1
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Midha T, Mallory JD, Kolomeisky AB, Igoshin OA. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy. J Phys Chem Lett 2023; 14:3422-3429. [PMID: 37010247 DOI: 10.1021/acs.jpclett.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cleavage of dinucleotides after the misincorporational pauses serves as a proofreading mechanism that increases transcriptional elongation accuracy. The accuracy is further improved by accessory proteins such as GreA and TFIIS. However, it is not clear why RNAP pauses and why cleavage-factor-assisted proofreading is necessary despite transcriptional errors in vitro being of the same order as those in downstream translation. Here, we developed a chemical-kinetic model that incorporates most relevant features of transcriptional proofreading and uncovers how the balance between speed and accuracy is achieved. We found that long pauses are essential for high accuracy, whereas cleavage-factor-stimulated proofreading optimizes speed. Moreover, in comparison to the cleavage of a single nucleotide or three nucleotides, RNAP backtracking and dinucleotide cleavage improve both speed and accuracy. Our results thereby show how the molecular mechanism and the kinetic parameters of the transcriptional process were evolutionarily optimized to achieve maximal speed and tolerable accuracy.
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Affiliation(s)
- Tripti Midha
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
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2
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
- Cluster of Excellence Physics of Life TU Dresden Dresden Germany
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3
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Kilic Z, Sgouralis I, Pressé S. Residence time analysis of RNA polymerase transcription dynamics: A Bayesian sticky HMM approach. Biophys J 2021; 120:1665-1679. [PMID: 33705761 DOI: 10.1016/j.bpj.2021.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
The time spent by a single RNA polymerase (RNAP) at specific locations along the DNA, termed "residence time," reports on the initiation, elongation, and termination stages of transcription. At the single-molecule level, this information can be obtained from dual ultrastable optical trapping experiments, revealing a transcriptional elongation of RNAP interspersed with residence times of variable duration. Successfully discriminating between long and short residence times was used by previous approaches to learn about RNAP's transcription elongation dynamics. Here, we propose an approach based on the Bayesian sticky hidden Markov model that treats all residence times for an Escherichia coli RNAP on an equal footing without a priori discriminating between long and short residence times. Furthermore, our method has two additional advantages: we provide full distributions around key point statistics and directly treat the sequence dependence of RNAP's elongation rate. By applying our approach to experimental data, we find assigned relative probabilities on long versus short residence times, force-dependent average residence time transcription elongation dynamics, ∼10% drop in the average backtracking durations in the presence of GreB, and ∼20% drop in the average residence time as a function of applied force in the presence of RNaseA.
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Affiliation(s)
- Zeliha Kilic
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Department of Physics and School of Molecular Sciences, Arizona State University, Tempe, Arizona. spresse@%20asu.edu
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4
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Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed. Sci Rep 2020; 10:16074. [PMID: 32999370 PMCID: PMC7527559 DOI: 10.1038/s41598-020-73069-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022] Open
Abstract
There is a growing appreciation for the diverse regulatory consequences of the family of proteins that bind to the secondary channel of E. coli RNA polymerase (RNAP), such as GreA, GreB or DksA. Similar binding sites could suggest a competition between them. GreA is characterised to rescue stalled RNAP complexes due to its antipause activity, but also it is involved in transcription fidelity and proofreading. Here, overexpression of GreA is noted to be lethal independent of its antipause activity. A library of random GreA variants has been used to isolate lethality suppressors to assess important residues for GreA functionality and its interaction with the RNA polymerase. Some mutant defects are inferred to be associated with altered binding competition with DksA, while other variants seem to have antipause activity defects that cannot reverse a GreA-sensitive pause site in a fliC::lacZ reporter system. Surprisingly, apparent binding and cleavage defects are found scattered throughout both the coiled-coil and globular domains. Thus, the coiled-coil of GreA is not just a measuring stick ensuring placement of acidic residues precisely at the catalytic centre but also seems to have binding functions. These lethality suppressor mutants may provide valuable tools for future structural and functional studies.
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5
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Meer KM, Nelson PG, Xiong K, Masel J. High Transcriptional Error Rates Vary as a Function of Gene Expression Level. Genome Biol Evol 2020; 12:3754-3761. [PMID: 31841128 PMCID: PMC6988749 DOI: 10.1093/gbe/evz275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Errors in gene transcription can be costly, and organisms have evolved to prevent their occurrence or mitigate their costs. The simplest interpretation of the drift barrier hypothesis suggests that species with larger population sizes would have lower transcriptional error rates. However, Escherichia coli seems to have a higher transcriptional error rate than species with lower effective population sizes, for example Saccharomyces cerevisiae. This could be explained if selection in E. coli were strong enough to maintain adaptations that mitigate the consequences of transcriptional errors through robustness, on a gene by gene basis, obviating the need for low transcriptional error rates and associated costs of global proofreading. Here, we note that if selection is powerful enough to evolve local robustness, selection should also be powerful enough to locally reduce error rates. We therefore predict that transcriptional error rates will be lower in highly abundant proteins on which selection is strongest. However, we only expect this result when error rates are high enough to significantly impact fitness. As expected, we find such a relationship between expression and transcriptional error rate for non-C→U errors in E. coli (especially G→A), but not in S. cerevisiae. We do not find this pattern for C→U changes in E. coli, presumably because most deamination events occurred during sample preparation, but do for C→U changes in S. cerevisiae, supporting the interpretation that C→U error rates estimated with an improved protocol, and which occur at rates comparable with E. coli non-C→U errors, are biological.
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Affiliation(s)
- Kendra M Meer
- Department of Ecology & Evolutionary Biology, University of Arizona.,Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Paul G Nelson
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Kun Xiong
- Department of Molecular & Cellular Biology, University of Arizona.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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6
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Li W, Lynch M. Universally high transcript error rates in bacteria. eLife 2020; 9:54898. [PMID: 32469307 PMCID: PMC7259958 DOI: 10.7554/elife.54898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
Errors can occur at any level during the replication and transcription of genetic information. Genetic mutations derived mainly from replication errors have been extensively studied. However, fundamental details of transcript errors, such as their rate, molecular spectrum, and functional effects, remain largely unknown. To globally identify transcript errors, we applied an adapted rolling-circle sequencing approach to Escherichia coli, Bacillus subtilis, Agrobacterium tumefaciens, and Mesoplasma florum, revealing transcript-error rates 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates. The majority of detected errors would result in amino-acid changes, if translated. With errors identified from 9929 loci, the molecular spectrum and distribution of errors were uncovered in great detail. A G→A substitution bias was observed in M. florum, which apparently has an error-prone RNA polymerase. Surprisingly, an increased frequency of nonsense errors towards the 3' end of mRNAs was observed, suggesting a Nonsense-Mediated Decay-like quality-control mechanism in prokaryotes.
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Affiliation(s)
- Weiyi Li
- Department of Biology, Indiana University, Bloomington, United States
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, United States.,Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, United States
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7
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Zhang B, Zhu Z, Jia W, Qu F, Huang B, Shan B, Yu H, Tang Y, Chen L, Du H. In vitro activity of aztreonam-avibactam against metallo-β-lactamase-producing Enterobacteriaceae-A multicenter study in China. Int J Infect Dis 2020; 97:11-18. [PMID: 32473388 DOI: 10.1016/j.ijid.2020.05.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/02/2020] [Accepted: 05/21/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES To study the molecular epidemiology of clinical metallo-β-lactamase (MBL)-producing Enterobacteriaceae isolates in China and to evaluate the antimicrobial susceptibility of MBL-Enterobacteriaceae isolates to aztreonam-avibactam. METHODS Bacterial speciation was determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. PCR was used to screen for common carbapenemase genes. Antimicrobial susceptibility testing of common clinical antibiotics and aztreonam-avibactam was performed using the standard broth microdilution method. RESULTS A total of 161 MBL-Enterobacteriaceae isolates were included, with Klebsiella pneumoniae (n = 73, 45.4%) and Escherichia coli (n = 53, 32.9%) being the most common species. Among the 161 isolates, blaNDM (n = 151), blaIMP (n = 13), and blaVIM (n = 2) were detected, including five strains (3.1%) co-harboring two MBLs. MBL-Enterobacteriaceae isolates frequently contained two (n = 55, 34.2%) or more (n = 89, 55.3%) additional serine β-lactamase genes (blaKPC, blaCTX-M, blaTEM, or blaSHV). Antimicrobial susceptibility testing showed that 81.4% of isolates (n = 131) were resistant to aztreonam. The rates of resistance to cefazolin, ceftazidime, ceftriaxone, cefotaxime, ampicillin-sulbactam, amoxicillin-clavulanic acid, and piperacillin-tazobactam were all over 90%. The addition of avibactam (4 μg/ml) significantly reduced the minimum inhibitory concentrations (MICs) of the aztreonam-resistant isolates by more than 8-fold (range ≤0.125 to 4 μg/ml), with a MIC50/MIC90 of ≤0.125/1 μg/ml among the 131 isolates. Overall, 96.9% (n = 156) of the total isolates were inhibited at an aztreonam-avibactam concentration of ≤1 μg/ml. Univariate and multivariate logistic regression analysis found that in patients with MBL-Enterobacteriaceae infections, the presence of pre-existing lung disease (adjusted odds ratio 8.267, 95% confidence interval 1.925-28.297; p = 0.004) was associated with a hazard effect on worse disease outcomes. CONCLUSIONS The combined use of aztreonam-avibactam is highly potent against MBL-Enterobacteriaceae and may serve as a new candidate for the treatment of infections caused by MBL-Enterobacteriaceae in China.
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Affiliation(s)
- Biying Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Jia
- Center of Medical Laboratory, The General Hospital of Ningxia Medical University, Yinchuan, China
| | - Fen Qu
- The Center of Clinical Diagnosis Laboratory, 302 Hospital of PLA, Beijing, China; China Aviation General Hospital of China Medical University, Beijing, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bin Shan
- Department of Laboratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Hua Yu
- Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yiwei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, USA; Cepheid Shanghai, Shanghai, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, NJ, USA; Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
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8
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Conditional down-regulation of GreA impacts expression of rRNA and transcription factors, affecting Mycobacterium smegmatis survival. Sci Rep 2020; 10:5802. [PMID: 32242064 PMCID: PMC7118132 DOI: 10.1038/s41598-020-62703-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
Gre, one of the conserved transcription factors in bacteria, modulates RNA polymerase (RNAP) activity to ensure processivity and fidelity of RNA synthesis. Gre factors regulate transcription by inducing the intrinsic-endonucleolytic activity of RNAP, allowing the enzyme to resume transcription from the paused and arrested sites. While Escherichia coli and a number of eubacteria harbor GreA and GreB, genus mycobacteria has a single Gre (GreA). To address the importance of the GreA in growth, physiology and gene expression of Mycobacterium smegmatis, we have constructed a conditional knock-down strain of GreA. The GreA depleted strain exhibited slow growth, drastic changes in cell surface phenotype, cell death, and increased susceptibility to front-line anti-tubercular drugs. Transcripts and 2D-gel electrophoresis (2D-PAGE) analysis of the GreA conditional knock-down strain showed altered expression of the genes involved in transcription regulation. Among the genes analysed, expression of RNAP subunits (β, β’ and ω), carD, hupB, lsr2, and nusA were affected to a large extent. Severe reduction in the expression of genes of rRNA operon in the knock-down strain reveal a role for GreA in regulating the core components of the translation process.
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9
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Miropolskaya N, Kulbachinskiy A, Esyunina D. Factor-specific effects of mutations in the active site of RNA polymerase on RNA cleavage. Biochem Biophys Res Commun 2020; 523:165-170. [PMID: 31837805 DOI: 10.1016/j.bbrc.2019.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022]
Abstract
Bacterial RNA polymerase (RNAP) relies on the same active site for RNA synthesis and co-transcriptional RNA proofreading. The intrinsic RNA proofreading activity of RNAP can be greatly stimulated by Gre factors, which bind within the secondary channel and directly participate in the RNA cleavage reaction in the active site of RNAP. Here, we characterize mutations in Escherichia coli RNAP that differentially affect intrinsic and Gre-stimulated RNA cleavage. Substitution of a highly conserved arginine residue that contacts nascent RNA upstream of the active site strongly impairs intrinsic and GreA-dependent cleavage, without reducing GreA affinity or catalytic Mg2+ binding. In contrast, substitutions of several nonconserved residues at the Gre-interacting interface in the secondary channel primarily affect GreB-dependent cleavage, by decreasing both the catalytic rate and GreB affinity. The results suggest that RNAP residues not directly involved in contacts with the reacting RNA groups or catalytic ions play essential roles in RNA cleavage and can modulate its regulation by transcription factors.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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10
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Riaz-Bradley A, James K, Yuzenkova Y. High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors. Nucleic Acids Res 2020; 48:1341-1352. [PMID: 31840183 PMCID: PMC7026648 DOI: 10.1093/nar/gkz1130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
The vast majority of organisms possess transcription elongation factors, the functionally similar bacterial Gre and eukaryotic/archaeal TFIIS/TFS. Their main cellular functions are to proofread errors of transcription and to restart elongation via stimulation of RNA hydrolysis by the active centre of RNA polymerase (RNAP). However, a number of taxons lack these factors, including one of the largest and most ubiquitous groups of bacteria, cyanobacteria. Using cyanobacterial RNAP as a model, we investigated alternative mechanisms for maintaining a high fidelity of transcription and for RNAP arrest prevention. We found that this RNAP has very high intrinsic proofreading activity, resulting in nearly as low a level of in vivo mistakes in RNA as Escherichia coli. Features of the cyanobacterial RNAP hydrolysis are reminiscent of the Gre-assisted reaction—the energetic barrier is similarly low, and the reaction involves water activation by a general base. This RNAP is resistant to ubiquitous and most regulatory pausing signals, decreasing the probability to go off-pathway and thus fall into arrest. We suggest that cyanobacterial RNAP has a specific Trigger Loop domain conformation, and isomerises easier into a hydrolytically proficient state, possibly aided by the RNA 3′-end. Cyanobacteria likely passed these features of transcription to their evolutionary descendants, chloroplasts.
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Affiliation(s)
- Amber Riaz-Bradley
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Katherine James
- Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.,Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
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11
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Dylewski M, Fernández-Coll L, Bruhn-Olszewska B, Balsalobre C, Potrykus K. Autoregulation of greA Expression Relies on GraL Rather than on greA Promoter Region. Int J Mol Sci 2019; 20:ijms20205224. [PMID: 31652493 PMCID: PMC6829880 DOI: 10.3390/ijms20205224] [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: 09/28/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
GreA is a well-characterized transcriptional factor that acts primarily by rescuing stalled RNA polymerase complexes, but has also been shown to be the major transcriptional fidelity and proofreading factor, while it inhibits DNA break repair. Regulation of greA gene expression itself is still not well understood. So far, it has been shown that its expression is driven by two overlapping promoters and that greA leader encodes a small RNA (GraL) that is acting in trans on nudE mRNA. It has been also shown that GreA autoinhibits its own expression in vivo. Here, we decided to investigate the inner workings of this autoregulatory loop. Transcriptional fusions with lacZ reporter carrying different modifications (made both to the greA promoter and leader regions) were made to pinpoint the sequences responsible for this autoregulation, while GraL levels were also monitored. Our data indicate that GreA mediated regulation of its own gene expression is dependent on GraL acting in cis (a rare example of dual-action sRNA), rather than on the promoter region. However, a yet unidentified, additional factor seems to participate in this regulation as well. Overall, the GreA/GraL regulatory loop seems to have unique but hard to classify properties.
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Affiliation(s)
- Maciej Dylewski
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, W. Stwosza 59, 80-299 Gdańsk, Poland.
| | - Llorenç Fernández-Coll
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Bożena Bruhn-Olszewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, W. Stwosza 59, 80-299 Gdańsk, Poland.
| | - Carlos Balsalobre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, W. Stwosza 59, 80-299 Gdańsk, Poland.
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12
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Bradley CC, Gordon AJE, Halliday JA, Herman C. Transcription fidelity: New paradigms in epigenetic inheritance, genome instability and disease. DNA Repair (Amst) 2019; 81:102652. [PMID: 31326363 DOI: 10.1016/j.dnarep.2019.102652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA transcription errors are transient, yet frequent, events that do have consequences for the cell. However, until recently we lacked the tools to empirically measure and study these errors. Advances in RNA library preparation and next generation sequencing (NGS) have allowed the spectrum of transcription errors to be empirically measured over the entire transcriptome and in nascent transcripts. Combining these powerful methods with forward and reverse genetic strategies has refined our understanding of transcription factors known to enhance RNA accuracy and will enable the discovery of new candidates. Furthermore, these approaches will shed additional light on the complex interplay between transcription fidelity and other DNA transactions, such as replication and repair, and explore a role for transcription errors in cellular evolution and disease.
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Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA; Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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13
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Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
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Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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14
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Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
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Koscielniak D, Wons E, Wilkowska K, Sektas M. Non-programmed transcriptional frameshifting is common and highly RNA polymerase type-dependent. Microb Cell Fact 2018; 17:184. [PMID: 30474557 PMCID: PMC6260861 DOI: 10.1186/s12934-018-1034-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Background The viral or host systems for a gene expression assume repeatability of the process and high quality of the protein product. Since level and fidelity of transcription primarily determines the overall efficiency, all factors contributing to their decrease should be identified and optimized. Among many observed processes, non-programmed insertion/deletion (indel) of nucleotide during transcription (slippage) occurring at homopolymeric A/T sequences within a gene can considerably impact its expression. To date, no comparative study of the most utilized Escherichia coli and T7 bacteriophage RNA polymerases (RNAP) propensity for this type of erroneous mRNA synthesis has been reported. To address this issue we evaluated the influence of shift-prone A/T sequences by assessing indel-dependent phenotypic changes. RNAP-specific expression profile was examined using two of the most potent promoters, ParaBAD of E. coli and φ10 of phage T7. Results Here we report on the first systematic study on requirements for efficient transcriptional slippage by T7 phage and cellular RNAPs considering three parameters: homopolymer length, template type, and frameshift directionality preferences. Using a series of out-of-frame gfp reporter genes fused to a variety of A/T homopolymeric sequences we show that T7 RNAP has an exceptional potential for generating frameshifts and is capable of slipping on as few as three adenine or four thymidine residues in a row, in a flanking sequence-dependent manner. In contrast, bacterial RNAP exhibits a relatively low ability to baypass indel mutations and requires a run of at least 7 tymidine and even more adenine residues. This difference comes from involvement of various intrinsic proofreading properties. Our studies demonstrate distinct preference towards a specific homopolymer in slippage induction. Whereas insertion slippage performed by T7 RNAP (but not deletion) occurs tendentiously on poly(A) rather than on poly(T) runs, strong bias towards poly(T) for the host RNAP is observed. Conclusions Intrinsic RNAP slippage properties involve trade-offs between accuracy, speed and processivity of transcription. Viral T7 RNAP manifests far greater inclinations to the transcriptional slippage than E. coli RNAP. This possibly plays an important role in driving bacteriophage adaptation and therefore could be considered as beneficial. However, from biotechnological and experimental viewpoint, this might create some problems, and strongly argues for employing bacterial expression systems, stocked with proofreading mechanisms. Electronic supplementary material The online version of this article (10.1186/s12934-018-1034-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawid Koscielniak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Karolina Wilkowska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Marian Sektas
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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Turtola M, Mäkinen JJ, Belogurov GA. Active site closure stabilizes the backtracked state of RNA polymerase. Nucleic Acids Res 2018; 46:10870-10887. [PMID: 30256972 PMCID: PMC6237748 DOI: 10.1093/nar/gky883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023] Open
Abstract
All cellular RNA polymerases (RNAP) occasionally backtrack along the template DNA as part of transcriptional proofreading and regulation. Here, we studied the mechanism of RNAP backtracking by one nucleotide using two complementary approaches that allowed us to precisely measure the occupancy and lifetime of the backtracked state. Our data show that the stability of the backtracked state is critically dependent on the closure of the RNAP active site by a mobile domain, the trigger loop (TL). The lifetime and occupancy of the backtracked state measurably decreased by substitutions of the TL residues that interact with the nucleoside triphosphate (NTP) substrate, whereas amino acid substitutions that stabilized the closed active site increased the lifetime and occupancy. These results suggest that the same conformer of the TL closes the active site during catalysis of nucleotide incorporation into the nascent RNA and backtracking by one nucleotide. In support of this hypothesis, we construct a model of the 1-nt backtracked complex with the closed active site and the backtracked nucleotide in the entry pore area known as the E-site. We further propose that 1-nt backtracking mimics the reversal of the NTP substrate loading into the RNAP active site during on-pathway elongation.
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Affiliation(s)
- Matti Turtola
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
| | - Janne J Mäkinen
- University of Turku, Department of Biochemistry, FIN-20014 Turku, Finland
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Traverse CC, Ochman H. A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli. G3 (BETHESDA, MD.) 2018; 8:2257-2264. [PMID: 29769292 PMCID: PMC6027873 DOI: 10.1534/g3.118.200209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/28/2018] [Indexed: 02/07/2023]
Abstract
Although mutations are the basis for adaptation and heritable genetic change, transient errors occur during transcription at rates that are orders of magnitude higher than the mutation rate. High rates of transcription errors can be detrimental by causing the production of erroneous proteins that need to be degraded. Two transcription fidelity factors, GreA and GreB, have previously been reported to stimulate the removal of errors that occur during transcription, and a third fidelity factor, DksA, is thought to decrease the error rate through an unknown mechanism. Because the majority of transcription-error assays of these fidelity factors were performed in vitro and on individual genes, we measured the in vivo transcriptome-wide error rates in all possible combinations of mutants of the three fidelity factors. This method expands measurements of these fidelity factors to the full spectrum of errors across the entire genome. Our assay shows that GreB and DksA have no significant effect on transcription error rates, and that GreA only influences the transcription error rate by reducing G-to-A errors.
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Affiliation(s)
- Charles C Traverse
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Howard Ochman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
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Gordon AJE, Sivaramakrishnan P, Halliday JA, Herman C. Transcription infidelity and genome integrity: the parallax view. Transcription 2018; 9:315-320. [PMID: 29929421 DOI: 10.1080/21541264.2018.1491251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
It was recently shown that removal of GreA, a transcription fidelity factor, enhances DNA break repair. This counterintuitive result, arising from unresolved backtracked RNA polymerase impeding DNA resection and thereby facilitating RecA-loading, leads to an interesting corollary: error-free full-length transcripts and broken chromosomes. Therefore, transcription fidelity may compromise genomic integrity.
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Affiliation(s)
- Alasdair J E Gordon
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Priya Sivaramakrishnan
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Department of Genetics , Perelman School of Medicine, University of Pennsylvania , Philadelphia , PA , USA
| | - Jennifer A Halliday
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Christophe Herman
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,c Department of Molecular Virology and Microbiology , Baylor College of Medicine , Houston , TX , USA.,d Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston , TX , USA
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19
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Cui G, Wang J, Qi X, Su J. Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida. Sci Rep 2018; 8:6895. [PMID: 29720697 PMCID: PMC5932009 DOI: 10.1038/s41598-018-25271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/18/2018] [Indexed: 01/24/2023] Open
Abstract
Francisella tularensis is a facultative intracellular Gram-negative bacterium that causes the zoonotic disease tularemia. We identified the transcription elongation factor GreA as a virulence factor in our previous study, but its role was not defined. Here, we investigate the effects of the inactivation of the greA gene, generating a greA mutant of F. tularensis subsp. novicida. Inactivation of greA impaired the bacterial invasion into and growth within host cells, and subsequently virulence in mouse infection model. A transcriptomic analysis (RNA-Seq) showed that the loss of GreA caused the differential expression of 196 bacterial genes, 77 of which were identified as virulence factors in previous studies. To confirm that GreA regulates the expression of virulence factors involved in cell invasion by Francisella, FTN_1186 (pepO) and FTN_1551 (ampD) gene mutants were generated. The ampD deletion mutant showed reduced invasiveness into host cells. These results strongly suggest that GreA plays an important role in the pathogenesis of Francisella by affecting the expression of virulence genes and provide new insights into the complex regulation of Francisella infection.
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Affiliation(s)
- Guolin Cui
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jun Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xinyi Qi
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jingliang Su
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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Transcription fidelity and its roles in the cell. Curr Opin Microbiol 2017; 42:13-18. [PMID: 28968546 PMCID: PMC5904569 DOI: 10.1016/j.mib.2017.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 12/21/2022]
Abstract
The Trigger Loop is one of the major determinants of transcription fidelity. Intrinsic proofreading occurs via transcript-assisted cleavage. Factor-assisted proofreading takes place via exchange of RNAP active centres. Misincorporation is a major source of transcription pausing. Another role of fidelity is the prevention of conflicts with other cellular processes.
Accuracy of transcription is essential for productive gene expression, and the past decade has brought new understanding of the mechanisms ensuring transcription fidelity. The discovery of a new catalytic domain, the Trigger Loop, revealed that RNA polymerase can actively choose the correct substrates. Also, the intrinsic proofreading activity was found to proceed via a ribozyme-like mechanism, whereby the erroneous nucleoside triphosphate (NTP) helps its own excision. Factor-assisted proofreading was shown to proceed through an exchange of active centres, a unique phenomenon among proteinaceous enzymes. Furthermore, most recent in vivo studies have revised the roles of transcription accuracy and proofreading factors, as not only required for production of errorless RNAs, but also for prevention of frequent misincorporation-induced pausing that may cause conflicts with fellow RNA polymerases and the replication machinery.
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