Correlative Escherichia coli Transcription Rate and Bubble Conformation Remodeled by NusA and NusG

• Published in: The journal of physical chemistry. B 2023-04, Vol.127 (13), p.2909-2917
• Main Authors: Zhang, Yuqiong, Han, Weijing, Wang, Lisha, Wang, Hao, Jia, Qi, Chen, Tongsheng, Wang, Shuang, Li, Ming
• Format: Article
• Language: English
• Subjects: B: Biophysical and Biochemical Systems and Processes; DNA-Directed RNA Polymerases - metabolism; Escherichia coli - genetics; Escherichia coli Proteins - genetics; Peptide Elongation Factors - genetics; Transcription Factors - genetics; Transcription, Genetic; Transcriptional Elongation Factors - genetics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.2c08771

Transcription is highly regulated by a variety of transcription factors, among which NusA and NusG act contradictorily in Escherichia coli (E. coli) that NusA stabilizes a paused RNA polymerase (RNAP) and NusG suppresses it. The mechanism of the NusA and NusG regulations on RNAP transcription has been addressed, but their effect on the conformational changes of the transcription bubble correlated with transcription kinetics remains elusive. By using single-molecule magnetic trap, we identify a reduction in the transcription rate of ∼40% events by NusA. Although the rest ∼60% of transcription events exhibit unaffected transcription rates, a NusA-enhanced standard deviation of the transcription rate is observed. NusA remodeling also increases the extent of DNA unwinding in the transcription bubble by 1–2 base pairs, which can be reduced by NusG. The NusG remodeling is more significant on the RNAP molecules with reduced transcription rates rather than those without. Our results provide a quantitative view on the mechanisms of transcriptional regulation by NusA and NusG factors.