The mechanisms of substrate selection, catalysis, and translocation by the elongating RNA polymerase

GA Belogurov, I Artsimovitch - Journal of molecular biology, 2019 - Elsevier
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs,
ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has …

Generation and repair of postreplication gaps in Escherichia coli

MM Cox, MF Goodman, JL Keck… - Microbiology and …, 2023 - Am Soc Microbiol
When replication forks encounter template lesions, one result is lesion skipping, where the
stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to …

Crucial role and mechanism of transcription-coupled DNA repair in bacteria

BK Bharati, M Gowder, F Zheng, K Alzoubi, V Svetlov… - Nature, 2022 - nature.com
Transcription-coupled DNA repair (TCR) is presumed to be a minor sub-pathway of
nucleotide excision repair (NER) in bacteria. Global genomic repair is thought to perform the …

Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges

W Wei, WC Ho, MG Behringer, SF Miller… - Nature …, 2022 - nature.com
Ecological and demographic factors can significantly shape the evolution of microbial
populations both directly and indirectly, as when changes in the effective population size …

Control of transcription elongation and DNA repair by alarmone ppGpp

JW Weaver, S Proshkin, W Duan, V Epshtein… - Nature Structural & …, 2023 - nature.com
Second messenger (p) ppGpp (collectively guanosine tetraphosphate and guanosine
pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating …

The clash of macromolecular titans: replication-transcription conflicts in bacteria

KS Lang, H Merrikh - Annual review of microbiology, 2018 - annualreviews.org
Within the last decade, it has become clear that DNA replication and transcription are
routinely in conflict with each other in growing cells. Much of the seminal work on this topic …

ppGpp and RNA-polymerase backtracking guide antibiotic-induced mutable gambler cells

Y Zhai, PJ Minnick, JP Pribis, L Garcia-Villada… - Molecular cell, 2023 - cell.com
Antibiotic resistance is a global health threat and often results from new mutations.
Antibiotics can induce mutations via mechanisms activated by stress responses, which both …

Replisome bypass of transcription complexes and R-loops

JG Brüning, KJ Marians - Nucleic acids research, 2020 - academic.oup.com
The vast majority of the genome is transcribed by RNA polymerases. G+ C-rich regions of
the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA …

[HTML][HTML] Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

HL Klein, G Bačinskaja, J Che, A Cheblal, R Elango… - Microbial …, 2019 - ncbi.nlm.nih.gov
Understanding the plasticity of genomes has been greatly aided by assays for
recombination, repair and mutagenesis. These assays have been developed in microbial …

DksA and ppGpp Regulate the σS Stress Response by Activating Promoters for the Small RNA DsrA and the Anti-Adapter Protein IraP

ME Girard, S Gopalkrishnan, ED Grace… - Journal of …, 2018 - Am Soc Microbiol
ABSTRACT σS is an alternative sigma factor, encoded by the rpoS gene, that redirects
cellular transcription to a large family of genes in response to stressful environmental …