151
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Zhang X, Li M, Liu Y. Optimization and characterization of position-selective labelling of RNA (PLOR) for diverse RNA and DNA sequences. RNA Biol 2020; 17:1009-1017. [PMID: 32249673 DOI: 10.1080/15476286.2020.1749797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Modifications of short RNAs at specific sites can be achieved commercially by solid-phase chemical synthesis method. However, labelling long RNAs is still challenging for the routine methods. Position-selective Labelling of RNA (PLOR) is a hybrid phase transcription method that allows to label RNAs at desired sites with great flexibility and decent efficiency. In principle, PLOR is a promising method for synthesis of long modified RNAs that are unable to be generated by solid-phase chemical synthesis and other methods. However, as a recently developed method, PLOR has been only applied to label a 71nt and a 104nt RNA, and the limited sequence applications of PLOR may hinder its potential usages. To extend PLOR to more RNAs, we tested the PLOR performances for various RNA sequences. Considering that the controlled transcriptional pauses at the initiation stage in PLOR may lead to different preferences on RNA sequences from in vitro transcription method, we here focused on identifying the effects of the 5'-end and initiated lengths of RNA on PLOR. In addition, our work demonstrated that PLOR efficiencies also varied with linker sizes of DNA templates. This work can facilitate PLOR to be the choice of synthesizing long modified RNAs for more users in the near future.
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Affiliation(s)
- Xiaoyu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
| | - Mengyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
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152
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Apura P, Saramago M, Peregrina A, Viegas SC, Carvalho SM, Saraiva LM, Arraiano CM, Domingues S. Tailor-made sRNAs: a plasmid tool to control the expression of target mRNAs in Pseudomonas putida. Plasmid 2020; 109:102503. [PMID: 32209400 DOI: 10.1016/j.plasmid.2020.102503] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 11/25/2022]
Abstract
Pseudomonas putida is a highly attractive production system for industrial needs. However, for its improvement as a biocatalyst at the industrial level, modulation of its gene expression is urgently needed. We report the construction of a plasmid expressing a small RNA-based system with the potential to be used for different purposes. Due to the small RNAs modular composition, the design facilities and ability to tune gene expression, they constitute a powerful tool in genetic and metabolic engineering. In the tool presented here, customized sRNAs are expressed from a plasmid and specifically directed to any region of a chosen target. Expression of these customized sRNAs is shown to differentially modulate the level of endogenous and heterologous reporter genes. The antisense interaction of the sRNA with the mRNA produces different outcomes. Depending on the particularity of each sRNA-target mRNA pair, we demonstrate the duality of this system, which is able either to decrease or increase the expression of the same given gene. This system combines high specificity with the potential to be widely applied, due to its predicted ability to modulate the expression of virtually any given gene. This plasmid can be used to redesign P. putida metabolism, fulfilling an important industrial gap.
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Affiliation(s)
- Patrícia Apura
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Margarida Saramago
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexandra Peregrina
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sandra C Viegas
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Sandra M Carvalho
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lígia M Saraiva
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Susana Domingues
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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153
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Nagy SK, Kállai BM, András J, Mészáros T. A novel family of expression vectors with multiple affinity tags for wheat germ cell-free protein expression. BMC Biotechnol 2020; 20:17. [PMID: 32169064 PMCID: PMC7071761 DOI: 10.1186/s12896-020-00610-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cell-free protein expression has become a widely used alternative of in vivo, cell-based systems in functional and structural studies of proteins. The wheat germ-based method outstands from the commercially available eukaryotic in vitro translation systems by its flexibility, high translation efficiency and success rate of properly folded eukaryotic protein synthesis. The original T7 promoter containing pEU3-NII vector was improved previously by addition of a ligation-independent cloning site, His6- and GST-tags, and a TEV protease cleavage site to facilitate the creation of recombinant plasmids, permit affinity purification, and enable production of purified, tag-free target proteins, respectively. RESULTS Here, we describe a further development of pEU3-NII vector by inserting the rare-cutting, NotI restriction enzyme cleavage site to simplify vector linearization step prior to in vitro transcription. Additionally, His12, FLAG, and Halo affinity tag coding vectors have been created to increase detection sensitivity, specificity of interaction studies, and provide covalently linkable ligands for pull-down assays, respectively. Finally, the presented GST-His6, and GST-biotin double-tagging vectors could broaden the range of possibilities of protein-protein interaction studies. CONCLUSIONS The new generation of pEU3-NII vector family allows a more rapid production of translationally active mRNA and wheat germ cell-free expression of target proteins with a wide variety of affinity tags thus enables designing flexible and diverse experimental arrangement for in vitro studies of proteins.
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Affiliation(s)
- Szilvia Krisztina Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Brigitta Margit Kállai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Judit András
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary.
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154
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Baksay S, Pornon A, Burrus M, Mariette J, Andalo C, Escaravage N. Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL. Sci Rep 2020; 10:4202. [PMID: 32144370 PMCID: PMC7060345 DOI: 10.1038/s41598-020-61198-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/18/2020] [Indexed: 11/09/2022] Open
Abstract
Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high-throughput sequence reads and how the relationship was affected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have different characteristics. We found a significant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with flow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantification.
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Affiliation(s)
- Sandra Baksay
- Laboratoire Evolution and Diversité Biologique EDB, CNRS, UMR 5174, Université Toulouse III Paul Sabatier, F-31062, Toulouse, France.
| | - André Pornon
- Laboratoire Evolution and Diversité Biologique EDB, CNRS, UMR 5174, Université Toulouse III Paul Sabatier, F-31062, Toulouse, France
| | - Monique Burrus
- Laboratoire Evolution and Diversité Biologique EDB, CNRS, UMR 5174, Université Toulouse III Paul Sabatier, F-31062, Toulouse, France
| | - Jérôme Mariette
- Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliqués INRA, UR875, Toulouse, F-31320, Castanet-Tolosan, France
| | - Christophe Andalo
- Laboratoire Evolution and Diversité Biologique EDB, CNRS, UMR 5174, Université Toulouse III Paul Sabatier, F-31062, Toulouse, France
| | - Nathalie Escaravage
- Laboratoire Evolution and Diversité Biologique EDB, CNRS, UMR 5174, Université Toulouse III Paul Sabatier, F-31062, Toulouse, France
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155
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Kulcsár PI, Tálas A, Tóth E, Nyeste A, Ligeti Z, Welker Z, Welker E. Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5'G-extended sgRNAs. Nat Commun 2020; 11:1223. [PMID: 32144253 PMCID: PMC7060260 DOI: 10.1038/s41467-020-15021-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Increased fidelity mutants of the SpCas9 nuclease constitute the most promising approach to mitigating its off-target effects. However, these variants are effective only in a restricted target space, and many of them are reported to work less efficiently when applied in clinically relevant, pre-assembled, ribonucleoprotein forms. The low tolerance to 5'-extended, 21G-sgRNAs contributes, to a great extent, to their decreased performance. Here, we report the generation of Blackjack SpCas9 variant that shows increased fidelity yet remain effective with 21G-sgRNAs. Introducing Blackjack mutations into previously reported increased fidelity variants make them effective with 21G-sgRNAs and increases their fidelity. Two "Blackjack" nucleases, eSpCas9-plus and SpCas9-HF1-plus are superior variants of eSpCas9 and SpCas9-HF1, respectively, possessing matching on-target activity and fidelity but retaining activity with 21G-sgRNAs. They facilitate the use of existing pooled sgRNA libraries with higher specificity and show similar activities whether delivered as plasmids or as pre-assembled ribonucleoproteins.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary.
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary
- Gene Design Ltd, Szeged, H-6726, Hungary
| | | | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
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156
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Guillen D, Schievelbein M, Patel K, Jose D, Ouellet J. A simple and affordable kinetic assay of nucleic acids with SYBR Gold gel staining. PLoS One 2020; 15:e0229527. [PMID: 32126098 PMCID: PMC7053750 DOI: 10.1371/journal.pone.0229527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/07/2020] [Indexed: 11/18/2022] Open
Abstract
Labeling substrates or products are paramount in determining enzymatic kinetic parameters. Several options are available; many laboratories use either radioactive or fluorescent labeling because of their high sensitivity. However, those methods have their own drawbacks such as half-life decay, expensive and hazardous. Here, we propose a novel, simple, economical and fast alternative to substrate labeling for studying the kinetics of nucleic acids: post-migration gel staining with SYBR Gold. Cleavage rates similar to the ones reported in the literature for the I-R3 DNA-cleaving DNA enzyme in the presence of zinc chloride are an indication of the quality of the new method. Moreover, the activity of the hammerhead ribozyme was also monitored by our method to illustrate its versatility. This labeling-free method has several advantages such as its ease of use as well as cost effective and versatility with both non-structured and structured RNAs or DNAs.
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Affiliation(s)
- Danielle Guillen
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Mika Schievelbein
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Kushkumar Patel
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Davis Jose
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
| | - Jonathan Ouellet
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey, United States of America
- * E-mail:
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157
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Feyrer H, Munteanu R, Baronti L, Petzold K. One-Pot Production of RNA in High Yield and Purity Through Cleaving Tandem Transcripts. Molecules 2020; 25:E1142. [PMID: 32143353 PMCID: PMC7179201 DOI: 10.3390/molecules25051142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/25/2020] [Accepted: 03/01/2020] [Indexed: 02/06/2023] Open
Abstract
There is an increasing demand for efficient and robust production of short RNA molecules in both pharmaceutics and research. A standard method is in vitro transcription by T7 RNA polymerase. This method is sequence-dependent on efficiency and is limited to products longer than ~12 nucleotides. Additionally, the native initiation sequence is required to achieve high yields, putting a strain on sequence variability. Deviations from this sequence can lead to side products, requiring laborious purification, further decreasing yield. We here present transcribing tandem repeats of the target RNA sequence followed by site-specific cleavage to obtain RNA in high purity and yield. This approach makes use of a plasmid DNA template and RNase H-directed cleavage of the transcript. The method is simpler and faster than previous protocols, as it can be performed as one pot synthesis and provides at the same time higher yields of RNA.
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Affiliation(s)
| | | | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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158
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Wu MZ, Asahara H, Tzertzinis G, Roy B. Synthesis of low immunogenicity RNA with high-temperature in vitro transcription. RNA (NEW YORK, N.Y.) 2020; 26:345-360. [PMID: 31900329 PMCID: PMC7025508 DOI: 10.1261/rna.073858.119] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/30/2019] [Indexed: 05/26/2023]
Abstract
The use of synthetic RNA for therapeutics requires that the in vitro synthesis process be robust and efficient. The technology used for the synthesis of these in vitro-transcribed RNAs, predominantly using phage RNA polymerases (RNAPs), is well established. However, transcripts synthesized with RNAPs are known to display an immune-stimulatory activity in vivo that is often undesirable. Previous studies have identified double-stranded RNA (dsRNA), a major by-product of the in vitro transcription (IVT) process, as a trigger of cellular immune responses. Here we describe the characterization of a high-temperature IVT process using thermostable T7 RNAPs to synthesize functional mRNAs that demonstrate reduced immunogenicity without the need for a post-synthesis purification step. We identify features that drive the production of two kinds of dsRNA by-products-one arising from 3' extension of the run-off product and one formed by the production of antisense RNAs-and demonstrate that at a high temperature, T7 RNAP has reduced 3'-extension of the run-off product. We show that template-encoded poly(A) tailing does not affect 3'-extension but reduces the formation of the antisense RNA by-products. Combining high-temperature IVT with template-encoded poly(A) tailing prevents the formation of both kinds of dsRNA by-products generating functional mRNAs with reduced immunogenicity.
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Affiliation(s)
- Monica Z Wu
- RNA and Genome Editing, New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Haruichi Asahara
- RNA and Genome Editing, New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - George Tzertzinis
- RNA and Genome Editing, New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Bijoyita Roy
- RNA and Genome Editing, New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
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159
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Chan CW, Badong D, Rajan R, Mondragón A. Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs. RNA (NEW YORK, N.Y.) 2020; 26:278-289. [PMID: 31848215 PMCID: PMC7025506 DOI: 10.1261/rna.073478.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem-loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.
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Affiliation(s)
- Clarence W Chan
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Deanna Badong
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
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160
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Yu AM, Batra N, Tu MJ, Sweeney C. Novel approaches for efficient in vivo fermentation production of noncoding RNAs. Appl Microbiol Biotechnol 2020; 104:1927-1937. [PMID: 31953559 PMCID: PMC7385725 DOI: 10.1007/s00253-020-10350-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 01/07/2023]
Abstract
Genome-derived noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), play an essential role in the control of target gene expression underlying various cellular processes, and dysregulation of ncRNAs is involved in the pathogenesis and progression of various diseases in virtually all species including humans. Understanding ncRNA biology has opened new avenues to develop novel RNA-based therapeutics. Presently, ncRNA research and drug development is dominated by the use of ncRNA mimics that are synthesized chemically in vitro and supplemented with extensive and various types of artificial modifications and thus may not necessarily recapitulate the properties of natural RNAs generated and folded in living cells in vivo. Therefore, there are growing interests in developing novel technologies for in vivo production of RNA molecules. The two most recent major breakthroughs in achieving an efficient, large-scale, and cost-effective fermentation production of recombinant or bioengineered RNAs (e.g., tens of milligrams from 1 L of bacterial culture) are (1) using stable RNA carriers and (2) direct overexpression in RNase III-deficient bacteria, while other approaches offer a low yield (e.g., nano- to microgram scales per liter). In this article, we highlight these novel microbial fermentation-based technologies that have shifted the paradigm to the production of true biological ncRNA molecules for research and development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA.
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
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161
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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162
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Hegelein A, Müller D, Größl S, Göbel M, Hengesbach M, Schwalbe H. Genetic Code Expansion Facilitates Position-Selective Labeling of RNA for Biophysical Studies. Chemistry 2020; 26:1800-1810. [PMID: 31692134 PMCID: PMC7027469 DOI: 10.1002/chem.201904623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Indexed: 12/13/2022]
Abstract
Nature relies on reading and synthesizing the genetic code with high fidelity. Nucleic acid building blocks that are orthogonal to the canonical A-T and G-C base-pairs are therefore uniquely suitable to facilitate position-specific labeling of nucleic acids. Here, we employ the orthogonal kappa-xanthosine-base-pair for in vitro transcription of labeled RNA. We devised an improved synthetic route to obtain the phosphoramidite of the deoxy-version of the kappa nucleoside in solid phase synthesis. From this DNA template, we demonstrate the reliable incorporation of xanthosine during in vitro transcription. Using NMR spectroscopy, we show that xanthosine introduces only minor structural changes in an RNA helix. We furthermore synthesized a clickable 7-deaza-xanthosine, which allows to site-specifically modify transcribed RNA molecules with fluorophores or other labels.
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Affiliation(s)
- Andreas Hegelein
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Sylvester Größl
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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163
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Jackson NAC, Kester KE, Casimiro D, Gurunathan S, DeRosa F. The promise of mRNA vaccines: a biotech and industrial perspective. NPJ Vaccines 2020; 5:11. [PMID: 32047656 PMCID: PMC7000814 DOI: 10.1038/s41541-020-0159-8] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
mRNA technologies have the potential to transform areas of medicine, including the prophylaxis of infectious diseases. The advantages for vaccines range from the acceleration of immunogen discovery to rapid response and multiple disease target manufacturing. A greater understanding of quality attributes that dictate translation efficiency, as well as a comprehensive appreciation of the importance of mRNA delivery, are influencing a new era of investment in development activities. The application of translational sciences and growing early-phase clinical experience continue to inform candidate vaccine selection. Here we review the state of the art for the prevention of infectious diseases by using mRNA and pertinent topics to the biotechnology and pharmaceutical industries.
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Affiliation(s)
- Nicholas A. C. Jackson
- Coalition for Epidemic Preparedness Innovations (CEPI), Gibbs building, 215 Euston Road, Bloomsbury, London, NW1 2BE UK
| | - Kent E. Kester
- Sanofi Pasteur, 1 Discovery Dr, Swiftwater, PA 18370 USA
| | | | | | - Frank DeRosa
- Translate Bio, 29 Hartwell Ave, Lexington, MA 02421 USA
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164
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Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies. Methods Mol Biol 2020. [PMID: 32006317 DOI: 10.1007/978-1-0716-0278-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many RNA architectures were discovered to be involved in essential biological pathways acting as catalysts and/or regulators of gene expression, transcription, translation, splicing, or viral infection. The key to understand their diverse biological functions is to investigate their structure and dynamic. Nuclear Magnetic Resonance (NMR) is a powerful method to gain insight into these properties. However, the study of high-molecular-weight RNAs by NMR remains challenging. Advances in biochemical and NMR methods over the recent years allow to overcome the limitation of NMR. In particular, the incorporation of paramagnetic probes, coupled to the measurement of the induced effects on nuclear spins, has become an efficient tool providing long-range distance restraints and information on dynamic in solution. At the same time, the use of spin label enabled the application of Electron Paramagnetic Resonance (EPR) to study biological macromolecules. Combining NMR and EPR is emerging as a new approach to investigate the architecture of biological systems.Here, we describe an efficient protocol to introduce a paramagnetic probe into a RNA at a specific position. This method enables various combinations of isotopic labeling for NMR and is also of interest for EPR studies.
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165
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Abstract
Virtually all in vitro transcription of DNA into RNA is performed with bacteriophage-encoded DNA-dependent RNA polymerases. These enzymes and their characteristics are introduced here.
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166
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Lapinaite A, Carlomagno T, Gabel F. Small-Angle Neutron Scattering of RNA-Protein Complexes. Methods Mol Biol 2020; 2113:165-188. [PMID: 32006315 DOI: 10.1007/978-1-0716-0278-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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167
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Welty R, Rau M, Pabit S, Dunstan MS, Conn GL, Pollack L, Hall KB. Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain. J Mol Biol 2019; 432:991-1007. [PMID: 31874150 DOI: 10.1016/j.jmb.2019.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/14/2023]
Abstract
The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg2+-dependent folded states, which we suggest lie along the folding pathway of the RNA. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael Rau
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, Clark Hall, Ithaca, NY, 14853, USA
| | - Mark S Dunstan
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta GA, 30322, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Clark Hall, Ithaca, NY, 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA.
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168
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Promoter Length Affects the Initiation of T7 RNA Polymerase In Vitro: New Insights into Promoter/Polymerase Co-evolution. J Mol Evol 2019; 88:179-193. [PMID: 31863129 DOI: 10.1007/s00239-019-09922-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
Polymerases are integral factors of gene expression and are essential for the maintenance and transmission of genetic information. RNA polymerases (RNAPs) differ from other polymerases in that they can bind promoter sequences and initiate transcription de novo and this promoter recognition requires the presence of specific DNA binding domains in the polymerase. Bacteriophage T7 RNA polymerase (T7RNAP) is the prototype for single subunit RNA polymerases which include bacteriophage and mitochondrial RNAPs, and the structure and mechanistic aspects of transcription by T7 RNAP are well characterized. Here, we describe experiments to determine whether the prototype T7 RNAP is able to recognize and initiate at truncated promoters similar to mitochondrial promoters. Using an in vitro oligonucleotide transcriptional system, we have assayed transcription initiation activity by T7 RNAP. These assays have not only defined the limits of conventional de novo initiation on truncated promoters, but have identified novel activities of initiation of RNA synthesis. We propose that these novel activities may be vestigial activities surviving from the transition of single subunit polymerase initiation using primers to de novo initiation using promoters.
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169
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Parsonnet NV, Lammer NC, Holmes ZE, Batey RT, Wuttke DS. The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity. Nucleic Acids Res 2019; 47:8180-8192. [PMID: 31147715 DOI: 10.1093/nar/gkz486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 01/04/2023] Open
Abstract
The glucocorticoid receptor (GR) binds the noncoding RNA Gas5 via its DNA-binding domain (DBD) with functional implications in pro-apoptosis signaling. Here, we report a comprehensive in vitro binding study where we have determined that GR-DBD is a robust structure-specific RNA-binding domain. GR-DBD binds to a diverse range of RNA hairpin motifs, both synthetic and biologically derived, with apparent mid-nanomolar affinity while discriminating against uniform dsRNA. As opposed to dimeric recognition of dsDNA, GR-DBD binds to RNA as a monomer and confers high affinity primarily through electrostatic contacts. GR-DBD adopts a discrete RNA-bound state, as assessed by NMR, distinct from both free and DNA-bound. NMR and alanine mutagenesis suggest a heightened involvement of the C-terminal α-helix of the GR-DBD in RNA-binding. RNA competes for binding with dsDNA and occurs in a similar affinity range as dimer binding to the canonical DNA element. Given the prevalence of RNA hairpins within the transcriptome, our findings strongly suggest that many RNAs have potential to impact GR biology.
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Affiliation(s)
- Nicholas V Parsonnet
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Nickolaus C Lammer
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Zachariah E Holmes
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
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170
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Liu X, Shen S, Wu P, Li F, Liu X, Wang C, Gong Q, Wu J, Yao X, Zhang H, Shi Y. Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. Nucleic Acids Res 2019; 47:7648-7665. [PMID: 31251801 PMCID: PMC6698656 DOI: 10.1093/nar/gkz505] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/16/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Mitochondria are essential molecular machinery for the maintenance of cellular energy supply by the oxidative phosphorylation system (OXPHOS). Mitochondrial transcription factor B1 (TFB1M) is a dimethyltransferase that maintains mitochondrial homeostasis by catalyzing dimethylation of two adjacent adenines located in helix45 (h45) of 12S rRNA. This m62A modification is indispensable for the assembly and maturation of human mitochondrial ribosomes. However, both the mechanism of TFB1M catalysis and the precise function of TFB1M in mitochondrial homeostasis are unknown. Here we report the crystal structures of a ternary complex of human (hs) TFB1M–h45–S-adenosyl-methionine and a binary complex hsTFB1M–h45. The structures revealed a distinct mode of hsTFB1M interaction with its rRNA substrate and with the initial enzymatic state involved in m62A modification. The suppression of hsTFB1M protein level or the overexpression of inactive hsTFB1M mutants resulted in decreased ATP production and reduced expression of components of the mitochondrial OXPHOS without affecting transcription of the corresponding genes and their localization to the mitochondria. Therefore, hsTFB1M regulated the translation of mitochondrial genes rather than their transcription via m62A modification in h45.
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Affiliation(s)
- Xiaodan Liu
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Shengqi Shen
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Pengzhi Wu
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Fudong Li
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Xing Liu
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Chongyuan Wang
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Qingguo Gong
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Jihui Wu
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Xuebiao Yao
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Huafeng Zhang
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
| | - Yunyu Shi
- School of Life Sciences, University of Science & Technology of China, Hefei 230027, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei 230027, China
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171
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Gholamalipour Y, Johnson WC, Martin CT. Efficient inhibition of RNA self-primed extension by addition of competing 3'-capture DNA-improved RNA synthesis by T7 RNA polymerase. Nucleic Acids Res 2019; 47:e118. [PMID: 31392994 PMCID: PMC6821179 DOI: 10.1093/nar/gkz700] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
In vitro synthesized RNA is used widely in studies of RNA biology, biotechnology and RNA therapeutics. However, in vitro synthesized RNA often contains impurities, such as RNAs with lengths shorter and longer than the expected runoff RNA. We have recently confirmed that longer RNA products are formed predominantly via cis self-primed extension, in which released runoff RNA folds back on itself to prime its own RNA-templated extension. In the current work, we demonstrate that addition of a DNA oligonucleotide (capture DNA) that is complementary to the 3′ end of the expected runoff RNA effectively prevents self-primed extension, even under conditions commonly used for high RNA yields. Moreover, the presence of this competing capture DNA during ‘high yield’ transcription, leads to an increase in the yield of expected runoff RNA by suppressing the formation of undesired longer RNA byproducts.
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Affiliation(s)
- Yasaman Gholamalipour
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - William C Johnson
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Craig T Martin
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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172
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PCR-based reverse genetics strategy for bluetongue virus recovery. Virol J 2019; 16:151. [PMID: 31805959 PMCID: PMC6896262 DOI: 10.1186/s12985-019-1261-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 11/28/2019] [Indexed: 11/21/2022] Open
Abstract
Background Bluetongue virus (BTV), an emerging insect vector mediated pathogen affecting both wild ruminants and livestock, has a genome consisting of 10 linear double-stranded RNA genome segments. BTV has a severe economic impact on agriculture in many parts of the world. Current reverse genetics (RG) strategy to rescue BTV mainly rely on in vitro synthesis of RNA transcripts from cloned complimentary DNA (cDNA) corresponding to viral genome segments with the aid of helper plasmids. RNA synthesis is a laborious job which is further complicated with a need for expensive reagents and a meticulous operational procedure. Additionally, the target genes must be cloned into a specific vector to prepare templates for RNA transcription. Result In this study, we have developed a PCR based BTV RG system with easy two-step transfection. Viable viruses were recovered following a first transfection with the seven helper plasmids and a second transfection with the 10 PCR products on the BSR cells. Further, recovered viruses were characterized with indirect immunofluorescence assays (IFA) and gene sequencing. And the proliferation properties of these viruses were also compared with wild type BTV. Interestingly, we have identified that viruses containing the segment 2 of the genome from reassortant BTV, grew slightly slower than the others. Conclusion In this study, a convenient PCR based RG platform for BTV is established, and this strategy could be an effective alternative to the original available BTV rescue methods. Furthermore, this RG strategy is likely applicable for other Orbiviruses.
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173
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Takakura M, Ishiguro K, Akichika S, Miyauchi K, Suzuki T. Biogenesis and functions of aminocarboxypropyluridine in tRNA. Nat Commun 2019; 10:5542. [PMID: 31804502 PMCID: PMC6895100 DOI: 10.1038/s41467-019-13525-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
Transfer (t)RNAs contain a wide variety of post-transcriptional modifications, which play critical roles in tRNA stability and functions. 3-(3-amino-3-carboxypropyl)uridine (acp3U) is a highly conserved modification found in variable- and D-loops of tRNAs. Biogenesis and functions of acp3U have not been extensively investigated. Using a reverse-genetic approach supported by comparative genomics, we find here that the Escherichia coli yfiP gene, which we rename tapT (tRNA aminocarboxypropyltransferase), is responsible for acp3U formation in tRNA. Recombinant TapT synthesizes acp3U at position 47 of tRNAs in the presence of S-adenosylmethionine. Biochemical experiments reveal that acp3U47 confers thermal stability on tRNA. Curiously, the ΔtapT strain exhibits genome instability under continuous heat stress. We also find that the human homologs of tapT, DTWD1 and DTWD2, are responsible for acp3U formation at positions 20 and 20a of tRNAs, respectively. Double knockout cells of DTWD1 and DTWD2 exhibit growth retardation, indicating that acp3U is physiologically important in mammals.
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Affiliation(s)
- Mayuko Takakura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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174
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Korniy N, Goyal A, Hoffmann M, Samatova E, Peske F, Pöhlmann S, Rodnina MV. Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance. Nucleic Acids Res 2019; 47:5210-5222. [PMID: 30968122 PMCID: PMC6547452 DOI: 10.1093/nar/gkz202] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/12/2019] [Accepted: 04/08/2019] [Indexed: 12/16/2022] Open
Abstract
A hallmark of translation in human immunodeficiency virus type 1 (HIV-1) is a –1 programmed ribosome frameshifting event that produces the Gag-Pol fusion polyprotein. The constant Gag to Gag-Pol ratio is essential for the virion structure and infectivity. Here we show that the frameshifting efficiency is modulated by Leu-tRNALeu that reads the UUA codon at the mRNA slippery site. This tRNALeu isoacceptor is particularly rare in human cell lines derived from T-lymphocytes, the cells that are targeted by HIV-1. When UUA decoding is delayed, the frameshifting follows an alternative route, which maintains the Gag to Gag-Pol ratio constant. A second potential slippery site downstream of the first one is normally inefficient but can also support –1-frameshifting when altered by a compensatory resistance mutation in response to current antiviral drug therapy. Together these different regimes allow the virus to maintain a constant –1-frameshifting efficiency to ensure successful virus propagation.
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Affiliation(s)
- Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Akanksha Goyal
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.,Faculty of Biology and Psychology, University of Göttingen, Wilhelm-Weber-Str. 2, 37073 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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175
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Identification of a radical SAM enzyme involved in the synthesis of archaeosine. Nat Chem Biol 2019; 15:1148-1155. [DOI: 10.1038/s41589-019-0390-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/16/2019] [Indexed: 01/27/2023]
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176
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Kanwal F, Chen T, Zhang Y, Simair A, Lu C. A Modified In Vitro Transcription Approach to Improve RNA Synthesis and Ribozyme Cleavage Efficiency. Mol Biotechnol 2019; 61:469-476. [PMID: 30868354 DOI: 10.1007/s12033-019-00167-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA elements such as catalytic RNA, riboswitch, microRNA, and long non-coding RNA perform a major role in cellular processes. A complete understanding of cellular processes is impossible without knowing the structure-function relationship of participating RNA molecules that ultimately requires large quantities of pure RNAs. Thus, structural/functional analyses of emerging RNAs necessitate revised protocols for improved RNA quantity and quality. Here we present a modified in vitro transcription protocol to enhance ribozyme cleaving efficiency and RNA yield by working on two variables, i.e., incubation temperature and limiting GTPs. Following an improved RNA synthesis, the target RNA is purified from transcription mixture components through denaturing size-exclusion chromatography. The protocol confirms that cyclic elevated incubation temperatures during transcription and increased concentrations of GTPs improve the production rate of RNA. Our modified in vitro transcription method improves the ribozyme cleaving efficiency and targets RNA yield by four- to fivefold that can benefit almost any RNA-related study from protein-RNA interaction analysis to crystallography.
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Affiliation(s)
- Fariha Kanwal
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Ting Chen
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Yunlong Zhang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Altaf Simair
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China.
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177
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Lu X, Wu H, Xia H, Huang F, Yan Y, Yu B, Cheng R, Drulis-Kawa Z, Zhu B. Klebsiella Phage KP34 RNA Polymerase and Its Use in RNA Synthesis. Front Microbiol 2019; 10:2487. [PMID: 31736920 PMCID: PMC6834552 DOI: 10.3389/fmicb.2019.02487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/15/2019] [Indexed: 11/28/2022] Open
Abstract
We have characterized the single subunit RNA polymerase from Klebsiella phage KP34. The enzyme is unique among known bacteriophage RNA polymerases in that it recognizes two unrelated promoter sequences, which provided clues for the evolution of phage single-subunit RNA polymerases. As the first representative enzyme from the “phiKMV-like viruses” cluster, its use in run-off RNA synthesis was investigated. RNA-Seq analysis revealed that the KP34 RNA polymerase does not possess the undesired self-templated RNA terminus extension known for T7 RNA polymerase and is suitable to synthesize RNAs with structured 3′ termini such as sgRNAs. A KP34 RNA polymerase Y603F mutant is engineered to incorporate deoxy- and 2′-fluoro ribonucleotide into RNA.
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Affiliation(s)
- Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Xia
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Sciences and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
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178
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Wu JM, Zheng RE, Zhang RJ, Ji JL, Yu XP, Xu YP. A Clip Domain Serine Protease Involved in Egg Production in Nilaparvata lugens: Expression Patterns and RNA Interference. INSECTS 2019; 10:insects10110378. [PMID: 31671577 PMCID: PMC6920836 DOI: 10.3390/insects10110378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/30/2022]
Abstract
Clip domain serine proteases play vital roles in various innate immune functions and in embryonic development. Nilaparvata lugens proclotting enzymes (NlPCEs) belong to this protease family. NlPCE1 was reported to be involved in innate immunity, whereas the role of other NlPCEs is unclear. In the present study, N. lugens proclotting enzyme-3 (NlPCE3) was cloned and characterized. NlPCE3 contains a signal peptide, a clip domain, and a trypsin-like serine protease domain. NlPCE3 was expressed in all tissues examined (gut, fat body, and ovary), and at all developmental stages. Immunofluorescence staining showed that NlPCE3 was mainly expressed in the cytoplasm and cytomembrane of follicular cells. Double stranded NlPCE3 RNA interference clearly inhibited the expression of NlPCE3, resulting in abnormal egg formation and obstruction of ovulation. These results indicate that NlPCE3 plays an important role in egg production in N. lugens.
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Affiliation(s)
- Jia-Min Wu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
| | - Rong-Er Zheng
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
| | - Rui-Juan Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
| | - Jin-Liang Ji
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
| | - Yi-Peng Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China.
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179
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Higuchi-Takeuchi M, Numata K. Marine Purple Photosynthetic Bacteria as Sustainable Microbial Production Hosts. Front Bioeng Biotechnol 2019; 7:258. [PMID: 31681740 PMCID: PMC6798066 DOI: 10.3389/fbioe.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/25/2019] [Indexed: 12/01/2022] Open
Abstract
Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.
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Affiliation(s)
- Mieko Higuchi-Takeuchi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan
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180
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Thermodynamic control of -1 programmed ribosomal frameshifting. Nat Commun 2019; 10:4598. [PMID: 31601802 PMCID: PMC6787027 DOI: 10.1038/s41467-019-12648-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Abstract
mRNA contexts containing a 'slippery' sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the -1 reading frame. In this study we build a thermodynamic model based on Bayesian statistics to explain how -1 programmed ribosome frameshifting can work. As training sets for the model, we measured frameshifting efficiencies on 64 dnaX mRNA sequence variants in vitro and also used 21 published in vivo efficiencies. With the obtained free-energy difference between mRNA-tRNA base pairs in the 0 and -1 frames, the frameshifting efficiency of a given sequence can be reproduced and predicted from the tRNA-mRNA base pairing in the two frames. Our results further explain how modifications in the tRNA anticodon modulate frameshifting and show how the ribosome tunes the strength of the base-pair interactions.
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181
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Kelly EK, Czekay DP, Kothe U. Base-pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar ribonucleoproteins. RNA (NEW YORK, N.Y.) 2019; 25:1393-1404. [PMID: 31311819 PMCID: PMC6800473 DOI: 10.1261/rna.071043.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/11/2019] [Indexed: 05/04/2023]
Abstract
H/ACA small nucleolar ribonucleoproteins (snoRNPs) pseudouridylate RNA in eukaryotes and archaea. They target many RNAs site-specifically through base-pairing interactions between H/ACA guide and substrate RNA. Besides ribosomal RNA (rRNA) and small nuclear RNA (snRNA), H/ACA snoRNPs are thought to also modify messenger RNA (mRNA) with potential impacts on gene expression. However, the base pairing between known target RNAs and H/ACA guide RNAs varies widely in nature, and therefore the rules governing substrate RNA selection are still not fully understood. To provide quantitative insight into substrate RNA recognition, we systematically altered the sequence of a substrate RNA target by the Saccharomyces cerevisiae H/ACA guide RNA snR34. Time courses measuring pseudouridine formation revealed a gradual decrease in the initial velocity of pseudouridylation upon reducing the number of base pairs between substrate and guide RNA. Changing or inserting nucleotides close to the target uridine severely impairs pseudouridine formation. Interestingly, filter binding experiments show that all substrate RNA variants bind to H/ACA snoRNPs with nanomolar affinity. Next, we showed that binding of inactive, near-cognate RNAs to H/ACA snoRNPs does not inhibit their activity for cognate RNAs, presumably because near-cognate RNAs dissociate rapidly. We discuss that the modulation of initial velocities by the base-pairing strength might affect the order and efficiency of pseudouridylation in rRNA during ribosome biogenesis. Moreover, the binding of H/ACA snoRNPs to near-cognate RNAs may be a mechanism to search for cognate target sites. Together, our data provide critical information to aid in the prediction of productive H/ACA guide-substrate RNA pairs.
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Affiliation(s)
- Erin K Kelly
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Dominic P Czekay
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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182
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RNA-based therapy for osteogenesis. Int J Pharm 2019; 569:118594. [DOI: 10.1016/j.ijpharm.2019.118594] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 02/06/2023]
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183
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Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy. Molecules 2019; 24:molecules24193476. [PMID: 31557861 PMCID: PMC6804060 DOI: 10.3390/molecules24193476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 02/05/2023] Open
Abstract
RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.
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184
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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185
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Schaffter SW, Schulman R. Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules. Nat Chem 2019; 11:829-838. [PMID: 31427767 DOI: 10.1038/s41557-019-0292-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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186
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Wang Q, Zhang D, Guan Z, Li D, Pei K, Liu J, Zou T, Yin P. DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli. Nucleic Acids Res 2019; 46:6880-6892. [PMID: 29931175 PMCID: PMC6061791 DOI: 10.1093/nar/gky528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/28/2018] [Indexed: 11/30/2022] Open
Abstract
mRNA decay is an important strategy by which bacteria can rapidly adapt to their ever-changing surroundings. The 5′-terminus state of mRNA determines the velocity of decay of many types of RNA. In Escherichia coli, RNA pyrophosphohydrolase (RppH) is responsible for the removal of the 5′-terminal triphosphate from hundreds of mRNAs and triggers its rapid degradation by ribonucleases. A diaminopimelate epimerase, DapF, can directly interact with RppH and stimulate its hydrolysis activity in vivo and in vitro. However, the molecular mechanism remains to be elucidated. Here, we determined the complex structure of DapF–RppH as a heterotetramer in a 2:2 molar ratio. DapF-bound RppH exhibits an RNA-favorable conformation similar to the RNA-bound state, suggesting that association with DapF promotes and stabilizes RppH in a conformation that facilitates substrate RNA binding and thus stimulates the activity of RppH. To our knowledge, this is the first published structure of an RNA–pyrophosphohydrolysis complex in bacteria. Our study provides a framework for further investigation of the potential regulators involved in the RNA–pyrophosphohydrolysis process in prokaryotes.
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Affiliation(s)
- Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Pei
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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187
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Gholamalipour Y, Karunanayake Mudiyanselage A, Martin CT. 3' end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character-RNA-Seq analyses. Nucleic Acids Res 2019; 46:9253-9263. [PMID: 30219859 PMCID: PMC6182178 DOI: 10.1093/nar/gky796] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
Synthetic RNA is widely used in basic science, nanotechnology and therapeutics research. The vast majority of this RNA is synthesized in vitro by T7 RNA polymerase or one of its close family members. However, the desired RNA is generally contaminated with products longer and shorter than the DNA-encoded product. To better understand these undesired byproducts and the processes that generate them, we analyze in vitro transcription reactions using RNA-Seq as a tool. The results unambiguously confirm that product RNA rebinds to the polymerase and self-primes (in cis) generation of a hairpin duplex, a process that favorably competes with promoter driven synthesis under high yield reaction conditions. While certain priming modes can be favored, the process is heterogeneous, both in initial priming and in the extent of priming, and already extended products can rebind for further extension, in a distributive process. Furthermore, addition of one or a few nucleotides, previously termed 'nontemplated addition,' also occurs via templated primer extension. At last, this work demonstrates the utility of RNA-Seq as a tool for in vitro mechanistic studies, providing information far beyond that provided by traditional gel electrophoresis.
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Affiliation(s)
- Yasaman Gholamalipour
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | - Craig T Martin
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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188
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:a032359. [PMID: 31262947 PMCID: PMC6601463 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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189
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Zhao S, Xing Z, Liu Z, Liu Y, Liu X, Chen Z, Li J, Yan R. Efficient somatic and germline genome engineering of Bactrocera dorsalis by the CRISPR/Cas9 system. PEST MANAGEMENT SCIENCE 2019; 75:1921-1932. [PMID: 30565410 DOI: 10.1002/ps.5305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/31/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Bactrocera dorsalis (Hendel), a very destructive insect pest of many fruits and vegetables, is widespread in many Asian countries. To facilitate control of this pest, it is essential to investigate its genetics and gene function using targeted gene disruption. RESULTS Here, we describe successful targeted mutagenesis of the white and transformer genes in B. dorsalis through use of the clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) system. Co-injection of the white sgRNA and Cas9 mRNA into B. dorsalis embryos caused eye color change, and the white mutations in the germline were heritable. CRISPR-mediated knockout of the sex determination gene transformer (tra) in B. dorsalis resulted in a male-biased sex ratio and adult flies with abnormal outer and interior reproductive organs. Small indels and substitutions were induced by CRIRPR for both genes. CONCLUSION Our data demonstrate that somatic and germline genome engineering of the pest B. dorsalis can be performed efficiently using the CRISPR/Cas9 system, opening the door to the use of the CRISPR-mediated method for functional annotations of genes in B. dorsalis and for its population control using, for example, such as gene drive. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Santao Zhao
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Zengzhu Xing
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Zhonggeng Liu
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Yanhui Liu
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Xiangrui Liu
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Zhe Chen
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Jiahui Li
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Rihui Yan
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
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190
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Aufdembrink LM, Hoog TG, Pawlak MR, Bachan BF, Heili JM, Engelhart AE. Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes. Methods Enzymol 2019; 623:23-43. [PMID: 31239049 DOI: 10.1016/bs.mie.2019.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Thermal denaturation is a common technique in the biophysical study of nucleic acids. These experiments are typically performed by monitoring the increase in absorbance (hyperchromism) of a sample at 260nm with temperature (Mergny & Lacroix, 2003; Puglisi & Tinoco, 1989). This wavelength is chosen as nucleic acids of mixed sequence typically exhibit their maximum absorbance here. Exceptions exist, however, some noncanonical nucleic acid structures exhibit differing spectral changes with temperature, resulting in other wavelengths being convenient reporters of secondary structure. In the case of nucleic acids that bind visible light-absorbing ligands, such as fluorogenic aptamers, another wavelength can be a convenient reporter of secondary structure stability and RNA-ligand recognition. As it can be difficult, if not impossible, to know which wavelength to employ a priori, we have developed a system for obtaining the full UV-visible spectrum of a sample at each wavelength, allowing for the subsequent extraction of the absorbance-temperature profile at the desired wavelength. Here, we describe the apparatus and software used to do so. We also describe another technique for the use of a qPCR instrument for measuring secondary structure stability of fluorescent nucleic acid-ligand complexes.
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Affiliation(s)
- Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Tanner G Hoog
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Matthew R Pawlak
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Benjamin F Bachan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Joseph M Heili
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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191
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Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
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192
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Abstract
RNA is a functionally rich and diverse biomaterial responsible for regulating several cellular processes. This functionality has been harnessed to build predominately small nanoscale structures for drug delivery and the treatment of disease. The understanding of design principles to build large RNA structures will allow for further control of stoichiometry and spatial arrangement drugs and ligands. We present the design and characterization of RNA nanotubes that self-assemble from programmable monomers, or tiles, formed by five distinct RNA strands. Tiles include double crossover junctions and assemble via single-stranded sticky-end domains. We find that nanotube formation is dependent on the intertile crossover distance. The average length observed for the annealed RNA nanotubes is ≈1.5 μm, with many nanotubes exceeding 10 μm, enabling the characterization of RNA nanotubes length distribution via fluorescence microscopy. Assembled tubes were observed to be stable for more than 24 h, however post-annealing growth under isothermal conditions does not occur. Nanotubes assemble also from RNA tiles modified to include a single-stranded overhang (toehold), suggesting that it may be possible to decorate these large RNA scaffolds with nanoparticles or other nucleic acid molecules.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering , University of California at Riverside , Riverside , California 92521 , United States
| | - Cody Geary
- Department of Bioengineering , California Institute of Technology , Pasadena , California 91125 , United States
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus C 08000 , Denmark
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 92521 , United States
- Department of Mechanical and Aerospace Engineering , University of California , Los Angeles , California 90095 , United States
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193
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Abstract
Here we have directly visualized conformational changes in the 5′UTR of the HIV-1 genome using single-molecule fluorescence techniques. We find that the monomeric 5′UTR can spontaneously transition between two conformations, which have distinct intramolecular base pairing. One of the observed conformations is competent for dimerization with a second 5′UTR molecule. Our results are consistent with a model in which dimerization initiates by way of localized intermolecular kissing-loop base pairing, which is promoted by tRNA primer annealing. The intermolecular interface then extends, giving rise to the putative extended dimer, which is stabilized by HIV-1 NC. Thus, the 5′UTR is intrinsically dynamic, and both viral and host factors play a role in modulating the RNA conformation and dynamics. The highly conserved 5′ untranslated region (5′UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5′UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed. According to this model the conformation of the 5′UTR determines the fate of the genome. In this work, the dynamics of this proposed conformational switch and the factors that regulate it were probed using multiple single-molecule and in-gel ensemble FRET assays. Our results show that the HIV-1 5′UTR intrinsically samples conformations that are stabilized by both viral and host factor binding. Annealing of tRNALys3, the primer for initiation of reverse transcription, can promote the kissing dimer but not the extended dimer. In contrast, HIV-1 nucleocapsid (NC) promotes formation of the extended dimer in both the absence and presence of tRNALys3. Our data are consistent with an ordered series of events that involves primer annealing, genome dimerization, and virion assembly.
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194
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Roura Frigolé H, Camacho N, Castellví Coma M, Fernández-Lozano C, García-Lema J, Rafels-Ybern À, Canals A, Coll M, Ribas de Pouplana L. tRNA deamination by ADAT requires substrate-specific recognition mechanisms and can be inhibited by tRFs. RNA (NEW YORK, N.Y.) 2019; 25:607-619. [PMID: 30737359 PMCID: PMC6467012 DOI: 10.1261/rna.068189.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/28/2019] [Indexed: 05/30/2023]
Abstract
Adenosine deaminase acting on transfer RNA (ADAT) is an essential eukaryotic enzyme that catalyzes the deamination of adenosine to inosine at the first position of tRNA anticodons. Mammalian ADATs modify eight different tRNAs, having increased their substrate range from a bacterial ancestor that likely deaminated exclusively tRNAArg Here we investigate the recognition mechanisms of tRNAArg and tRNAAla by human ADAT to shed light on the process of substrate expansion that took place during the evolution of the enzyme. We show that tRNA recognition by human ADAT does not depend on conserved identity elements, but on the overall structural features of tRNA. We find that ancestral-like interactions are conserved for tRNAArg, while eukaryote-specific substrates use alternative mechanisms. These recognition studies show that human ADAT can be inhibited by tRNA fragments in vitro, including naturally occurring fragments involved in important regulatory pathways.
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MESH Headings
- Adenosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Deamination
- Evolution, Molecular
- Gene Expression
- Humans
- Inosine/metabolism
- Nucleic Acid Conformation
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- Sequence Alignment
- Substrate Specificity
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Affiliation(s)
- Helena Roura Frigolé
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Maria Castellví Coma
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Carla Fernández-Lozano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Jorge García-Lema
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - Albert Canals
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Catalonia, Spain
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195
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A review on native and denaturing purification methods for non-coding RNA (ncRNA). J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:71-79. [PMID: 31071581 DOI: 10.1016/j.jchromb.2019.04.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.
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196
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Dai Y, Peralta AN, Wynn JE, Sherpa C, Li H, Verma A, Le Grice SFJ, Santos WL. Molecular recognition of a branched peptide with HIV-1 Rev Response Element (RRE) RNA. Bioorg Med Chem 2019; 27:1759-1765. [PMID: 30879859 PMCID: PMC6476629 DOI: 10.1016/j.bmc.2019.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/27/2023]
Abstract
Interaction of HIV-1 rev response element (RRE) RNA with its cognate protein, Rev, is critical for HIV-1 replication. Understanding the mode of interaction between RRE RNA and ligands at the binding site can facilitate RNA molecular recognition as well as provide a strategy for developing anti-HIV therapeutics. Our approach utilizes branched peptides as a scaffold for multivalent binding to RRE IIB (high affinity rev binding site) with incorporation of unnatural amino acids to increase affinity via non-canonical interactions with the RNA. Previous high throughput screening of a 46,656-member library revealed several hits that bound RRE IIB RNA in the sub-micromolar range. In particular, the lead compound, 4B3, displayed a Kd value of 410 nM and demonstrated selectivity towards RRE. A ribonuclease protection assay revealed that 4B3 binds to the stem-loop structure of RRE IIB RNA, which was confirmed by SHAPE analysis with 234 nt long NL4-3 RRE RNA. Our studies further indicated interaction of 4B3 with both primary and secondary Rev binding sites.
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Affiliation(s)
- Yumin Dai
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Ashley N Peralta
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Hao Li
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Astha Verma
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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197
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Otsu M, Kawai G. Distinct RNA recognition mechanisms in closely related LINEs from zebrafish. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:294-304. [PMID: 30942141 DOI: 10.1080/15257770.2018.1527348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Long interspersed nuclear element (LINE) is known to be transposed by the reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. We focused on the RNA recognition by RT from two related LINEs, ZfL2-1 and ZfL2-2, from zebrafish. Previous study showed that RT from ZfL2-2 recognizes a single residue in the specific position of the RNA loop. In the present study, it was found that RT from ZfL2-1 recognizes the inserted stem-loop of ZfL2-1 RNA. Thus, these related RTs recognize the same region of LINE RNAs but discriminate them by different mechanism.
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Affiliation(s)
- Maina Otsu
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Japan
| | - Gota Kawai
- a Department of Life and Environmental Sciences, Faculty of Engineering , Chiba Institute of Technology , Narashino , Japan
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198
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Milisavljevič N, Perlíková P, Pohl R, Hocek M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org Biomol Chem 2019; 16:5800-5807. [PMID: 30063056 DOI: 10.1039/c8ob01498a] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We synthesized a small library of eighteen 5-substituted pyrimidine or 7-substituted 7-deazapurine nucleoside triphosphates bearing methyl, ethynyl, phenyl, benzofuryl or dibenzofuryl groups through cross-coupling reactions of nucleosides followed by triphosphorylation or through direct cross-coupling reactions of halogenated nucleoside triphosphates. We systematically studied the influence of the modification on the efficiency of T7 RNA polymerase catalyzed synthesis of modified RNA and found that modified ATP, UTP and CTP analogues bearing smaller modifications were good substrates and building blocks for the RNA synthesis even in difficult sequences incorporating multiple modified nucleotides. Bulky dibenzofuryl derivatives of ATP and GTP were not substrates for the RNA polymerase. In the case of modified GTP analogues, a modified procedure using a special promoter and GMP as initiator needed to be used to obtain efficient RNA synthesis. The T7 RNA polymerase synthesis of modified RNA can be very efficiently used for synthesis of modified RNA but the method has constraints in the sequence of the first three nucleotides of the transcript, which must contain a non-modified G in the +1 position.
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Affiliation(s)
- Nemanja Milisavljevič
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic.
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199
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Baiersdörfer M, Boros G, Muramatsu H, Mahiny A, Vlatkovic I, Sahin U, Karikó K. A Facile Method for the Removal of dsRNA Contaminant from In Vitro-Transcribed mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 15:26-35. [PMID: 30933724 PMCID: PMC6444222 DOI: 10.1016/j.omtn.2019.02.018] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 01/12/2023]
Abstract
The increasing importance of in vitro-transcribed (IVT) mRNA for synthesizing the encoded therapeutic protein in vivo demands the manufacturing of pure mRNA products. The major contaminant in the IVT mRNA is double-stranded RNA (dsRNA), a transcriptional by-product that can be removed only by burdensome procedure requiring special instrumentation and generating hazardous waste. Here we present an alternative simple, fast, and cost-effective method involving only standard laboratory techniques. The purification of IVT mRNA is based on the selective binding of dsRNA to cellulose in an ethanol-containing buffer. We demonstrate that at least 90% of the dsRNA contaminants can be removed with a good, >65% recovery rate, regardless of the length, coding sequence, and nucleoside composition of the IVT mRNA. The procedure is scalable; purification of microgram or milligram amounts of IVT mRNA is achievable. Evaluating the impact of the mRNA purification in vivo in mice, increased translation could be measured for the administered transcripts, including the 1-methylpseudouridine-containing IVT mRNA, which no longer induced interferon (IFN)-α. The cellulose-based removal of dsRNA contaminants is an effective, reliable, and safe method to obtain highly pure IVT mRNA suitable for in vivo applications.
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Affiliation(s)
| | - Gábor Boros
- BioNTech RNA Pharmaceuticals, 55131 Mainz, Germany
| | | | - Azita Mahiny
- BioNTech RNA Pharmaceuticals, 55131 Mainz, Germany
| | | | - Ugur Sahin
- BioNTech RNA Pharmaceuticals, 55131 Mainz, Germany
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200
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Van Hoecke L, Roose K. How mRNA therapeutics are entering the monoclonal antibody field. J Transl Med 2019; 17:54. [PMID: 30795778 PMCID: PMC6387507 DOI: 10.1186/s12967-019-1804-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/17/2019] [Indexed: 01/06/2023] Open
Abstract
In 1975, Milstein and Köhler revolutionized the medical world with the development of the hybridoma technique to produce monoclonal antibodies. Since then, monoclonal antibodies have entered almost every branch of biomedical research. Antibodies are now used as frontline therapeutics in highly divergent indications, ranging from autoimmune disease over allergic asthma to cancer. Wider accessibility and implementation of antibody-based therapeutics is however hindered by manufacturing challenges and high development costs inherent to protein-based drugs. For these reasons, alternative ways are being pursued to produce and deliver antibodies more cost-effectively without hampering safety. Over the past decade, messenger RNA (mRNA) based drugs have emerged as a highly appealing new class of biologics that can be used to encode any protein of interest directly in vivo. Whereas current clinical efforts to use mRNA as a drug are mainly situated at the level of prophylactic and therapeutic vaccination, three recent preclinical studies have addressed the feasibility of using mRNA to encode therapeutic antibodies directly in vivo. Here, we highlight the potential of mRNA-based approaches to solve several of the issues associated with antibodies produced and delivered in protein format. Nonetheless, we also identify key hurdles that mRNA-based approaches still need to take to fulfill this potential and ultimately replace the current protein antibody format.
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Affiliation(s)
- Lien Van Hoecke
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Kenny Roose
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium.,Departement of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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