Diverse and unified mechanisms of transcription initiation in bacteria

J Chen, H Boyaci, EA Campbell - Nature Reviews Microbiology, 2021 - nature.com
Transcription of DNA is a fundamental process in all cellular organisms. The enzyme
responsible for transcription, RNA polymerase, is conserved in general architecture and …

Mechanisms of transcriptional pausing in bacteria

JY Kang, TV Mishanina, R Landick, SA Darst - Journal of molecular biology, 2019 - Elsevier
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all
domains of life. In this review, we recap the history of transcriptional pausing discovery …

DeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning

J Thomsen, MB Sletfjerding, SB Jensen, S Stella… - Elife, 2020 - elifesciences.org
Single-molecule Förster Resonance energy transfer (smFRET) is an adaptable method for
studying the structure and dynamics of biomolecules. The development of high throughput …

Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase

SB Jensen, S Thodberg, S Parween, ME Moses… - Nature …, 2021 - nature.com
Metabolic control is mediated by the dynamic assemblies and function of multiple redox
enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates …

Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase

IC Nova, JM Craig, A Mazumder, AH Laszlo… - Proceedings of the …, 2024 - pnas.org
RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology
by transcribing DNA into RNA. Despite their importance, much about how RNAPs work …

[HTML][HTML] Mechanisms of σ54-dependent transcription initiation and regulation

AE Danson, M Jovanovic, M Buck, X Zhang - Journal of molecular biology, 2019 - Elsevier
Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene
transcription, a highly regulated process conserved from bacteria to humans. In bacteria …

[HTML][HTML] Recent advances in understanding σ70-dependent transcription initiation mechanisms

A Mazumder, AN Kapanidis - Journal of molecular biology, 2019 - Elsevier
Prokaryotic transcription is one of the most studied biological systems, with relevance to
many fields including the development and use of antibiotics, the construction of synthetic …

CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase

D Jensen, AR Manzano, J Rammohan… - Nucleic Acids …, 2019 - academic.oup.com
Abstract The pathogen Mycobacterium tuberculosis (Mtb), the causative agent of
tuberculosis, enacts unique transcriptional regulatory mechanisms when subjected to host …

Can DyeCycling break the photobleaching limit in single-molecule FRET?

B Vermeer, S Schmid - Nano Research, 2022 - Springer
Biomolecular systems, such as proteins, crucially rely on dynamic processes at the
nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a …

Structural basis of ECF-σ-factor-dependent transcription initiation

W Lin, S Mandal, D Degen, MS Cho, Y Feng… - Nature …, 2019 - nature.com
Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to
primary σ factors, but have simpler structures, comprising only two of six conserved …