scholarly journals The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 976 ◽  
Author(s):  
Pieter-Jan Ceyssens ◽  
Jeroen De Smet ◽  
Jeroen Wagemans ◽  
Natalia Akulenko ◽  
Evgeny Klimuk ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Alpha Subunit ◽  
Regulation Mechanism ◽  
Post Translational Modification ◽  
Α Subunit ◽  
Bacterial Transcription ◽  
Highly Active ◽  
Bacterial Rna

In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism.

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

RNA Biology ◽  
2021 ◽  
pp. 1-10
Author(s):  
Anastasiya Oguienko ◽  
Ivan Petushkov ◽  
Danil Pupov ◽  
Daria Esyunina ◽  
Andrey Kulbachinskiy
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Universal Functions ◽  
Bacterial Rna

scholarly journals Interactions between the Escherichia coli cAMP receptor protein and the C-terminal domain of the α subunit of RNA polymerase at Class I promoters

1999 ◽  
Vol 337 (3) ◽  
pp. 415-423 ◽  
Author(s):  
Emma C. LAW ◽  
Nigel J. SAVERY ◽  
Stephen J. W. BUSBY
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Class I ◽  
Receptor Protein ◽  
Camp Receptor Protein ◽  
Α Subunit ◽  
Terminal Domain ◽  
Up Elements ◽  
Camp Receptor

The Escherichia coli cAMP receptor protein (CRP) is a factor that activates transcription at over 100 target promoters. At Class I CRP-dependent promoters, CRP binds immediately upstream of RNA polymerase and activates transcription by making direct contacts with the C-terminal domain of the RNA polymerase α subunit (αCTD). Since αCTD is also known to interact with DNA sequence elements (known as UP elements), we have constructed a series of semi-synthetic Class I CRP-dependent promoters, carrying both a consensus DNA-binding site for CRP and a UP element at different positions. We previously showed that, at these promoters, the CRP–αCTD interaction and the CRP–UP element interaction contribute independently and additively to transcription initiation. In this study, we show that the two halves of the UP element can function independently, and that, in the presence of the UP element, the best location for the DNA site for CRP is position -69.5. This suggests that, at Class I CRP-dependent promoters where the DNA site for CRP is located at position -61.5, the two αCTDs of RNA polymerase are not optimally positioned. Two experiments to test this hypothesis are presented.

scholarly journals Sigma factor 1 in chloroplast gene transcription and photosynthetic light acclimation

2019 ◽  
Vol 71 (3) ◽  
pp. 1029-1038 ◽  
Author(s):  
Lauren A Macadlo ◽  
Iskander M Ibrahim ◽  
Sujith Puthiyaveetil
Keyword(s):  
Rna Polymerase ◽  
Gene Transcription ◽  
Sigma Factor ◽  
Transcription Initiation ◽  
Sigma Factors ◽  
Transcriptional Level ◽  
Gene Promoters ◽  
Chloroplast Genes ◽  
Specific Subset ◽  
Bacterial Rna

Abstract Sigma factors are dissociable subunits of bacterial RNA polymerase that ensure efficient transcription initiation from gene promoters. Owing to their prokaryotic origin, chloroplasts possess a typical bacterial RNA polymerase together with its sigma factor subunit. The higher plant Arabidopsis thaliana contain as many as six sigma factors for the hundred or so of its chloroplast genes. The role of this relatively large number of transcription initiation factors for the miniature chloroplast genome, however, is not fully understood. Using two Arabidopsis T-DNA insertion mutants, we show that sigma factor 1 (SIG1) initiates transcription of a specific subset of chloroplast genes. We further show that the photosynthetic control of PSI reaction center gene transcription requires complementary regulation of the nuclear SIG1 gene at the transcriptional level. This SIG1 gene regulation is dependent on both a plastid redox signal and a light signal transduced by the phytochrome photoreceptor.

scholarly journals Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation

2018 ◽  
Vol 70 (6) ◽  
pp. 1111-1120.e3 ◽  
Author(s):  
Robert Glyde ◽  
Fuzhou Ye ◽  
Milija Jovanovic ◽  
Ioly Kotta-Loizou ◽  
Martin Buck ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Bacterial Rna

scholarly journals Bacterial RNA polymerase can retain σ70 throughout transcription

2016 ◽  
Vol 113 (3) ◽  
pp. 602-607 ◽  
Author(s):  
Timothy T. Harden ◽  
Christopher D. Wells ◽  
Larry J. Friedman ◽  
Robert Landick ◽  
Ann Hochschild ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Single Molecule ◽  
Transcription Initiation ◽  
Messenger Rna ◽  
Initiation Factors ◽  
Bacterial Rna ◽  
Direct Measurements ◽  
Promoter Recognition ◽  
Σ Factor ◽  
Transcript Elongation

Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated initiation factors. However, the primary σ factor in Escherichia coli, σ70, can remain associated with RNAP during the transition from initiation to elongation, influencing events that occur after initiation. Quantitative studies on the extent of σ70 retention have been limited to complexes halted during early elongation. Here, we used multiwavelength single-molecule fluorescence-colocalization microscopy to observe the σ70–RNAP complex during initiation from the λ PR′ promoter and throughout the elongation of a long (>2,000-nt) transcript. Our results provide direct measurements of the fraction of actively transcribing complexes with bound σ70 and the kinetics of σ70 release from actively transcribing complexes. σ70 release from mature elongation complexes was slow (0.0038 s−1); a substantial subpopulation of elongation complexes retained σ70 throughout transcript elongation, and this fraction depended on the sequence of the initially transcribed region. We also show that elongation complexes containing σ70 manifest enhanced recognition of a promoter-like pause element positioned hundreds of nucleotides downstream of the promoter. Together, the results provide a quantitative framework for understanding the postinitiation roles of σ70 during transcription.

scholarly journals Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes

2009 ◽  
Vol 75 (9) ◽  
pp. 2705-2711 ◽  
Author(s):  
Daniel Klein-Marcuschamer ◽  
Christine Nicole S. Santos ◽  
Huimin Yu ◽  
Gregory Stephanopoulos
Keyword(s):  
Rna Polymerase ◽  
Underlying Mechanism ◽  
Strain Engineering ◽  
Alpha Subunit ◽  
Physiological Changes ◽  
Core Enzyme ◽  
Complex Phenotypes ◽  
Bacterial Rna ◽  
Tolerant Mutant ◽  
Solvent Tolerant

ABSTRACT Combinatorial or random methods for strain engineering have been extensively used for the improvement of multigenic phenotypes and other traits for which the underlying mechanism is not fully understood. Although the preferred method has traditionally been mutagenesis and selection, our laboratory has successfully used mutant transcription factors, which direct the RNA polymerase (RNAP) during transcription, to engineer complex phenotypes in microbial cells. Here, we show that it is also possible to impart new phenotypes by altering the RNAP core enzyme itself, in particular through mutagenesis of the alpha subunit of the bacterial polymerase. We present the use of this tool for improving tolerance of Escherichia coli to butanol and other solvents and for increasing the titers of two commercially relevant products, l-tyrosine and hyaluronic acid. In addition, we explore the underlying physiological changes that give rise to the solvent-tolerant mutant.

scholarly journals Ureidothiophene inhibits interaction of bacterial RNA polymerase with –10 promotor element

2020 ◽  
Vol 48 (14) ◽  
pp. 7914-7923
Author(s):  
John Harbottle ◽  
Nikolay Zenkin
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Early Stage ◽  
Chemical Compounds ◽  
Initiation Factor ◽  
Promoter Element ◽  
Bacterial Transcription ◽  
Bacterial Rna ◽  
Novel Target

Abstract Bacterial RNA polymerase is a potent target for antibiotics, which utilize a plethora of different modes of action, some of which are still not fully understood. Ureidothiophene (Urd) was found in a screen of a library of chemical compounds for ability to inhibit bacterial transcription. The mechanism of Urd action is not known. Here, we show that Urd inhibits transcription at the early stage of closed complex formation by blocking interaction of RNA polymerase with the promoter –10 element, while not affecting interactions with –35 element or steps of transcription after promoter closed complex formation. We show that mutation in the region 1.2 of initiation factor σ decreases sensitivity to Urd. The results suggest that Urd may directly target σ region 1.2, which allosterically controls the recognition of –10 element by σ region 2. Alternatively, Urd may block conformational changes of the holoenzyme required for engagement with –10 promoter element, although by a mechanism distinct from that of antibiotic fidaxomycin (lipiarmycin). The results suggest a new mode of transcription inhibition involving the regulatory domain of σ subunit, and potentially pinpoint a novel target for development of new antibacterials.

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