1
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Lau MH, Madika A, Zhang Y, Minton NP. Parageobacillus thermoglucosidasius Strain Engineering Using a Theophylline Responsive RiboCas for Controlled Gene Expression. ACS Synth Biol 2024; 13:1237-1245. [PMID: 38517011 PMCID: PMC11036489 DOI: 10.1021/acssynbio.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The relentless increase in atmospheric greenhouse gas concentrations as a consequence of the exploitation of fossil resources compels the adoption of sustainable routes to chemical and fuel manufacture based on biological fermentation processes. The use of thermophilic chassis in such processes is an attractive proposition; however, their effective exploitation will require improved genome editing tools. In the case of the industrially relevant chassis Parageobacillus thermoglucosidasius, CRISPR/Cas9-based gene editing has been demonstrated. The constitutive promoter used, however, accentuates the deleterious nature of Cas9, causing decreased transformation and low editing efficiencies, together with an increased likelihood of off-target effects or alternative mutations. Here, we rectify this issue by controlling the expression of Cas9 through the use of a synthetic riboswitch that is dependent on the nonmetabolized, nontoxic, and cheap inducer, theophylline. We demonstrate that the riboswitches are dose-dependent, allowing for controlled expression of the target gene. Through their use, we were then able to address the deleterious nature of Cas9 and produce an inducible system, RiboCas93. The benefits of RiboCas93 were demonstrated by increased transformation efficiency of the editing vectors, improved efficiency in mutant generation (100%), and a reduction of Cas9 toxicity, as indicated by a reduction in the number of single nucleotide polymorphisms (SNPs) observed. This new system provides a quick and efficient way to produce mutants in P. thermoglucosidasius.
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Affiliation(s)
- Matthew
S. H. Lau
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Abubakar Madika
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- Department
of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Ying Zhang
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- NIHR
Nottingham Biomedical Research Centre, Nottingham
University Hospitals NHS Trust and The University of Nottingham, Nottingham NG7 2RD, U.K.
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2
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Kreckel HD, Samuels FMD, Bonnart R, Volk GM, Stich DG, Levinger NE. Tracking Permeation of Dimethyl Sulfoxide (DMSO) in Mentha × piperita Shoot Tips Using Coherent Raman Microscopy. PLANTS (BASEL, SWITZERLAND) 2023; 12:2247. [PMID: 37375873 DOI: 10.3390/plants12122247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
Cryopreservation has emerged as a low-maintenance, cost-effective solution for the long-term preservation of vegetatively propagated crops. Shoot tip cryopreservation often makes use of vitrification methods that employ highly concentrated mixtures of cryoprotecting agents; however, little is understood as to how these cryoprotecting agents protect cells and tissues from freezing. In this study, we use coherent anti-Stokes Raman scattering microscopy to directly visualize where dimethyl sulfoxide (DMSO) localizes within Mentha × piperita shoot tips. We find that DMSO fully penetrates the shoot tip tissue within 10 min of exposure. Variations in signal intensities across images suggest that DMSO may interact with cellular components, leading to its accumulation in specific regions.
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Affiliation(s)
- Heidi D Kreckel
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Fionna M D Samuels
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Remi Bonnart
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA
| | - Gayle M Volk
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA
| | - Dominik G Stich
- Advanced Light Microscopy Center, University of Colorado, Denver, CO 80045, USA
| | - Nancy E Levinger
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA
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3
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Xue T, Lu Y, Yang H, Hu X, Zhang K, Ren Y, Wu C, Xia X, Deng R, Wang Y. Isothermal RNA Amplification for the Detection of Viable Pathogenic Bacteria to Estimate the Salmonella Virulence for Causing Enteritis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1670-1678. [PMID: 35099949 DOI: 10.1021/acs.jafc.1c07182] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Viable foodborne pathogens can cause intestinal infection and food poisoning. Herein, we reported an RNA assay allowing for sensitive (close to 1 CFU and 1% viable bacteria detectable) and rapid (within 2.5 h) detection of viable pathogenic bacteria by coupling isothermal RNA amplification (nucleic acid sequence-based amplification, NASBA) with a CRISPR/Cas13a system. NASBA allowed direct amplification of 16S rRNA extracted from viable S. enterica (RNAs degrade rapidly in dead bacteria), and the specificity of amplification was ensured using Cas13a/crRNA to recognize the amplicons. We used the CRISPR/Cas13-based NASBA assay (termed cNASBA assay) to investigate the in vivo colonization and intestinal infection of S. enterica in mice. We found that S. enterica was mainly colonized at the cecum, colon, and rectum, and the severity of enteritis caused by S. enterica was determined by the number of viable S. enterica rather than the total count of S. enterica. The cNASBA assay can quantify viable S. enterica and thus can improve the accuracy of virulence estimation compared to qPCR. It shows promise as a reliable tool for monitoring pathogen contamination and biosafety control.
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Affiliation(s)
- Ting Xue
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Lu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xinyue Hu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Chengyong Wu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
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4
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Kawang K, Naoudom U, Kowitdamrong E, Kerr SJ, Ruxrungtham K, Nilaratanakul V. Sensitivity and specificity of anti-double-stranded RNA immunofluorescence for universal detection of viral infection in respiratory specimens. Heliyon 2021; 7:e08471. [PMID: 34977399 PMCID: PMC8689082 DOI: 10.1016/j.heliyon.2021.e08471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022] Open
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5
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Liu Z, Wang S, Tapeinos C, Torrieri G, Känkänen V, El-Sayed N, Python A, Hirvonen JT, Santos HA. Non-viral nanoparticles for RNA interference: Principles of design and practical guidelines. Adv Drug Deliv Rev 2021; 174:576-612. [PMID: 34019958 DOI: 10.1016/j.addr.2021.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/15/2021] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid interference (RNAi) is an innovative treatment strategy for a myriad of indications. Non-viral synthetic nanoparticles (NPs) have drawn extensive attention as vectors for RNAi due to their potential advantages, including improved safety, high delivery efficiency and economic feasibility. However, the complex natural process of RNAi and the susceptible nature of oligonucleotides render the NPs subject to particular design principles and requirements for practical fabrication. Here, we summarize the requirements and obstacles for fabricating non-viral nano-vectors for efficient RNAi. To address the delivery challenges, we discuss practical guidelines for materials selection and NP synthesis in order to maximize RNA encapsulation efficiency and protection against degradation, and to facilitate the cytosolic release of oligonucleotides. The current status of clinical translation of RNAi-based therapies and further perspectives for reducing the potential side effects are also reviewed.
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Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol 2020; 11:845-859. [PMID: 31336384 PMCID: PMC6917512 DOI: 10.1093/jmcb/mjz086] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
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7
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Zhu C, Varona M, Anderson JL. Magnetic Ionic Liquids as Solvents for RNA Extraction and Preservation. ACS OMEGA 2020; 5:11151-11159. [PMID: 32455238 PMCID: PMC7241037 DOI: 10.1021/acsomega.0c01098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/23/2020] [Indexed: 05/24/2023]
Abstract
Ribonucleic acid (RNA) is particularly sensitive to enzymatic degradation by endonucleases prior to sample analysis. In-field preservation has been a challenge for RNA sample preparation. Very recently, hydrophobic magnetic ionic liquids (MIL) have shown significant promise in the area of RNA extraction. In this study, MILs were synthesized and employed as solvents for the extraction and preservation of RNA in aqueous solution. RNA samples obtained from yeast cells were extracted and preserved by the trihexyl(tetradecyl) phosphonium tris(hexafluoroacetylaceto)cobaltate(II) ([P66614 +][Co(hfacac)3 -]) and trihexyl(tetradecyl) phosphonium tris(phenyltrifluoroacetylaceto)cobaltate(II) ([P66614 +][Co(Phtfacac)3 -]) MIL with a dispersion of the supporting media, polypropylene glycol, at room temperature for up to a 7 and 15 day period, respectively. High-quality RNA treated with ribonuclease A (RNase A) was recovered from the tetra(1-octylimidazole)cobaltate(II) di(l-glutamate) ([Co(OIM)4 2+][Glu-]2) and tetra(1-octylimidazole)cobaltate(II) di(l-aspartate) ([Co(OIM)4 2+][Asp-]2) MILs after a 24 h period at room temperature. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and agarose gel electrophoresis were used to determine the effect of RNA preservation. Furthermore, the preservation mechanism was investigated by exploring the partitioning of RNase A into the MIL using high-performance liquid chromatography.
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8
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Wilcox AH, Delwart E, Díaz-Muñoz SL. Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO. Microb Genom 2020; 5. [PMID: 31738702 PMCID: PMC6927307 DOI: 10.1099/mgen.0.000315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
dsRNA is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. DMSO has been used to denature dsRNA prior to the reverse-transcription stage to improve reverse transcriptase PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve the sequencing yield of a dsRNA virus (Φ6) in a short-read next-generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a ssRNA viral genome (influenza A/California/07/2009). We suggest that up to 50 % DMSO treatment be used prior to cDNA synthesis when samples of interest are composed of or may contain dsRNA.
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Affiliation(s)
- Alexander H Wilcox
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Vitalant Research Institute, San Francisco, CA, USA
| | - Samuel L Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.,Genome Center, University of California, Davis, CA, USA
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9
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Nwokeoji AO, Kilby PM, Portwood DE, Dickman MJ. Accurate Quantification of Nucleic Acids Using Hypochromicity Measurements in Conjunction with UV Spectrophotometry. Anal Chem 2017; 89:13567-13574. [PMID: 29141408 DOI: 10.1021/acs.analchem.7b04000] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
UV absorbance spectrophotometry is widely used for the quantification of nucleic acids. For accurate quantification, it is important to determine the hypochromicity of the oligonucleotide or complex nucleic acid structure. The use of thermal denaturation studies in conjunction with UV spectrophotometry to determine hypochromicity requires prolonged, elevated temperatures, which may cause partial hydrolysis of RNA. In addition, dsRNA is difficult to denature even at elevated temperature, and the extinction coefficients of nucleic acids are also affected by temperature, which makes it difficult to accurately determine the nucleic acid concentration. To overcome these caveats, we have utilized the chemical denaturant dimethyl sulfoxide which, in conjunction with a short thermal denaturation, prevents renaturation of the duplex nucleic acids (dsDNA/RNA). Using this approach, we have measured the absorbance of both the unstructured and structured nucleic acids to accurately measure their hypochromicity and determine their extinction coefficients. For a range of different dsRNA, we have for the first time determined values of 46.18-47.29 μg/mL/A260 for the quantification of dsRNA using UV spectrophotometry. Moreover, this approach enables the accurate determination of the relative proportion of duplex nucleic acids in mixed ds/ss nucleic acid solutions, demonstrating significant advantages over current methods.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield , Mappin Street, Sheffield S1 3JD, U.K
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, U.K
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, U.K
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield , Mappin Street, Sheffield S1 3JD, U.K
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10
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An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system. Sci Rep 2017; 7:7732. [PMID: 28798404 PMCID: PMC5552694 DOI: 10.1038/s41598-017-07870-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/04/2017] [Indexed: 11/08/2022] Open
Abstract
Riboswitches are bacterial RNA elements that regulate gene expression in response to metabolite or ion abundance and are considered as potential drug targets. In recent years a number of methods to find non-natural riboswitch ligands have been described. Here we report a high-throughput in vivo screening system that allows identifying OFF-riboswitch modulators in a 384 well bioluminescence assay format. We use a reverse reporter gene setup in Bacillus subtilis, consisting of a primary screening assay, a secondary assay as well as counter assays to detect compounds in a library of 1,280 molecules that act on the guanine-responsive xpt riboswitch from B. anthracis. With this in vivo high-throughput approach we identified several hit compounds and could validate the impact of one of them on riboswitch-mediated gene regulation, albeit this might not be due to direct binding to the riboswitch. However, our data demonstrate the capability of our screening assay for bigger high-throughput screening campaigns. Furthermore, the screening system described here can not only be generally employed to detect non-natural ligands or compounds influencing riboswitches acting as genetic OFF switches, but it can also be used to investigate natural ligands of orphan OFF-riboswitches.
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11
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Hansen MMK, Ventosa Rosquelles M, Yelleswarapu M, Maas RJM, van Vugt-Jonker AJ, Heus HA, Huck WTS. Protein Synthesis in Coupled and Uncoupled Cell-Free Prokaryotic Gene Expression Systems. ACS Synth Biol 2016; 5:1433-1440. [PMID: 27306580 DOI: 10.1021/acssynbio.6b00010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Secondary structure formation of mRNA, caused by desynchronization of transcription and translation, is known to impact gene expression in vivo. Yet, inactivation of mRNA by secondary structures in cell-free protein expression is frequently overlooked. Transcription and translation rates are often not highly synchronized in cell-free expression systems, leading to a temporal mismatch between the processes and a drop in efficiency of protein production. By devising a cell-free gene expression platform in which transcriptional and translational elongation are successfully performed independently, we determine that sequence-dependent mRNA secondary structures are the main cause of mRNA inactivation in in vitro gene expression.
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Affiliation(s)
- Maike M. K. Hansen
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Marta Ventosa Rosquelles
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Maaruthy Yelleswarapu
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Aafke J. van Vugt-Jonker
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
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12
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Schmitz BW, Kitajima M, Campillo ME, Gerba CP, Pepper IL. Virus Reduction during Advanced Bardenpho and Conventional Wastewater Treatment Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:9524-32. [PMID: 27447291 DOI: 10.1021/acs.est.6b01384] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The present study investigated wastewater treatment for the removal of 11 different virus types (pepper mild mottle virus; Aichi virus; genogroup I, II, and IV noroviruses; enterovirus; sapovirus; group-A rotavirus; adenovirus; and JC and BK polyomaviruses) by two wastewater treatment facilities utilizing advanced Bardenpho technology and compared the results with conventional treatment processes. To our knowledge, this is the first study comparing full-scale treatment processes that all received sewage influent from the same region. The incidence of viruses in wastewater was assessed with respect to absolute abundance, occurrence, and reduction in monthly samples collected throughout a 12 month period in southern Arizona. Samples were concentrated via an electronegative filter method and quantified using TaqMan-based quantitative polymerase chain reaction (qPCR). Results suggest that Plant D, utilizing an advanced Bardenpho process as secondary treatment, effectively reduced pathogenic viruses better than facilities using conventional processes. However, the absence of cell-culture assays did not allow an accurate assessment of infective viruses. On the basis of these data, the Aichi virus is suggested as a conservative viral marker for adequate wastewater treatment, as it most often showed the best correlation coefficients to viral pathogens, was always detected at higher concentrations, and may overestimate the potential virus risk.
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Affiliation(s)
- Bradley W Schmitz
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 West Calle Agua Nueva, Tucson, Arizona 85745, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University , Kita 13 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Maria E Campillo
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 West Calle Agua Nueva, Tucson, Arizona 85745, United States
| | - Charles P Gerba
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 West Calle Agua Nueva, Tucson, Arizona 85745, United States
| | - Ian L Pepper
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 West Calle Agua Nueva, Tucson, Arizona 85745, United States
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13
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Xu J, Xu Y, Yonezawa T, Li L, Hasegawa M, Lu F, Chen J, Zhang W. Polymorphism and evolution of ribosomal DNA in tea (Camellia sinensis, Theaceae). Mol Phylogenet Evol 2015; 89:63-72. [DOI: 10.1016/j.ympev.2015.03.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 01/18/2023]
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14
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Fluorescence assays for monitoring RNA-ligand interactions and riboswitch-targeted drug discovery screening. Methods Enzymol 2014; 550:363-83. [PMID: 25605395 DOI: 10.1016/bs.mie.2014.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches and other noncoding regulatory RNA are intriguing targets for the development of therapeutic agents. A significant challenge in the drug discovery process, however, is the identification of potent compounds that bind the target RNA specifically and disrupt its function. Essential to this process is an effectively designed cascade of screening assays. A screening cascade for identifying compounds that target the T box riboswitch antiterminator element is described. In the primary assays, moderate to higher throughput screening of compound libraries is achieved by combining the sensitivity of fluorescence techniques with functionally relevant assays. Active compounds are then validated and the binding to target RNA further characterized in secondary assays. The cascade of assays monitor ligand-induced changes in the steady-state fluorescence of an attached dye or internally incorporated 2-aminopurine; the fluorescence anisotropy of an RNA complex; and, the thermal denaturation fluorescence profile of a fluorophore-quencher labeled RNA. While the assays described have been developed for T box riboswitch-targeted drug discovery, the fluorescence methods and screening cascade design principles can be applied to drug discovery efforts targeted toward other medicinally relevant noncoding RNA.
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15
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Lee J, Vogt CE, McBrairty M, Al-Hashimi HM. Influence of dimethylsulfoxide on RNA structure and ligand binding. Anal Chem 2013; 85:9692-8. [PMID: 23987474 DOI: 10.1021/ac402038t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough analysis of how lower concentrations (<10%) of DMSO typically used in binding assays affects RNA structure and ligand binding has not been undertaken. Here, we use NMR and 2-aminopurine fluorescence spectroscopy to examine how DMSO affects the structure, dynamics, and ligand binding properties of two flexible hairpin RNAs: the transactivation response element from HIV-1 and bacterial ribosomal A-site. In both cases, 5-10% DMSO decreased stacking interactions and increased local disorder in noncanonical residues within bulges and loops and resulted in 0.3-4-fold reduction in the measured binding affinities for different small molecules, with the greatest reduction observed for an intercalating compound that binds RNA nonspecifically. Our results suggest that, by competing for hydrophobic interactions, DMSO can have a small but significant effect on RNA structure and ligand binding. These effects should be considered when developing ligand binding assays and high throughput screens.
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Affiliation(s)
- Janghyun Lee
- Department of Chemistry and Biophysics, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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16
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Kwok CK, Ding Y, Sherlock ME, Assmann SM, Bevilacqua PC. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Anal Biochem 2013; 435:181-6. [PMID: 23399535 DOI: 10.1016/j.ab.2013.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/09/2013] [Accepted: 01/12/2013] [Indexed: 01/11/2023]
Abstract
Single-stranded DNA (ssDNA) ligation is a crucial step in many biochemical assays. Efficient ways of carrying out this reaction, however, are lacking. We show here that existing ssDNA ligation methods suffer from slow kinetics, poor yield, and severe nucleotide preference. To resolve these issues, we introduce a hybridization-based strategy that provides efficient and low-bias ligation of ssDNA. Our method uses a hairpin DNA to hybridize to any incoming acceptor ssDNA with low bias, with ligation of these strands mediated by T4 DNA ligase. This technique potentially can be applied in protocols that require ligation of ssDNA, including ligation-mediated polymerase chain reaction (LMPCR) and complementary DNA (cDNA) library construction.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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17
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Zhou S, Acquaah-Harrison G, Jack KD, Bergmeier SC, Hines JV. Ligand-induced changes in T box antiterminator RNA stability. Chem Biol Drug Des 2011; 79:202-8. [PMID: 22117759 DOI: 10.1111/j.1747-0285.2011.01274.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
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Affiliation(s)
- Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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18
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Burr B, Burr FA, Rubenstein I, Simon MN. Purification and translation of zein messenger RNA from maize endosperm protein bodies. Proc Natl Acad Sci U S A 2010; 75:696-700. [PMID: 16592496 PMCID: PMC411323 DOI: 10.1073/pnas.75.2.696] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The messenger RNAs coding for the zein storage protein have been purified from other contaminating RNAs. The average molecular lengths are 1.1-1.2 kilobases, as determined by polyacrylamide gel electrophoresis and by electron microscopy. Products of messenger-dependent protein synthesis in vitro appear to be 1100 and 2000 daltons heavier than the native polypeptides. Zein is like secretory proteins in having a precursor with an additional amino-terminal sequence. Although only one mRNA is seen in polyacrylamide gel electrophoresis, the combined size of the polypeptide products formed exceeds the coding capacity for one message of the size determined in this study. This suggests that there are at least two mRNAs of similar sizes for the zein polypeptides rather than one dicistronic message.
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Affiliation(s)
- B Burr
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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19
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Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA (NEW YORK, N.Y.) 2007; 13:151-9. [PMID: 17105992 PMCID: PMC1705746 DOI: 10.1261/rna.234507] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We have developed a sensitive, accurate, and multiplexed microRNA (miRNA) profiling assay that is based on a highly efficient labeling method and novel microarray probe design. The probes provide both sequence and size discrimination, yielding in most cases highly specific detection of closely related mature miRNAs. Using a simple, single-vial experimental protocol, 120 ng of total RNA is directly labeled using Cy3 or Cy5, without fractionation or amplification, to produce precise and accurate measurements that span a linear dynamic range from 0.2 amol to 2 fmol of input miRNA. The results can provide quantitative estimates of the miRNA content for the tissues studied. The assay is also suitable for use with formalin-fixed paraffin-embedded clinical samples. Our method allows rapid design and validation of probes for simultaneous quantitative measurements of all human miRNA sequences in the public databases and to new miRNA sequences as they are reported.
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Affiliation(s)
- Hui Wang
- Agilent Technologies, Inc., Agilent Laboratories, Santa Clara, California 95051, USA.
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20
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Jackson A, Jiao PE, Ni I, Fu GK. Agarose gel size fractionation of RNA for the cloning of full-length cDNAs. Anal Biochem 2003; 323:252-5. [PMID: 14656534 DOI: 10.1016/j.ab.2003.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Alan Jackson
- Incyte Corp, 3160 Porter Dr, Palo Alto, CA 94304, USA
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21
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Shumyatsky GP, Tillib SV, Kramerov DA. B2 RNA and 7SK RNA, RNA polymerase III transcripts, have a cap-like structure at their 5' end. Nucleic Acids Res 1990; 18:6347-51. [PMID: 1700854 PMCID: PMC332502 DOI: 10.1093/nar/18.21.6347] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We found that hydrolysates of poly(A)+ RNA from Ehrlich ascites carcinoma cells which were transcribed by RNA polymerase III contained an unusual component designated as X. It was part of B2 RNA representing a transcript of B2 retroposon, typical of rodents. The component X possesses a cap-like structure, xppp5'G, where x has a non-nucleotide structure. About half of all B2 RNAs contained this group at the 5' end. Previously, Epstein et al. (1) detected a similar structure at the 5' end of small nuclear U6 RNA. Later, Singh and Reddy (2) showed methyl to be the blocking group in the component x of U6 RNA. Besides B2 RNA, we found 5' ends containing methyl groups in 7SK RNA.
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Affiliation(s)
- G P Shumyatsky
- Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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22
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Kramerov DA, Tillib SV, Shumyatsky GP, Georgiev GP. The most abundant nascent poly(A) + RNAs are transcribed by RNA polymerase III in murine tumor cells. Nucleic Acids Res 1990; 18:4499-506. [PMID: 1697065 PMCID: PMC331270 DOI: 10.1093/nar/18.15.4499] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Twelve to twenty percent of newly synthesized poly(A) + RNA is transcribed by RNA polymerase III in Ehrlich ascites carcinoma and P3O1 plasmocytoma mouse tumors. Most of this RNA designated as pol IIIpoly(A) + RNA has a size of 160 to 800 nucleotides with a maximum of distribution of ca. 300 nucleotides. Pol IIIpoly(A) + RNA fraction consists of two major classes of molecules corresponding to previously described B1 RNA and B2 RNA with the ratio of 1:4 to 2:3. All B2 RNAs present in poly(A) + fraction contain a long poly(A) segments at the 3' ends. Thus, RNA polymerase III transcripts can be polyadenylated. Several transcripts that hybridize with B2 probe were also observed in poly(A)- RNA. The major components consist of 180, 160, 120 and 95 nucleotides. The 180-nucleotide B2 RNA seems to be a primary transcript from B2 repeat. We suggest that other B2 RNAs are transcribed from truncated copies of B2 element.
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Affiliation(s)
- D A Kramerov
- Engelhardt Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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23
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24
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Nash MA, Johnson M, Knesek JE, Chan JC, East JL. Molecular weight determination of glyoxalated RNA by sedimentation centrifugation. Anal Biochem 1981; 111:376-84. [PMID: 6264819 DOI: 10.1016/0003-2697(81)90576-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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25
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Castro C, Hernández R, Castañeda M. Trypanosoma cruzi ribosomal RNA: internal break in the large-molecular-mass species and number of genes. Mol Biochem Parasitol 1981; 2:219-33. [PMID: 7012618 DOI: 10.1016/0166-6851(81)90102-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The large-molecular-mass ribosomal ribonucleic acid from Trypanosoma cruzi probably contains an internal break. The molecule can be obtained in its intact form or in its two fragments depending on the denaturing agents used for its purification and/or display. This break appears to be an in vivo late processing step rather than a random nucleolytic cleavage during in vitro manipulations. Calculations of mass, from gel electrophoretograms, for the large and small main ribosomal ribonucleic acid species and for the two chains derived from the large species gave values of 1.37, 0.84, 0.70 and 0.57 X 10(6) daltons, respectively. Sedimentation velocity measurements in sucrose gradients and in the analytical ultracentrifuge indicated sedimentation coefficients of 24 and 18 S for the large and small main species, respectively. Saturation hybridization curves showed that the nuclear genome, quantified by chemical analysis, contains about 114 ribosomal ribonucleic acid gene copies.
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26
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Lee AS, Thomas TL, Lev Z, Britten RJ, Davidson EH. Four sizes of transcript produced by a single sea urchin gene expressed in early embryos. Proc Natl Acad Sci U S A 1980; 77:3259-63. [PMID: 6997875 PMCID: PMC349594 DOI: 10.1073/pnas.77.6.3259] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This report concerns a set of sea urchin egg and embryo transcripts complementary to a single-copy region of a cloned DNA fragment (Sp88). Three distinct 16-cell embryo polysomal RNA species were found to hybridize with this fragment. These RNAs are about 1700, 3000, and 4000 nucleotides (nt) in length, and the same species were identified in unfertilized eggs. A significant fraction of all three species of the egg and early embryo transcripts is polyadenylylated. At gastrula stage Sp88 transcripts are almost completely confined to the nucleus [Lev, Z., Thomas, T. L., Lee, A. S., Angerer, R. C., Britten, R. J. & Davidson, E. H. (1980) Dev. Biol, 75, in press]. The Sp88 transcripts of gastrulae are present as a fourth RNA species approximately 5800 nt in length. The four species share a sequence element of cloned DNA fragment that is about 1000 nt long. These RNAs constitute a set of alternative partially overlapping transcripts from the same genomic region.
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27
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28
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29
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Maxwell IH, Maxwell F, Hahn WE. Use of CH3HgOH-agarose gels for the electrophoresis of heterogeneous nuclear RNA and messenger RNA from mammalian cells. Anal Biochem 1979; 99:146-60. [PMID: 532955 DOI: 10.1016/0003-2697(79)90056-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Scherrer K, Imaizumi-Scherrer MT, Reynaud CA, Therwath A. On pre-messenger RNA and transcriptions. A review. Mol Biol Rep 1979; 5:5-28. [PMID: 379595 DOI: 10.1007/bf00777484] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
From the present review integrating old and new data emerge a few principles of gene expression in eukaryotes, and an infinite variety of possible mechanistic details generating the overal pattern. The few principles, most of which are not fundamentally new, may thus be summarized. 1) The eukaryotic genome is subdivided into transcriptional units: into transcriptons which are subject to individual activation controlled at DNA level. 2) Viral genomes may contain one or a few transcriptons, while cells of multicellular organisms contain from 3 x 10(3) in diptera up to an estimated 2 x 10(5) in birds and mammals. 3) Transcriptons may include one or several coding sequences. 4) Transcriptons vary considerably in size: in mammals and birds their size spectrum falls into the 2,000 to 20,000 bp range. 5) Units of coding information constituting one message (genes) and, possibly, units of regulative information are frequently broken up and stored within the transcripton in sub-genic blocks (of so far unknown significance) in general located at a certain distance from the 5' and 3' transcript terminals which are determined by the promotor and terminator signals. 6) The gene, in its specific definition as the functional unit underlying the phenotype, is in general constituted posttranscriptionally by the processing mechanisms from the mosaic of its genomic subunits in the transcripton; segments of coding, service and regulative sequences are recombined within themselves and with each other, polygenic transcripts separate into their unit messages. 7) Activated transcriptons produce pre-mRNA; these primary transcripts are colinear with the DNA of the transcriptional unit. 8) Primary pre-mRNA is processed into secondary pre-mRNA's by extragenic cleavage and intragenic ("splicing") processing, giving rise stepwise to functional mRNA. During this process chemical modifications as methylation, 5'-terminal capping and 3'-terminal polyadenylation take place. 9) Translation yields either potentially functional polypeptides or polycistronic polyproteins subject to further processing. 10) Processing is a regulated process; it involves many of the possible phases and mechanisms of post-transcriptional regulation (cf. 39, 40).
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31
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Nevins JR, Darnell JE. Steps in the processing of Ad2 mRNA: poly(A)+ nuclear sequences are conserved and poly(A) addition precedes splicing. Cell 1978; 15:1477-93. [PMID: 729004 DOI: 10.1016/0092-8674(78)90071-5] [Citation(s) in RCA: 403] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The conservation of nuclear Ad2 sequences during nucleocytoplasmic transport has been estimated from the accumulation of 3H-uridine in nuclear and cytoplasmic Ad2-specific RNA from the major late transcription unit. From 10-28% is conserved of the total Ad2 nuclear RNA synthesized from each of five regions of the genome that specify groups of 3' co-terminal mRNAs. The sum of the conservation of all the regions was equivalent to 100%, signifying the conservation of at least a part of each transcript or all of about one fifth to one sixth of the transcripts. The conservation of poly(A)+ Ad2 nuclear RNA is about 4 times greater than of total Ad2 nuclear RNA, approaching 100% conservation of poly(A)+ nuclear sequences. Since each mRNA contains three "spliced" sequences that are probably encoded only once per transcript, these data on conservation of the Ad2 sequences suggest that each transcriptional event from the 16-99 transcription unit gives rise to one of a possible 13-14 mRNA molecules with destruction of the remainder of the transcribed RNA. The portion which is conserved resides next to the region to which which poly(A) is added. Three models for the choice of poly(A) sites were considered: termination at the poly(A) site, cleavage shortly after synthesis of one of the sites before transcription was complete, and cleavage after completion of transcription. The first model was ruled out by the demonstration of equimolar synthesis over the 16-99 region. The second model is strongly supported because 3H-uridine label appears equally rapidly in the time range 2-10 min in each of the five 3' poly(A) addition sites, whereas chain completion before cleavage would lead to a faster appearance of label in the most promoter-distal site. Furthermore, briefly labeled RNA molecules extending from 16 to each of several poly(A) addition sites were the first poly(A)- terminated 3H-uridine-labeled molecules detected, demonstrating that poly(A) addition precedes splicing. The choice of which mRNA emerges from each transcriptional event would appear to depend upon first choosing one of five 3' mRNA ends followed by a 5' splicing event.
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32
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Niessing J. Globin messenger precursor RNA in duck immature red blood cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 91:587-98. [PMID: 729583 DOI: 10.1111/j.1432-1033.1978.tb12712.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A procedure is described for the chromatographic analysis of RNA under fully denaturing conditions on cross-linked Sepharose. Chromatography of DNA . RNA hybrids, poly(C) . poly(G) hybrids and complexes of poly(C) . hnRNA on Sepharose CL in pure formamide at 46 degrees C leads to denaturation and strand separation of the hybrid structures. Using this procedure, nuclear RNA from duck immature red blood cells was resolved according to molecular size and assayed for the presence of globin mRNA sequences by hybridization with complementary DNA. Two size classes of putative globin mRNA precursor molecules were detected at an elution position corresponding to 14--18 S and 23--28 S. As judged from chromatographic analysis on poly(U)-Sepharose, about 70% of the 14--18-S globin precursor RNA is polyadenylated while only 11% of the putative 23--28-S precursor RNA has a poly(A) tract. Inhibition of transcription by actinomycin D and pulse-chase experiments indicate a half-life of less than 7.5 min for these precursor RNA species.
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33
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Smith MM, Reeve AE, Huang RC. Analysis of RNA initiated in isolated mouse myeloma nuclei using purine nucleoside 5'[gamma-S]triphosphates as affinity probes. Cell 1978; 15:615-26. [PMID: 719754 DOI: 10.1016/0092-8674(78)90030-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The purine ribonucleoside triphosphate analogues adenosine 5'[gamma-S]triphosphate and guanosine 5'[gamma-T]triphosphate were used as affinity probes for studying RNA chain initiation in isolated nuclei from the mouse myeloma 66.2 cell line. Transcripts initiated with either nucleotide analogue were isolated by affinity chromatography on a mercury-agarose affinity column. The binding was specific and dependent upon the inclusion of the sulfur nucleotide analogues in the in vitro synthetic reaction. Several lines of evidence indicate that the affinity-labeled RNA is initiated in vitro. First, the sulfur nucleotide is recovered in high yield as a single nucleoside 5'[gamma-S]triphosphate 2',3'-monophosphate product following alkaline hydrolysis of RNA bound to the affinity column. Second, authentic ribosomal 5S RNA is known to initiate with GTP; in vitro 5S RNA is bound to mercury-agarose only if [gamma-S]GTP is used as the affinity label in the synthesis, and not if [gamma-S]ATP is used. Under the conditions studied, nuclei incorporated 1.2--2.4 pmole of UMP per 10(6) nuclei per min, and the rate of synthesis was unaffected by substitution of the nucleotide analogues for the normal nucleotides. The percentage of the total RNA synthesized that was incorporated into sequences initiated in vitro was 7.8 +/- 1.5% with [gamma-S]ATP and 9.6 +/- 6.4% with [gamma-S]GTP. The size of the total RNA synthesized, determined by sedimentation on sucrose density gradients containing dimethylsulfoxide, ranged from less than 5S to 45S, and the size of the affinity-labeled sequences ranged from less than 5S to 28S. Approximately half of the incorporation into RNA initiated in vitro was sensitive to a concentration of alpha-amanitin which selectively inhibits polymerase II activity. Most of the remaining incorporation into initiated sequences can be abolished by concentrations of alpha-amanitin that are inhibitory for polymerase III activity. Over 70% of the total incorporation into ribosomal 5S RNA transcripts was into sequences initiated in vitro. This initiation was catalyzed by polymerase III and was specific for GTP as the initiating nucleotide. The RNAase T1 fingerprint of the newly initiated 5S RNA indicates that this gene is accurately initiated and faithfully elongated in vitro. The use of these affinity label probes provides much greater sensitivity for studying the initiation of RNA in vitro.
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34
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Costantini FD, Scheller RH, Britten RJ, Davidson EH. Repetitive sequence transcripts in the mature sea urchin oocyte. Cell 1978; 15:173-87. [PMID: 568031 DOI: 10.1016/0092-8674(78)90093-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The expression of interspersed repetitive sequences in the RNA of mature sea urchin oocytes was investigated. 3H-DNA tracers representing short interspersed repetitive sequences a few hundred nucleotides long, and long repetitive sequences approximately 2000 nucleotides long, were prepared from genomic DNA of the sea urchin, Strongylocentrotus purpuratus. These tracers were reacted with excess RNA from the mature oocyte. About 80% of the reactable short repeat tracer and 35% of the long repeat tracer hybridized. Thus most of the repetitive sequence families in the short repeat tracer are represented in oocyte RNA, and transcripts complementary to both strands of many repeat sequences are present. The kinetics of the reaction show that some transcripts are highly prevalent (greater than 10(5) copies per oocyte), while others are rare (approximately 10(3) copies per oocyte). Nine cloned repetitive sequences were labeled, strand-separated and reacted with the oocyte RNA. Transcripts of both strands of all nine repeats were found in the RNA. The prevalence of transcripts of the cloned repeat families varied from approximately 3000 to 100,000 copies per oocyte. Studies with both cloned and genomic tracers show that transcript prevalence is independent of the genomic reiteration frequency of the transcribed repetitive sequences. Most of the families represented by prevalent transcripts have fewer than 200 copies per haploid genome. The RNA molecules with which the cloned repeats react are at least 1000-2000 nucleotides in length. Other experiments show that a majority of the members of repeat families represented by prevalent transcripts in the oocyte RNA are interspersed among single-copy sequence elements in the genome.
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35
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Fried AH. Synthesis and degradiation of simian virus 40 RNA sequences not found in the mRNA population. Virology 1978; 88:286-99. [PMID: 211713 DOI: 10.1016/0042-6822(78)90286-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Vizard DL, Ansevin AT, Thornton GB, Mandel M, Arlinghaus RB. Saltatory thermal denaturation of double-stranded viral RNAs. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 519:138-48. [PMID: 208611 DOI: 10.1016/0005-2787(78)90068-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The double-stranded RNAs from bacteriophage phi6 and the replicative form of mengovirus denature upon heating in a series of abrupt steps which resemble the subtransitions (thermalites) observed within the high resolution profiles of small, naturally occurring DNA molecules. Such RNA thermalites are approximately an order of magnitude narrower than typical thermal subtransitions of nominally single-stranded RNA. We conclude that the same features of nucleotide sequence that give rise to cooperative denaturation in DNA genomes are to be found also in RNA genomes. Thus, high resolution thermal denaturation profiles are useful for characterizing double-stranded RNA molecules as well as native DNA in the size range of common viruses. A medium containing dimethylsulfoxide was required to lower the Tm of the RNA samples to a satisfactory temperature range. For double-stranded RNA in 50% dimethylsulfoxide, the dependence of Tm on G . C composition was greater than that of DNA in the same medium and also greater than that of double-stranded RNA in an aqueous medium. The fact that RNA thermalites are broader than DNA thermalites and that the melting temperature of double-stranded RNA has a greater dependence on base composition than that of DNA, indicates that at least one of the thermodynamic parameters for double helix formation in RNA is different from that in DNA.
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37
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Pachl CA, Yound ET. The size and messenger RNA activity of bacteriophage T7 late transcripts synthesized in vivo. J Mol Biol 1978; 122:69-101. [PMID: 671552 DOI: 10.1016/0022-2836(78)90109-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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38
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Molloy G, Puckett L. The metabolism of heterogeneous nuclear RNA and the formation of cytoplasmic messenger RNA in animal cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978; 31:1-38. [PMID: 785543 DOI: 10.1016/0079-6107(78)90003-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Zimmerman SB, Davies DR, Navia MA. An ordered single-stranded structure for polyadenylic acid in denaturing solvents. An X-ray fiber diffraction and model building study. J Mol Biol 1977; 116:317-30. [PMID: 599560 DOI: 10.1016/0022-2836(77)90219-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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41
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Koenig P, Reines SA, Cantor CR. Pyrene derivatives as fluorescent probes of conformation near the 3' termini of polyribonucleotides. Biopolymers 1977; 16:2231-42. [PMID: 911999 DOI: 10.1002/bip.1977.360161011] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Aronson AI. Alterations of RNA metabolism in sea urchin embryos by an inhibitor of protein synthesis initiation. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 477:334-42. [PMID: 889828 DOI: 10.1016/0005-2787(77)90252-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An inhibitor of the initiation of protein synthesis, 2-(4-methyl-2,6 dinitroanilino)-N-methyl propionamide, (MDMP), inhibits incorporation of amino acids by 85--95% without altering the rate of incorporation of uridine into sea-urchin-hatched blastula embryos. Since the inhibition is readily reversible up to at least 90 min after addition, extensive secondary effects are unlikely. Newly synthesized RNA accumulates in polyribosome-like structures in amount and with a size distribution very similar to the control. The polyadenylation of total, cytoplasmic and polyribosomal RNA are only slightly different from the controls. While the size distribution of 9-S of approx. 30-S RNA is about the same, there is relatively less low molecular weight RNA (approx. 4-S). There is also a greater accumulation of greater than 30-S RNA in the cytoplasm of treated embryos due either to leakage and/or improper processing of nuclear RNA. The latter possibility is consistent with the decrease in 4-S RNA which is a presumed degradation product of nuclear HnRNA. While the initial rate of RNA synthesis and much of the accumulation of RNA in polyribosomes are not affected, the inhibition of protein synthesis per se or a secondary effect of MDMP results in altered patterns of RNA transport and processing.
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43
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44
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45
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Abstract
Hybridization of labeled RNA with excess amounts of DNA complementary to globin mRNA, in conjunction with a pulse-chase technique, were used to investigate the biosynthetic pathway of globin mRNA in erythroid cells. Three species of molecules sharing common sequences with globin mRNA were detected in the nuclei of these cells, two of which are larger than the cytoplasmic globin mRNA. One species was approximately 7 times larger than globin mRNA ("27S"), and the other ("15S") was only about twice the size of cytoplasmic globin mRNA. The largest species lacked poly(A) sequences, while the others contained poly(A), After chase, the large RNA species gradually disappeared ( 1/2 = 5 min), while the cytoplasmic 10S species accumulated. From these results a model is proposed describing the biosynthetic pathway of globin RNA transcription: an early transcription product is the large molecule "27S" (approximately 5000 nucleotides long) which is then cleaved into a smaller species "15S" (approximately 1500 nucleotides). This intermediate precursor is then clipped, presumably at the 5' end, and finally converted to the exported "10S" molecule (approximately 750 nucleotides) which accumulates in the cytoplasm.
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Knöchel W, Grundmann U. Nuclear steady-state RNA from chicken immature red blood cells. Distribution of globin-coding and poly (A) sequences. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 476:47-56. [PMID: 557995 DOI: 10.1016/0005-2787(77)90284-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nuclear steady-state RNA and polysomal RNA of chicken immature red blood cells were isolated and separated on formamide sucrose gradients. For comparison the distribution of 9 S globin mRNA was investigated by gradient centrifugation of 125I-labelled mRNA. The material was either pooled into two fractions (less than 20 S; greater than 20 S) and translated in an Ehrlich ascites cell-free system or each gradient fraction was analyzed by hybridization with [3H]-poly (U) or [3H]-labelled DNA complementary to purified 9 S globin mRNA (globin cDNA). In neither case could evidence be obtained for the existence of a high molecular weight RNA as a probable globin mRNA precursor. Further analysis was performed by electrophoresis of RNA on exponential polyacrylamide gels in formamide and subsequent hybridization with cDNA. The results are consistent with those of gradient centrifugation and demonstrate that the distribution of globin-coding sequences in nuclear steady state RNA corresponds to that of cytoplasmic 9 S globin mRNA.
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Levis R, Penman S. The metabolism of poly (A)+ and poly(A)-hnRNA in cultured Drosophila cells studied with a rapid uridine pulse-chase. Cell 1977; 11:105-13. [PMID: 872216 DOI: 10.1016/0092-8674(77)90321-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Rapidly sedimenting hnRNA complexes contain regions of stable intermolecular duplex. Disruption of such complexes, as judged by a reduction in sedimentation rate, requires conditions sufficient to denature the duplex regions. Rapidly sedimenting molecules reappear only when the complementary sequences reanneal-that is, the formation of such complexes is dependent upon time and the concentration of homologous RNA. These experiments lead us to the conclusion that rapidly sedimenting hnRNA complexes consist of two or more largely single-stranded RNA molecules held together by short duplex regions. Precisely such structures have been visualized in the electron microscope. Rapidly sedimenting fractions of native nuclear RNA from preparative sucrose gradients consist primarily of large, multi-molecular complexes interconnected by duplex regions averaging 300 base pairs in length. Exposure of the RNA to severely denaturing conditions eliminates such complexes. Reannealing of the RNA reconstitutes complexes which are indistinguishable from those observed in preparations before denaturation.
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