradation by yeast RNase III (Rnt1p) and characterized the kinetic bottlenecks controlling the reactivity of different substrates. Surprisingly, the results indicate that Rnt1p cleavage reaction is not only limited by the rate of catalysis but can also depend on base-pairing of product termini. Cleavage products terminating with paired nucleotides, like the degradation signals found in coding mRNA sequence, were less reactive and more prone to inhibition than products having unpaired nucleotides found in non-coding RNA substrates. Mutational analysis of U5 snRNA and Mig2 mRNA confirms the pairing of the cleavage site as a major determinant for the difference between cleavage rates of coding and non-coding RNA. Together the data indicate that the base-pairing of Rnt1p substrates encodes reactivity determinants that permit both constitutive processing of non-coding RNA while limiting the rate of mRNA degradation.
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Affiliation(s)
- Marc-Andre Comeau
- Département de biologie, Faculté de science, Université de Sherbrooke, Sherbrooke, Québec J1E 2R1, Canada
| | - Daniel A Lafontaine
- Département de biologie, Faculté de science, Université de Sherbrooke, Sherbrooke, Québec J1E 2R1, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Pavillon de recherche appliquée sur le cancer, Sherbrooke, Québec J1E 4K8, Canada
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Gagnon J, Lavoie M, Catala M, Malenfant F, Elela SA. Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals. PLoS Genet 2015; 11:e1005000. [PMID: 25680180 PMCID: PMC4334505 DOI: 10.1371/journal.pgen.1005000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 01/13/2015] [Indexed: 12/11/2022] Open
Abstract
Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome, and encompass a wide variety of sequences, indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes, and their impact on RNA expression is linked to growth conditions. Together, the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. RNA degradation is essential for gene regulation. The amount and timing of protein synthesis is determined, at least in part, by messenger RNA stability. Although RNA stability is determined by specific structural and sequence motif, the distribution of the degradation signals in eukaryotic genomes remains unclear. In this study, we describe the genomic distribution of the RNA degradation signals required for selective nuclear degradation in yeast. The results indicate that most RNAs in the yeast transcriptome are predisposed for degradation, but only few are catalytically active. The catalytic reactivity of messenger RNAs were mostly determined by the overall structural context of the degradation signals. Strikingly, most active RNA degradation signals are found in genes associated with respiration and fermentation. Overall, the findings reported here demonstrate how certain RNA are selected for cleavage and illustrated the importance of this selective RNA degradation for fine tuning gene expression in response to changes in growth condition.
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Affiliation(s)
- Jules Gagnon
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mathieu Lavoie
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mathieu Catala
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Francis Malenfant
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sherif Abou Elela
- Université de Sherbrooke Centre of Excellence in RNA Biology, Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Liang YH, Lavoie M, Comeau MA, Abou Elela S, Ji X. Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection. Mol Cell 2014; 54:431-44. [PMID: 24703949 DOI: 10.1016/j.molcel.2014.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/23/2013] [Accepted: 02/27/2014] [Indexed: 11/19/2022]
Abstract
Ribonuclease III (RNase III) enzymes are a family of double-stranded RNA (dsRNA)-specific endoribonucleases required for RNA maturation and gene regulation. Prokaryotic RNase III enzymes have been well characterized, but how eukaryotic RNase IIIs work is less clear. Here, we describe the structure of the Saccharomyces cerevisiae RNase III (Rnt1p) postcleavage complex and explain why Rnt1p binds to RNA stems capped with an NGNN tetraloop. The structure shows specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain (dsRBD) and the guanine nucleotide in the second position of the loop. Strikingly, structural and biochemical analyses indicate that the dsRBD and N-terminal domains (NTDs) of Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site. These findings provide a framework for understanding eukaryotic RNase IIIs.
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Affiliation(s)
- Yu-He Liang
- Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mathieu Lavoie
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marc-Andre Comeau
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou Elela
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
| | - Xinhua Ji
- Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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7
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Nicholson AW. Ribonuclease III mechanisms of double-stranded RNA cleavage. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:31-48. [PMID: 24124076 PMCID: PMC3867540 DOI: 10.1002/wrna.1195] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/09/2013] [Accepted: 08/10/2013] [Indexed: 12/22/2022]
Abstract
Double-stranded(ds) RNA has diverse roles in gene expression and regulation, host defense, and genome surveillance in bacterial and eukaryotic cells. A central aspect of dsRNA function is its selective recognition and cleavage by members of the ribonuclease III (RNase III) family of divalent-metal-ion-dependent phosphodiesterases. The processing of dsRNA by RNase III family members is an essential step in the maturation and decay of coding and noncoding RNAs, including miRNAs and siRNAs. RNase III, as first purified from Escherichia coli, has served as a biochemically well-characterized prototype, and other bacterial orthologs provided the first structural information. RNase III family members share a unique fold (RNase III domain) that can dimerize to form a structure that binds dsRNA and cleaves phosphodiesters on each strand, providing the characteristic 2 nt, 3′-overhang product ends. Ongoing studies are uncovering the functions of additional domains, including, inter alia, the dsRNA-binding and PAZ domains that cooperate with the RNase III domain to select target sites, regulate activity, confer processivity, and support the recognition of structurally diverse substrates. RNase III enzymes function in multicomponent assemblies that are regulated by diverse inputs, and at least one RNase III-related polypeptide can function as a noncatalytic, dsRNA-binding protein. This review summarizes the current knowledge of the mechanisms of catalysis and target site selection of RNase III family members, and also addresses less well understood aspects of these enzymes and their interactions with dsRNA. WIREs RNA 2014, 5:31–48. doi: 10.1002/wrna.1195
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Affiliation(s)
- Allen W Nicholson
- Department of Biology and Chemistry, College of Science & Technology, Temple University, Philadelphia, PA, USA
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Feng Y, Zhang X, Graves P, Zeng Y. A comprehensive analysis of precursor microRNA cleavage by human Dicer. RNA (NEW YORK, N.Y.) 2012; 18:2083-92. [PMID: 22984192 PMCID: PMC3479397 DOI: 10.1261/rna.033688.112] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/07/2012] [Indexed: 05/20/2023]
Abstract
Dicer cleaves double-stranded RNAs (dsRNAs) or precursor microRNAs (pre-miRNAs) to yield ≈ 22-nt RNA duplexes. The pre-miRNA structure requirement for human Dicer activity is incompletely understood. By large-scale in vitro dicing assays and mutagenesis studies, we showed that human Dicer cleaves most, although not all, of the 161 tested human pre-miRNAs efficiently. The stable association of RNAs with Dicer, as examined by gel shift assays, appears important but is not sufficient for cleavage. Human Dicer tolerates remarkable structural variation in its pre-miRNA substrates, although the dsRNA feature in the stem region and the 2-nt 3'-overhang structure in a pre-miRNA contribute to its binding and cleavage by Dicer, and a large terminal loop further enhances pre-miRNA cleavage. Dicer binding protects the terminal loop from digestion by S1 nuclease, suggesting that Dicer interacts directly with the terminal loop region.
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Affiliation(s)
- Yong Feng
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430070, P.R. China
| | - Xiaoxiao Zhang
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Paul Graves
- Department of Radiation Oncology, New York Methodist Hospital, Weill Cornell Medical College, Brooklyn, New York 11215, USA
| | - Yan Zeng
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Corresponding authorE-mail
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9
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Babiskin AH, Smolke CD. Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nucleic Acids Res 2011; 39:8651-64. [PMID: 21737428 PMCID: PMC3201855 DOI: 10.1093/nar/gkr445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The design of synthetic gene networks requires an extensive genetic toolbox to control the activities and levels of protein components to achieve desired cellular functions. Recently, a novel class of RNA-based control modules, which act through post-transcriptional processing of transcripts by directed RNase III (Rnt1p) cleavage, were shown to provide predictable control over gene expression and unique properties for manipulating biological networks. Here, we increase the regulatory range of the Rnt1p control elements, by modifying a critical region for enzyme binding to its hairpin substrates, the binding stability box (BSB). We used a high throughput, cell-based selection strategy to screen a BSB library for sequences that exhibit low fluorescence and thus high Rnt1p processing efficiencies. Sixteen unique BSBs were identified that cover a range of protein expression levels, due to the ability of the sequences to affect the hairpin cleavage rate and to form active cleavable complexes with Rnt1p. We further demonstrated that the activity of synthetic Rnt1p hairpins can be rationally programmed by combining the synthetic BSBs with a set of sequences located within a different region of the hairpin that directly modulate cleavage rates, providing a modular assembly strategy for this class of RNA-based control elements.
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Affiliation(s)
- Andrew H Babiskin
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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Bergeron L, Perreault JP, Abou Elela S. Short RNA duplexes guide sequence-dependent cleavage by human Dicer. RNA (NEW YORK, N.Y.) 2010; 16:2464-73. [PMID: 20974746 PMCID: PMC2995407 DOI: 10.1261/rna.2346510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/16/2010] [Indexed: 05/30/2023]
Abstract
Dicer is a member of the double-stranded (ds) RNA-specific ribonuclease III (RNase III) family that is required for RNA processing and degradation. Like most members of the RNase III family, Dicer possesses a dsRNA binding domain and cleaves long RNA duplexes in vitro. In this study, Dicer substrate selectivity was examined using bipartite substrates. These experiments revealed that an RNA helix possessing a 2-nucleotide (nt) 3'-overhang may bind and direct sequence-specific Dicer-mediated cleavage in trans at a fixed distance from the 3'-end overhang. Chemical modifications of the substrate indicate that the presence of the ribose 2'-hydroxyl group is not required for Dicer binding, but some located near the scissile bonds are needed for RNA cleavage. This suggests a flexible mechanism for substrate selectivity that recognizes the overall shape of an RNA helix. Examination of the structure of natural pre-microRNAs (pre-miRNAs) suggests that they may form bipartite substrates with complementary mRNA sequences, and thus induce seed-independent Dicer cleavage. Indeed, in vitro, natural pre-miRNA directed sequence-specific Dicer-mediated cleavage in trans by supporting the formation of a substrate mimic.
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Affiliation(s)
- Lucien Bergeron
- RNA group/Groupe ARN, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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