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You searched for: Subject DNA-directed RNA polymerase Remove constraint Subject: DNA-directed RNA polymerase Subject Escherichia coli Remove constraint Subject: Escherichia coli Subject term Escherichia coli Remove constraint Subject term: Escherichia coli Text availability Citation in PubAg Remove constraint Text availability: Citation in PubAg
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1. Enhancing transcription in Escherichia coli and Pseudomonas putida using bacteriophage lambda anti-terminator protein Q

Author:
Jibran A. Khan; Adam M. Guss; Katy C. Kao
Source:
Biotechnology letters 2022 v.44 no.2 pp. 253-258
ISSN:
0141-5492
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; Lactobacillus plantarum; Pseudomonas putida; bacteriophages; biotechnology; fluorescence; metagenomics; polysaccharides; transcription initiation site
Abstract:
... Functional characterization of metagenomic DNA often involves expressing heterologous DNA in genetically tractable microorganisms such as Escherichia coli. Functional expression of heterologous genes can suffer from limitations due to the lack of recognition of foreign promoters or presence of intrinsic terminators on foreign DNA between a vector-based promoter and the transcription start site. An ...
DOI:
10.1007/s10529-021-03206-x

2. De Novo Design of the ArsR Regulated Pₐᵣₛ Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination

Author:
Sheng-Yan Chen; Yan Zhang; Renjie Li; Baojun Wang; Bang-Ce Ye
Source:
Analytical chemistry 2022 v.94 no.20 pp. 7210-7218
ISSN:
1520-6882
Subject:
DNA-directed RNA polymerase; Escherichia coli; analytical chemistry; arsenic; biosensors; colorimetry; detection limit; fluorescence; gene regulatory networks; groundwater; mobile telephones; reporter genes
Abstract:
... Whole-cell biosensors for arsenic contamination are typically designed based on natural bacterial sensing systems, which are often limited by their poor performance for precisely tuning the genetic response to environmental stimuli. Promoter design remains one of the most important approaches to address such issues. Here, we use the arsenic-responsive ArsR-Pₐᵣₛ regulation system from Escherichia c ...
DOI:
10.1021/acs.analchem.2c00055

3. PromoterLCNN: A Light CNN-Based Promoter Prediction and Classification Model

Author:
Daryl Hernández; Nicolás Jara; Mauricio Araya; Roberto E. Durán; Carlos Buil-Aranda
Source:
Genes 2022 v.13 no.7 pp. -
ISSN:
2073-4425
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; data collection; genes; prediction
Abstract:
... Promoter identification is a fundamental step in understanding bacterial gene regulation mechanisms. However, accurate and fast classification of bacterial promoters continues to be challenging. New methods based on deep convolutional networks have been applied to identify and classify bacterial promoters recognized by sigma (σ) factors and RNA polymerase subunits which increase affinity to specif ...
DOI:
10.3390/genes13071126

4. Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis

Author:
Dylan Plaskon; Claire Evensen; Kate Henderson; Benjamin Palatnik; Takahiro Ishikuri; Hao-Che Wang; Sarah Doughty; M. Thomas Record Jr.
Source:
Journal of molecular biology 2022 v.434 no.13 pp. 167621
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; RNA; antibiotics; byproducts; gene expression regulation; molecular biology; transcription initiation; uridine
Abstract:
... An understanding of the kinetics and mechanism of bacterial transcription initiation is needed to understand regulation of gene expression and advance fields from antibiotic discovery to promoter design. The step-by-step forward kinetics and mechanism of initiation and RNA-DNA hybrid growth, made irreversible by omitting pyrophosphate (PPi) byproduct, were determined recently for E. coli RNA polym ...
DOI:
10.1016/j.jmb.2022.167621

5. Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs

Author:
Anthony L. Shiver; Hendrik Osadnik; Jason M. Peters; Rachel A. Mooney; Peter I. Wu; Kemardo K. Henry; Hannes Braberg; Nevan J. Krogan; James C. Hu; Robert Landick; Kerwyn Casey Huang; Carol A. Gross
Source:
Molecular cell 2021 v.81 no.10 pp. 2201-2215.e9
ISSN:
1097-2765
Subject:
DNA-directed RNA polymerase; Escherichia coli; biotechnology; mutants
Abstract:
... The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated RNAP mechanism, and RNAP mutations drive Escherichia coli adaptation to many health- and industry-relevant environments, yet a paucity of systematic analyses hampers our understanding of the fitness trade-offs from alter ...
DOI:
10.1016/j.molcel.2021.04.027

6. Determination of glutathione-binding to proteins by fluorescence spectroscopy

Author:
Taner Duysak; Aqeel Rana Afzal; Che-Hun Jung
Source:
Biochemical and biophysical research communications 2021 v.557 pp. 329-333
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Escherichia coli; arabinose; dissociation; fluorescence; fluorescence emission spectroscopy; fumarate hydratase; glutathione; isomerases; malate dehydrogenase; research; thiols
Abstract:
... Glutathione (GSH) is the most abundant non-protein thiol and its cellular concentration has been reported as 17 mM in Escherichia coli. This study introduces a label-free method to determine the binding affinity of GSH to proteins, utilizing the intrinsic fluorescence of proteins; the dissociation constants of GSH for d-arabinose 5-phosphate isomerase KdsD, fumarase C, malate dehydrogenase, and RN ...
DOI:
10.1016/j.bbrc.2021.04.016

7. Efforts toward Further Integration of an Unnatural Base Pair into the Biology of a Semisynthetic Organism

Author:
Koji Hashimoto; Emil C. Fischer; Floyd E. Romesberg
Source:
Journal of the American Chemical Society 2021 v.143 no.23 pp. 8603-8607
ISSN:
1520-5126
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; bacteriophages; heterologous gene expression
Abstract:
... We have developed semisynthetic organisms (SSOs) that by virtue of a family of synthetic, unnatural base pairs (UBPs), store and retrieve increased information. To date, transcription in the SSOs has relied on heterologous expression of the RNA polymerase from T7 bacteriophage; here, we explore placing transcription under the control of the endogenous host multisubunit RNA polymerase. The results ...
DOI:
10.1021/jacs.1c03860

8. Enhancing n-Butanol Tolerance of Escherichia coli by Overexpressing of Stress-Responsive Molecular Chaperones

Author:
Guochao Xu; Lin Xiao; Anning Wu; Ruizhi Han; Ye Ni
Source:
Applied biochemistry and biotechnology 2021 v.193 no.1 pp. 257-270
ISSN:
0273-2289
Subject:
DNA-directed RNA polymerase; Escherichia coli; RNA; biofuels; biotechnology; butanol; cell structures; genes; molecular chaperones; specific growth rate; viability
Abstract:
... Microbial tolerance to organic solvents is critical for efficient production of biofuels. In this study, n-butanol tolerance of Escherichia coli JM109 was improved by overexpressing of genes encoding stress-responsive small RNA-regulator, RNA chaperone, and molecular chaperone. Gene rpoS, coding for sigma S subunit of RNA polymerase, was the most efficient in improving n-butanol tolerance of E. co ...
DOI:
10.1007/s12010-020-03417-4

9. Functional expression of an echinocandin B deacylase from Actinoplanes utahensis in Escherichia coli

Author:
Shu-Ping Zou; Xin Han; Han-Yue Zhu; Qi Sheng; Heng Tang; Zhi-Qiang Liu; Yu-Guo Zheng
Source:
International journal of biological macromolecules 2021 v.187 pp. 850-857
ISSN:
0141-8130
Subject:
Actinoplanes utahensis; DNA-directed RNA polymerase; Escherichia coli; Streptomyces; anidulafungin; electrostatic interactions; industrial applications; pH; plasmids; solubility; temperature
Abstract:
... Echinocandin B deacylase (ECBD) from Actinoplanes utahensis can be applied to produce echinocandin B nucleus (ECBN), an essential intermediate of the echinocandins antifungal drugs such as anidulafungin. To date, the expression of ECBD has been limited to Streptomyces. To achieve the active expression of ECBD in Escherichia coli (E. coli), we constructed a plasmid carrying two subunits of ECBD for ...
DOI:
10.1016/j.ijbiomac.2021.07.146

10. Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure

Author:
S Selveshwari; Kasturi Lele; Sutirth Dey
Source:
Journal of evolutionary biology 2021 v.34 no.6 pp. 953-967
ISSN:
1010-061X
Subject:
DNA repair; DNA-directed RNA polymerase; Escherichia coli; ancestry; cell adhesion; cell membrane structures; directed evolution; genomics; phenotype; physiological state; selection pressure; sequence analysis; signal transduction; transcription (genetics); ultraviolet radiation
Abstract:
... Physiological states can determine the ability of organisms to handle stress. Does this mean that the same selection pressure will lead to different evolutionary outcomes, depending on the organisms’ physiological state? If yes, what will be the genomic signatures of such adaptation(s)? We used experimental evolution in Escherichia coli followed by whole‐genome whole‐population sequencing to inves ...
DOI:
10.1111/jeb.13764

11. Maturation of 23S rRNA includes removal of helix H1 in many bacteria

Author:
Elan A. Shatoff; Bryan T. Gemler; Ralf Bundschuh; Kurt Fredrick
Source:
RNA biology 2021 v.18 no.S2 pp. 856-865
ISSN:
1555-8584
Subject:
Bacillus subtilis; DNA-directed RNA polymerase; Escherichia coli; Flavobacterium johnsoniae; operon; ribonucleases; ribosomal proteins; ribosomes; sequence analysis; transcriptomics
Abstract:
... In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as the nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails ribosomal protein binding, rRNA folding, rRNA modification, and rRNA processing. In the model organisms Escherichia coli and Bacillus subtilis, rRNA processing results in ...
DOI:
10.1080/15476286.2021.2000793

12. Natural biflavonoids as potential therapeutic agents against microbial diseases

Author:
José C.J.M.D.S. Menezes; Vinícius R. Campos
Source:
Science of the total environment 2021 v.769 pp. 145168
ISSN:
0048-9697
Subject:
DNA-directed DNA polymerase; DNA-directed RNA polymerase; Escherichia coli; Garcinia; Human gammaherpesvirus 4; Plasmodium falciparum; Protozoa; RNA; RNA-directed DNA polymerase; antigens; bioactive properties; bioavailability; biosphere; candidiasis; cross infection; cysteine proteinases; cytokines; dengue; fatty-acid synthase; flavones; fungi; gene expression; hepatitis; humans; influenza; leishmaniasis; malaria; mechanism of action; methicillin-resistant Staphylococcus aureus; mitochondria; oxidoreductases; sialidase; therapeutics
Abstract:
... Microbes broadly constitute several organisms like viruses, protozoa, bacteria, and fungi present in our biosphere. Fast-paced environmental changes have influenced contact of human populations with newly identified microbes resulting in diseases that can spread quickly. These microbes can cause infections like HIV, SARS-CoV2, malaria, nosocomial Escherichia coli, methicillin-resistant Staphylococ ...
DOI:
10.1016/j.scitotenv.2021.145168

13. Novel self-regulation strategy of a small heat shock protein for prodigious and rapid expression on demand

Author:
Tsukumi Miwa; Hideki Taguchi
Source:
Current genetics 2021 v.67 no.5 pp. 723-727
ISSN:
0172-8083
Subject:
DNA-directed RNA polymerase; Escherichia coli; eukaryotic cells; heat; heat shock proteins; heat stress
Abstract:
... In this mini-review, we summarize the known and novel regulation mechanisms of small heat shock proteins (sHsps). sHsps belong to a well-conserved family of ATP-independent oligomeric chaperones that protect denatured proteins from forming irreversible aggregates by co-aggregation. The functions of sHsps as a first line of defense against acute stresses require the high abundance of sHsps on deman ...
DOI:
10.1007/s00294-021-01185-0

14. Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase

Author:
Anastasiya Oguienko; Ivan Petushkov; Danil Pupov; Daria Esyunina; Andrey Kulbachinskiy
Source:
RNA biology 2021 v.18 no.11 pp. 2028-2037
ISSN:
1555-8584
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; RNA; stress response; transcription initiation; transcription initiation site
Abstract:
... The bacterial σ factor plays the central role in promoter recognition by RNA polymerase (RNAP). The primary σ factor, involved in transcription of housekeeping genes, was also shown to participate in the initiation of RNA synthesis and promoter escape by RNAP. In the open promoter complex, the σ finger formed by σ region 3.2 directly interacts with the template DNA strand upstream of the transcrip ...
DOI:
10.1080/15476286.2021.1889254

15. The construction of a dual-functional strain that produces both polysaccharides and sulfotransferases

Author:
Xiaomei Li; Yanying Yu; Jiaqing Tang; Bingxue Gong; Wenjing Li; Tingting Chen; Xianxuan Zhou
Source:
Biotechnology letters 2021 v.43 no.9 pp. 1831-1844
ISSN:
0141-5492
Subject:
DNA-directed RNA polymerase; Escherichia coli; active sites; batch fermentation; biotechnology; culture media; drugs; elemental composition; heparin; humans; mice; nuclear magnetic resonance spectroscopy; plasmids; probiotics; sulfotransferases
Abstract:
... OBJECTIVES: Heparosan is used as the starting polysaccharide sulfated using sulfotransferase to generate fully elaborate heparin, a widely used clinical drug. However, the preparation of heparosan and enzymes was considered tedious since such material must be prepared in separate fermentation batches. In this study, a commonly admitted probiotic, Escherichia coli strain Nissle 1917 (EcN), was engi ...
DOI:
10.1007/s10529-021-03156-4

16. A counting-strategy together with a spatial structured model describes RNA polymerase and ribosome availability in Escherichia coli

Author:
Andreas Kremling
Source:
Metabolic engineering 2021 v.67 pp. 145-152
ISSN:
1096-7176
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; bacterial growth; gene expression; models; proteome; ribosomes
Abstract:
... The allocation of resources during bacterial growth is strongly related to the availability of ribosomes and RNA polymerase molecules. Here, coarse-grained models offer a promising start due to their simple structure and the limited number of kinetic parameters. Based on published data sets for proteome and mRNA data in Escherichia coli, and together with mass balance equations describing gene exp ...
DOI:
10.1016/j.ymben.2021.06.006

17. An efficient dsRNA constitutive expression system in Escherichia coli

Author:
Josemaría Delgado-Martín; Leonardo Velasco
Source:
Applied microbiology and biotechnology 2021 v.105 no.16-17 pp. 6381-6393
ISSN:
0175-7598
Subject:
DNA-directed RNA polymerase; Escherichia coli; Nicotiana benthamiana; biotechnology; gene expression; genes; promoter regions; reverse genetics; viruses
Abstract:
... Synthetic dsRNA are valuable tools for reverse genetics research and virus silencing applications. Its synthesis can be performed both in vivo or in vitro. Whilst the latter presents the drawback of high production cost, the former has the advantage of being less expensive and suitable for scalable production. In general, dsRNAs are obtained in vivo from Escherichia coli heterologous systems that ...
DOI:
10.1007/s00253-021-11494-6

18. A plant CitPITP1 protein-coding exon sequence serves as a promoter in bacteria

Author:
Qingjiang Wu; Jialing Fu; Juan Sun; Xia Wang; Xiaomei Tang; Wenjia Lu; Chen Tan; Li Li; Xiuxin Deng; Qiang Xu
Source:
Journal of biotechnology 2021 v.339 pp. 1-13
ISSN:
0168-1656
Subject:
Amborella; Arabidopsis; Citrus; DNA-directed RNA polymerase; Escherichia coli; animals; biotechnology; exons; genetically modified plants; molecular biology; mutational analysis; nucleotides; prokaryotic cells
Abstract:
... Genetic manipulation of plant genes in prokaryotes has been widely used in molecular biology, but the function of a DNA sequence is far from being fully known. Here, we discovered that a plant protein-coding gene containing the CRAL_TRIO domain serves as a promoter in bacteria. We firstly characterized CitPITP1 from Citrus, which contains the CRAL_TRIO domain, and identified a 64-bp sequence (key6 ...
DOI:
10.1016/j.jbiotec.2021.07.011

19. A unique binding between SspA and RNAP β’NTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation

Author:
Fulin Wang; Yu Feng; Zhuo Shang; Wei Lin
Source:
Biochemical and biophysical research communications 2021 v.583 pp. 86-92
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Escherichia coli; acid tolerance; coevolution; data collection; metabolism; phylogeny; research; starvation; transcription (genetics); transcription factors; virulence; zinc
Abstract:
... Stringent starvation protein A (SspA) involved in nucleotide metabolism, acid tolerance and virulence of bacteria has been demonstrated to function as a transcription factor to regulate σ⁷⁰-dependent gene transcription through interacting with σ⁷⁰ region 4 and the zinc binding domain (ZBD) of E. coli RNA polymerase (EcoRNAP) β′ subunit simultaneously. Despite extensive biochemical and structural a ...
DOI:
10.1016/j.bbrc.2021.10.048

20. Antimicrobial antisense RNA delivery to F-pili producing multidrug-resistant bacteria via a genetically engineered bacteriophage

Author:
Yuya Suzuki; Takumi Ishimoto; Shouta Fujita; Sachie Kiryu; Mamoru Wada; Takahiro Akatsuka; Mineki Saito; Mitsuoki Kawano
Source:
Biochemical and biophysical research communications 2020 v.530 no.3 pp. 533-540
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Escherichia coli; Klebsiella pneumoniae; antisense RNA; bacterial infections; bacteriophages; death; genes; genetic engineering; multiple drug resistance; research; ribosomal proteins; sigma factors
Abstract:
... Multidrug-resistant bacteria are a growing issue worldwide. This study developed a convenient and effective method to downregulate the expression of a specific gene to produce a novel antimicrobial tool using a small (140 nucleotide) RNA with a 24-nucleotide antisense (as) region from an arabinose-inducible expression phagemid vector in Escherichia coli. Knockdown effects of rpoS encoding RNA poly ...
DOI:
10.1016/j.bbrc.2020.06.088

21. Efficient heterologous expression of nicotinate dehydrogenase in Comamonas testosteroni CNB-2 with transcriptional, folding enhancement strategy

Author:
Zhen-Hua Lu; Li-Rong Yang; Jian-Ping Wu
Source:
Enzyme and microbial technology 2020 v.134 pp. 109478
ISSN:
0141-0229
Subject:
Comamonas testosteroni; DNA-directed RNA polymerase; Escherichia coli; Komagataella pastoris; catalytic activity; electron transfer; enzyme activity; heterologous gene expression; hydroxylation; membrane proteins; molecular chaperones; oxidoreductases; plasmids; protein synthesis; synthesis; technology; transcription (genetics)
Abstract:
... Nicotinate dehydrogenase (NDHase) from Comamonas testosteroni JA1 catalyzes the C6 hydroxylation of 3-cyanopyridine with high regional selectivity, which is a very difficult and complex reaction for chemical synthesis. However, because NDHase is a membrane protein with three subunits (ndhS, ndhL and ndhM), it is difficult to express the enzyme in a functional form using common hosts such as Escher ...
DOI:
10.1016/j.enzmictec.2019.109478

22. Factor-specific effects of mutations in the active site of RNA polymerase on RNA cleavage

Author:
Nataliya Miropolskaya; Andrey Kulbachinskiy; Daria Esyunina
Source:
Biochemical and biophysical research communications 2020 v.523 no.1 pp. 165-170
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Escherichia coli; RNA; active sites; arginine; research
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 diff ...
DOI:
10.1016/j.bbrc.2019.12.045

23. Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex

Author:
Raashi Sreenivasan; Irina A. Shkel; Munish Chhabra; Amanda Drennan; Sara Heitkamp; Hao-Che Wang; Malavika A. Sridevi; Dylan Plaskon; Christina McNerney; Katelyn Callies; Clare K. Cimperman; M. Thomas Record
Source:
Biochemistry 2020 v.59 no.16 pp. 1565-1581
ISSN:
1520-4995
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; energy transfer; fluorescence; isomerization
Abstract:
... FRET (fluorescence resonance energy transfer) between far-upstream (−100) and downstream (+14) cyanine dyes (Cy3, Cy5) showed extensive bending and wrapping of λPR promoter DNA on Escherichia coli RNA polymerase (RNAP) in closed and open complexes (CC and OC, respectively). Here we determine the kinetics and mechanism of DNA bending and wrapping by FRET and of formation of RNAP contacts with −100 ...
DOI:
10.1021/acs.biochem.0c00098

24. Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network

Author:
Joon Young Park; Hemraj Rimal; Ina Bang; Linh Khanh Nong; Donghyuk Kim
Source:
Biotechnology and bioprocess engineering 2020 v.25 no.6 pp. 944-954
ISSN:
1226-8372
Subject:
DNA-directed RNA polymerase; Escherichia coli; bioprocessing; biotechnology; chromatin immunoprecipitation; digestion; epigenetics; gene expression regulation; microarray technology; transcription (genetics)
Abstract:
... The development and innovative use of next-generation sequencing technologies have opened the doors for genetic and epigenetic research at the next level. These technologies can be used to study gene expression regulation at the transcriptional and post-transcriptional levels in both prokaryotic and eukaryotic systems. In this review, we focused on the various tools and techniques for DNA-binding ...
DOI:
10.1007/s12257-020-0030-9

25. A Kayvirus Distant Homolog of Staphylococcal Virulence Determinants and VISA Biomarker Is a Phage Lytic Enzyme

Author:
Aleksandra Głowacka-Rutkowska; Magdalena Ulatowska; Joanna Empel; Magdalena Kowalczyk; Jakub Boreczek; Małgorzata Łobocka
Source:
Viruses 2020 v.12 no.3 pp. -
ISSN:
1999-4915
Subject:
DNA-directed RNA polymerase; Escherichia coli; antibiotic resistance; bacteriophages; biomarkers; cell walls; endolysin; gametolysin; genes; nisin; signal peptide; therapeutics; transcription (genetics); vancomycin; virulence
Abstract:
... Staphylococcal bacteriophages of the Kayvirus genus are candidates for therapeutic applications. One of their proteins, Tgl, is slightly similar to two staphylococcal virulence factors, secreted autolysins of lytic transglycosylase motifs IsaA and SceD. We show that Tgl is a lytic enzyme secreted by the bacterial transport system and localizes to cell peripheries like IsaA and SceD. It causes lysi ...
DOI:
10.3390/v12030292

26. Linking bacterial growth, survival, and multicellularity – small signaling molecules as triggers and drivers

Author:
Regine Hengge
Source:
Current opinion in microbiology 2020 v.55 pp. 57-66
ISSN:
1369-5274
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteria; bacterial growth; biofilm; cyclic AMP; extracellular matrix; models; polymers; second messengers; stress tolerance; transcription (genetics)
Abstract:
... An overarching theme of cellular regulation in bacteria arises from the trade-off between growth and stress resilience. In addition, the formation of biofilms contributes to stress survival, since these dense multicellular aggregates, in which cells are embedded in an extracellular matrix of self-produced polymers, represent a self-constructed protective and homeostatic 'niche'. As shown here for ...
DOI:
10.1016/j.mib.2020.02.007

27. Novel Escherichia coli RNA Polymerase Binding Protein Encoded by Bacteriophage T5

Author:
Evgeny Klimuk; Vladimir Mekler; Darya Lavysh; Marina Serebryakova; Natalia Akulenko; Konstantin Severinov
Source:
Viruses 2020 v.12 no.8 pp. -
ISSN:
1999-4915
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteriophages; binding proteins; genes; messenger RNA; mutants; transcription (genetics); virion
Abstract:
... The Escherichia coli bacteriophage T5 has three temporal classes of genes (pre-early, early, and late). All three classes are transcribed by host RNA polymerase (RNAP) containing the σ⁷⁰ promoter specificity subunit. Molecular mechanisms responsible for the switching of viral transcription from one class to another remain unknown. Here, we find the product of T5 gene 026 (gpT5.026) in RNAP prepara ...
DOI:
10.3390/v12080807

28. Preparation of a ribosomally synthesized fungal peptide toxin precursor and its in-vitro cyclization

Author:
Duleepa Pathiraja; Juan Byun; Saeyoung Lee; In-Geol Choi
Source:
Journal of biotechnology 2020 v.308 pp. 124-129
ISSN:
0168-1656
Subject:
DNA-directed RNA polymerase; Escherichia coli; alpha-amanitin; biomass; enzyme inhibitors; genes; macrocyclization reactions; mushrooms; poisonous fungi; post-translational modification; prolyl oligopeptidase; proteins; solubility; transcription (genetics)
Abstract:
... Amatoxins are ribosomally synthesized and post-translationally modified peptides (RiPPs) found in poisonous mushrooms. These cyclic peptides are potent inhibitors of RNA polymerase II transcriptional activity. Though the macrocyclization of amatoxin is extensively studied, little is known about its subsequent post-translational modifications. However, studies and the potential use of amatoxins has ...
DOI:
10.1016/j.jbiotec.2019.12.004

29. The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element

Author:
Samuel Lara-Gonzalez; Ana Carolina Dantas Machado; Satyanarayan Rao; Andrew A. Napoli; Jens Birktoft; Rosa Di Felice; Remo Rohs; Catherine L. Lawson
Source:
Biochemistry 2020 v.59 no.48 pp. 4523-4532
ISSN:
1520-4995
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; alanine; amino acid sequences; arginine; crystal structure; crystallization; guanidinium; length; molecular dynamics; mutation; promoter regions; shape; transcription factors
Abstract:
... We demonstrate here that the α subunit C-terminal domain of Escherichia coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of αCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A₆-tract), each with the ...
DOI:
10.1021/acs.biochem.0c00571

30. RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time

Author:
Menglin Chen; Kurt Fredrick
Source:
Journal of molecular biology 2020 v.432 no.14 pp. 3981-3986
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteria; messenger RNA; ribosomes; transcription termination; translation (genetics)
Abstract:
... In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide ...
DOI:
10.1016/j.jmb.2020.03.018

31. Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories

Author:
Yingxi Chen; Erin E. Boggess; Efrain Rodriguez Ocasio; Aric Warner; Lucas Kerns; Victoria Drapal; Chloe Gossling; Wilma Ross; Richard L. Gourse; Zengyi Shao; Julie Dickerson; Thomas J. Mansell; Laura R. Jarboe
Source:
Metabolic engineering 2020 v.61 pp. 120-130
ISSN:
1096-7176
Subject:
DNA-directed RNA polymerase; Escherichia coli; acid tolerance; amino acids; butanol; cell membranes; evolution; furfural; hydrophobicity; lipopolysaccharides; mutation; octanoic acid; polymers; stress response; vanillin
Abstract:
... Adaptive laboratory evolution is often used to improve the performance of microbial cell factories. Reverse engineering of evolved strains enables learning and subsequent incorporation of novel design strategies via the design-build-test-learn cycle. Here, we reverse engineer a strain of Escherichia coli previously evolved for increased tolerance of octanoic acid (C8), an attractive biorenewable c ...
DOI:
10.1016/j.ymben.2020.05.001

32. Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination

Author:
Ezaz Ahmad; Shubhada R. Hegde; Valakunja Nagaraja
Source:
Biochemical and biophysical research communications 2020 v.522 no.1 pp. 226-232
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Escherichia coli; RNA; computer simulation; research; transcription termination
Abstract:
... In Escherichia coli, G/C-rich hairpin structure followed by a U-tract in the 3′ region of the nascent RNA are crucial determinants for intrinsic or factor independent transcription termination. In mycobacteria, there is a scarcity of such intrinsic terminators. However, secondary structures having G/C-rich stem devoid of any U’s or with suboptimal U-tracts were identified earlier as terminators an ...
DOI:
10.1016/j.bbrc.2019.11.062

33. Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti

Author:
Olga Y. Burenina; Daria A. Elkina; Anzhela Y. Migur; Tatiana S. Oretskaya; Elena Evguenieva-Hackenberg; Roland K. Hartmann; Elena A. Kubareva
Source:
journal of microbiology 2020 v.58 no.11 pp. 945-956
ISSN:
1225-8873
Subject:
Bradyrhizobium japonicum; DNA-directed RNA polymerase; Ensifer meliloti; Escherichia coli; Rhodobacter sphaeroides; dissociation; gene expression; nitrogen fixation; non-coding RNA; nucleotides; sequence analysis; symbionts
Abstract:
... 6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobial ...
DOI:
10.1007/s12275-020-0283-1

34. Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis

Author:
Yong-Heng Huang; Tarek Hilal; Bernhard Loll; Jörg Bürger; Thorsten Mielke; Christoph Böttcher; Nelly Said; Markus C. Wahl
Source:
Molecular cell 2020 v.79 no.6 pp. 1024-1036.e5
ISSN:
1097-2765
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; amino acid sequences; biosynthesis; cryo-electron microscopy; inositols; ribosomal RNA; ribosomal proteins; ribosomes
Abstract:
... Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia col ...
DOI:
10.1016/j.molcel.2020.08.010

35. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing

Author:
Jared T. Winkelman; Chirangini Pukhrambam; Irina O. Vvedenskaya; Yuanchao Zhang; Deanne M. Taylor; Premal Shah; Richard H. Ebright; Bryce E. Nickels
Source:
Molecular cell 2020 v.79 no.5 pp. 797-811.e8
ISSN:
1097-2765
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; consensus sequence
Abstract:
... Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a “stepping” mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a “scrunching” mechanism, has not. We report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolutio ...
DOI:
10.1016/j.molcel.2020.07.006

36. Arabinose Alters Both Local and Distal H–D Exchange Rates in the Escherichia coli AraC Transcriptional Regulator

Author:
Alexander Tischer; Matthew J. Brown; Robert F. Schleif; Matthew Auton
Source:
Biochemistry 2019 v.58 no.26 pp. 2875-2882
ISSN:
1520-4995
Subject:
DNA; DNA-binding domains; DNA-directed RNA polymerase; Escherichia coli; arabinose; dimerization; hydrogen bonding; mass spectrometry; metabolism; operon; peptides; probability; regulatory proteins; transcription (genetics); transcription factors
Abstract:
... In the absence of arabinose, the dimeric Escherichia coli regulatory protein of the l-arabinose operon, AraC, represses expression by looping the DNA between distant half-sites. Binding of arabinose to the dimerization domains forces AraC to preferentially bind two adjacent DNA half-sites, which stimulates RNA polymerase transcription of the araBAD catabolism genes. Prior genetic and biochemical s ...
DOI:
10.1021/acs.biochem.9b00389

37. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase

Author:
Danil Pupov; Artem Ignatov; Aleksei Agapov; Andrey Kulbachinskiy
Source:
Biochemical and biophysical research communications 2019 v.510 no.1 pp. 122-127
ISSN:
0006-291X
Subject:
DNA; DNA damage; DNA repair; DNA-directed RNA polymerase; Escherichia coli; RNA; active sites; adenine nucleotides; cell death; genome; mutation; thymine; transcription (genetics)
Abstract:
... DNA lesions can severely compromise genome stability and lead to cell death if unrepaired. RNA polymerase (RNAP) is known to serve as a sensor of DNA damage and to attract DNA repair factors to the damaged template sites. Here, we systematically investigated the ability of Escherichia coli RNAP to transcribe DNA templates containing various types of DNA lesions, and analyzed their effects on trans ...
DOI:
10.1016/j.bbrc.2019.01.062

38. DksA and DNA double-strand break repair

Author:
Kamila K. Myka; Max E. Gottesman
Source:
Current genetics 2019 v.65 no.6 pp. 1297-1300
ISSN:
0172-8083
Subject:
DNA; DNA damage; DNA repair; DNA replication; DNA-directed DNA polymerase; DNA-directed RNA polymerase; Escherichia coli; RNA primers; genome; mitomycin; nalidixic acid; transcription factors; ultraviolet radiation
Abstract:
... We use genetic assays to suggest that transcription-coupled repair or new origin formation in Escherichia coli involves removal of RNAP to create an RNA primer for DNA synthesis. Transcription factor DksA was shown to play a role in numerous reactions involving RNA polymerase. Some, but not all, of the activities of DksA at promoters or during transcription elongation require (p)ppGpp. In addition ...
DOI:
10.1007/s00294-019-00983-x

39. Evolutionary engineering of Escherichia coli for improved anaerobic growth in minimal medium accelerated lactate production

Author:
Baowei Wang; Xiaoxia Zhang; Xinlei Yu; Zhenzhen Cui; Zhiwen Wang; Tao Chen; Xueming Zhao
Source:
Applied microbiology and biotechnology 2019 v.103 no.5 pp. 2155-2170
ISSN:
0175-7598
Subject:
DNA-directed RNA polymerase; Escherichia coli; acetolactate synthase; batch fermentation; bioreactors; ethanol; lactic acid; metabolic engineering; mutation; protein subunits
Abstract:
... Anaerobic fermentation is a favorable process for microbial production of bulk chemicals like ethanol and organic acids. Low productivity is the bottleneck of several anaerobic processes which has significant impact on the technique competitiveness of production strain. Improving growth rate of production strain can speed up the total production cycle and may finally increase productivity of anaer ...
DOI:
10.1007/s00253-018-09588-9

40. Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

Author:
Steen Pedersen; Thilde Bagger Terkelsen; Mette Eriksen; Magnus Krarup Hauge; Casper Carstens Lund; Kim Sneppen; Namiko Mitarai
Source:
Journal of molecular biology 2019 v.431 no.6 pp. 1088-1097
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; amino acids; codons; messenger RNA; models; ribosomal proteins; ribosomes; transcription termination; translation (genetics)
Abstract:
... We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The only difference between the two inserts was that the first base in one was moved to ...
DOI:
10.1016/j.jmb.2019.01.026

41. Growth phase-specific changes in the composition of E. coli transcription complexes

Author:
Isaac R. Eason; Harman P. Kaur; Katherine A. Alexander; Maxim V. Sukhodolets
Source:
Journal of chromatography 2019 v.1109 pp. 155-165
ISSN:
1570-0232
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; RNA; cell membranes; chromatography; isolation techniques; lipopolysaccharides; mass spectrometry; metabolism; phospholipids; proteins; protocols; ribosomes; transcription (genetics)
Abstract:
... In E. coli, a single oligomeric enzyme transcribes the genomic DNA, while multiple auxiliary proteins and regulatory RNA interact with the core RNA polymerase (RP) during different stages of the transcription cycle to influence its function. In this work, using fast protein isolation techniques combined with mass spectrometry (MS) and immuno-analyses, we studied growth phase-specific changes in th ...
DOI:
10.1016/j.jchromb.2019.01.014

42. Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading

Author:
Daria Esyunina; Andrey Kulbachinskiy
Source:
Biochemical and biophysical research communications 2019 v.509 no.1 pp. 161-166
ISSN:
0006-291X
Subject:
DNA-directed RNA polymerase; Deinococcus radiodurans; Escherichia coli; active sites; bacteria; genome; hydrolysis; messenger RNA; metal ions; nucleotides; transcription (genetics)
Abstract:
... Co-transcriptional RNA proofreading by RNA polymerase (RNAP) is essential for accurate mRNA synthesis and reactivation of stalled transcription complexes, which can otherwise compromise genome integrity. RNAP from the stress-resistant bacterium Deinococcus radiodurans exhibits high levels of RNA cleavage in comparison with RNAP from Escherichia coli, which allows it to remove misincorporated nucle ...
DOI:
10.1016/j.bbrc.2018.12.095

43. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

Author:
Sangjin Kim; Bruno Beltran; Irnov Irnov; Christine Jacobs-Wagner
Source:
Cell 2019 v.179 no.1 pp. 106-119.e16
ISSN:
0092-8674
Subject:
DNA; DNA topoisomerase; DNA-directed RNA polymerase; Escherichia coli; RNA; environmental factors; genes; proteins; transcription (genetics)
Abstract:
... Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when ...
DOI:
10.1016/j.cell.2019.08.033

44. Mycobacterial transcript cleavage factor Gre, exhibits chaperone-like activity

Author:
Abyson Joseph; Valakunja Nagaraja; Ramanathan Natesh
Source:
Biochimica et biophysica acta 2019 v.1867 no.9 pp. 757-764
ISSN:
1570-9639
Subject:
DNA-directed RNA polymerase; Escherichia coli; Mycobacterium smegmatis; Mycobacterium tuberculosis; circular dichroism spectroscopy; enzyme activity; heat; heat stress; hydrophobicity; messenger RNA; oligomerization; oxidative stress; proteins; stress response; sulfonates; transcription (genetics)
Abstract:
... Gre factors reactivate stalled elongation complexes by enhancing the intrinsic transcript cleavage activity of RNA polymerase. Previous work by us has shown that unlike in Escherichia coli (E.coli), Mycobacterium tuberculosis Gre factor is essential for its survival. Apart from their role in transcription regulation Gre factors have been implicated in stress response. A recent study has shown the ...
DOI:
10.1016/j.bbapap.2019.05.008

45. Purification of Tag-Free Chlamydia trachomatis Scc4 for Structural Studies Using Sarkosyl-Assisted on-Column Complex Dissociation

Author:
Thilini O. Ukwaththage; Octavia Y. Goodwin; Abigael C. Songok; Alexa M. Tafaro; Li Shen; Megan A. Macnaughtan
Source:
Biochemistry 2019 v.58 no.42 pp. 4284-4292
ISSN:
1520-4995
Subject:
Chlamydia trachomatis; DNA-directed RNA polymerase; Escherichia coli; affinity chromatography; bacteria; cells; detergents; dissociation; nuclear magnetic resonance spectroscopy; pathogens; sodium; solubility; spectral analysis; type III secretion system; virulence
Abstract:
... Chlamydia trachomatis is an obligate intracellular bacterial pathogen that causes the most common sexually transmitted bacterial disease in the world. The bacterium has a unique biphasic developmental cycle with a type III secretion system (T3SS) to invade host cells. Scc4 is a class I T3SS chaperone forming a heterodimer complex with Scc1 to chaperone the essential virulence effector, CopN. Scc4 ...
DOI:
10.1021/acs.biochem.9b00665

46. The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase

Author:
Masahiko Imashimizu; Maria L. Kireeva; Lucyna Lubkowska; Mikhail Kashlev; Nobuo Shimamoto
Source:
Journal of molecular biology 2019 v.431 no.14 pp. 2528-2542
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; RNA; nucleotides
Abstract:
... RNA polymerase can cleave a phosphodiester bond at the 3′ end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition ...
DOI:
10.1016/j.jmb.2019.04.020

47. Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation

Author:
Mo’men Abdelkareem; Charlotte Saint-André; Maria Takacs; Gabor Papai; Corinne Crucifix; Xieyang Guo; Julio Ortiz; Albert Weixlbaumer
Source:
Molecular cell 2019 v.75 no.2 pp. 298-309.e4
ISSN:
1097-2765
Subject:
DNA; DNA-directed RNA polymerase; Escherichia coli; active sites; catalytic activity; eukaryotic cells; messenger RNA; regulatory sequences; transcription (genetics); transcription factors
Abstract:
... Regulatory sequences or erroneous incorporations during DNA transcription cause RNA polymerase backtracking and inactivation in all kingdoms of life. Reactivation requires RNA transcript cleavage. Essential transcription factors (GreA and GreB, or TFIIS) accelerate this reaction. We report four cryo-EM reconstructions of Escherichia coli RNA polymerase representing the entire reaction pathway: (1) ...
DOI:
10.1016/j.molcel.2019.04.029

48. Unveiling the molecular basis for pleiotropy in selected rif mutants of Escherichia coli: Possible role for Tyrosine in the Rif binding pocket and fast movement of RNA polymerase

Author:
Maruthan Karthik; Shanmugaraja Meenakshi; M.Hussain Munavar
Source:
Gene 2019 v.713 pp. 143951
ISSN:
0378-1119
Subject:
DNA-directed RNA polymerase; Escherichia coli; antimicrobial properties; combination drug therapy; drugs; gene expression; gene expression regulation; genes; mutants; mutation; mycobacterial diseases; pH; phenotype; pleiotropy; polysaccharides; rifampicin; sodium chloride; temperature; transcription (genetics); transcriptome; tyrosine
Abstract:
... Rifampicin (RIF) is still a first line of antibiotic in the treatment of bacterial diseases, in particular the Mycobacterial infections. The antimicrobial activity of RIF is attributed to its ability to inhibit transcription by binding to the β subunit of bacterial RNA polymerase (encoded by rpoB). Continued use of this drug resulted in the emergence of RIF resistant rpoB mutations in a high frequ ...
DOI:
10.1016/j.gene.2019.143951

49. Xenogeneic Regulation of the Bacterial Transcription Machinery

Author:
Aline Tabib-Salazar; Nancy Mulvenna; Konstantin Severinov; Steve J. Matthews; Sivaramesh Wigneshweraraj
Source:
Journal of molecular biology 2019 v.431 no.20 pp. 4078-4092
ISSN:
0022-2836
Subject:
DNA-directed RNA polymerase; Escherichia coli; bacteria; bacteriology; bacteriophages; biosynthesis; progeny; proteins; transcription (genetics)
Abstract:
... The parasitic life cycle of viruses involves the obligatory subversion of the host's macromolecular processes for efficient viral progeny production. Viruses that infect bacteria, bacteriophages (phages), are no exception and have evolved sophisticated ways to control essential biosynthetic machineries of their bacterial prey to benefit phage development. The xenogeneic regulation of bacterial cel ...
DOI:
10.1016/j.jmb.2019.02.008

50. Cytochromes bd-I and bo3 are essential for the bactericidal effect of microcin J25 on Escherichia coli cells

Author:
A.E. Galván; M.C. Chalón; L.A. Schurig-Briccio; R.A. Salomón; C.J. Minahk; R.B. Gennis; A. Bellomio
Source:
Biochimica et biophysica acta 2018 v.1859 no.2 pp. 110-118
ISSN:
0005-2728
Subject:
DNA-directed RNA polymerase; Escherichia coli; antibacterial properties; bacteria; cell respiration; cytochromes; electron transport chain; mechanism of action; mutants; oxygen; oxygen consumption; peptides
Abstract:
... Microcin J25 has two targets in sensitive bacteria, the RNA polymerase, and the respiratory chain through inhibition of cellular respiration. In this work, the effect of microcin J25 in E. coli mutants that lack the terminal oxidases cytochrome bd-I and cytochrome bo₃ was analyzed. The mutant strains lacking cytochrome bo₃ or cytochrome bd-I were less sensitive to the peptide. In membranes obtaine ...
DOI:
10.1016/j.bbabio.2017.10.006