RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences

A Agapov, A Olina, A Kulbachinskiy - Nucleic Acids Research, 2022 - academic.oup.com
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases
(RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the …

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

A Dhakal, R Gyawali, L Wang, J Cheng - Scientific Data, 2023 - nature.com
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of
biological macromolecular complexes. Picking single-protein particles from cryo-EM …

Structural basis for intrinsic transcription termination

L You, EO Omollo, C Yu, RA Mooney, J Shi, L Shen… - Nature, 2023 - nature.com
Efficient and accurate termination is required for gene transcription in all living organisms,.
Cellular RNA polymerases in both bacteria and eukaryotes can terminate their transcription …

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

A Dhakal, R Gyawali, L Wang, J Cheng - Bioinformatics, 2024 - academic.oup.com
Motivation Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the
structures of large protein complexes. Picking single protein particles from cryo-EM …

Processing of stalled replication forks in Bacillus subtilis

B Carrasco, R Torres… - FEMS microbiology …, 2024 - academic.oup.com
Accurate DNA replication and transcription elongation are crucial for preventing the
accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple …

The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling

HH Pei, T Hilal, ZA Chen, YH Huang, Y Gao… - Nature …, 2020 - nature.com
Cellular RNA polymerases (RNAPs) can become trapped on DNA or RNA, threatening
genome stability and limiting free enzyme pools, but how RNAP recycling into active states …

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

T Kouba, T Koval', P Sudzinová, J Pospíšil… - Nature …, 2020 - nature.com
RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors
for recovery from stalled states and adaptation to environmental changes. Here, we …

Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase

L Yuan, Q Liu, L Xu, B Wu, Y Feng - Nature Communications, 2024 - nature.com
Bacterial RNAP needs to form holoenzyme with σ factors to initiate transcription. While
Staphylococcus aureus σA controls housekeeping functions, S. aureus σB regulates …

RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation

JJ Brewer, K Inlow, RA Mooney, B Bosch… - Nature Structural & …, 2025 - nature.com
Following transcript release during intrinsic termination, Escherichia coli RNA polymerase
(RNAP) often remains associated with DNA in a post-termination complex (PTC). RNAPs in …

Mycobacterial HelD connects RNA polymerase recycling with transcription initiation

T Kovaľ, N Borah, P Sudzinová, B Brezovská… - Nature …, 2024 - nature.com
Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from
nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however …