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 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 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 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 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.

Investigations of the modular structure of bacterial promoters

2006 ◽  
Vol 73 ◽  
pp. 1-10 ◽  
Author(s):  
Nora S. Miroslavova ◽  
Stephen J.W. Busby
Keyword(s):  
Rna Polymerase ◽  
Dna Sequence ◽  
Transcription Initiation ◽  
Promoter Activity ◽  
Modular Structure ◽  
Bacterial Rna ◽  
Sequence Elements ◽  
Promoter Dna ◽  
Transcript Initiation ◽  
Rna Polymerase Holoenzyme

Bacterial RNA polymerase holoenzyme carries different determinants that contact different promoter DNA sequence elements. These contacts are essential for the recognition of promoters prior to transcript initiation. Here, we have investigated how active promoters can be built from different combinations of elements. Our results show that the contribution of different contacts to promoter activity is critically dependent on the overall promoter context, and that certain combinations of contacts can hinder transcription initiation.

scholarly journals GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Yu Zhang ◽  
David Degen ◽  
Mary X Ho ◽  
Elena Sineva ◽  
Katherine Y Ebright ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Binding Site ◽  
Active Center ◽  
Transcription Initiation ◽  
Cyclic Peptide ◽  
Cross Resistance ◽  
Peptide Antibiotic ◽  
Nucleotide Binding Sites ◽  
Bacterial Rna ◽  
Polymerase I

Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance.

scholarly journals Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme

2014 ◽  
Vol 289 (35) ◽  
pp. 24549-24559 ◽  
Author(s):  
Ritwika S. Basu ◽  
Brittany A. Warner ◽  
Vadim Molodtsov ◽  
Danil Pupov ◽  
Daria Esyunina ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Structural Basis ◽  
Bacterial Rna ◽  
Rna Polymerase Holoenzyme

Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase

2017 ◽  
Vol 474 (24) ◽  
pp. 4053-4064 ◽  
Author(s):  
Ivan Petushkov ◽  
Daria Esyunina ◽  
Vladimir Mekler ◽  
Konstantin Severinov ◽  
Danil Pupov ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Molecular Beacon ◽  
Secondary Channel ◽  
Enzyme Active Site ◽  
Promoter Escape ◽  
Bacterial Rna ◽  
Transcription Complexes ◽  
Kinetics Of ◽  
Rnap Binding

In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5′-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ70 subunit of Escherichia coli RNAP. We show that substitutions and deletions in σ region 3.2 decrease the rate of promoter escape and lead to accumulation of inactive complexes during transcription initiation. Secondary channel factors differentially regulate this process depending on the promoter and mutations in σ region 3.2. GreA generally increase the rate of promoter escape; DksA also stimulates promoter escape on certain templates, while GreB either stimulates or inhibits this process depending on the template. When observed, the stimulation of promoter escape correlates with the accumulation of stressed transcription complexes with scrunched DNA, while changes in the RNA 5′-end structure modulate promoter clearance. Thus, the initiation-to-elongation transition is controlled by a complex interplay between RNAP-binding protein factors and the growing RNA chain.

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