Robust regulation of transcription pausing in  Escherichia coli by the ubiquitous elongation factor NusG

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 120; no. 24; p. e2221114120
• Main Authors: Yakhnin, Alexander V, Bubunenko, Mikhail, Mandell, Zachary F, Lubkowska, Lucyna, Husher, Sara, Babitzke, Paul, Kashlev, Mikhail
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 13.06.2023
• Subjects: Antisense RNA; Biological Sciences; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; E coli; Elongation; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Gene mapping; Gene regulation; Genes; Genomes; Open reading frames; Operons; Peptide Elongation Factors - genetics; Peptide Elongation Factors - metabolism; Ribonucleic acid; RNA; rRNA; Transcription Factors - genetics; Transcription, Genetic; Translation; Translocation; RNA polymerase pausing; backtracking; translocation; NusG; RNET-seq
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.2221114120

Transcription elongation by multi-subunit RNA polymerases (RNAPs) is regulated by auxiliary factors in all organisms. NusG/Spt5 is the only universally conserved transcription elongation factor shared by all domains of life. NusG is a component of antitermination complexes controlling ribosomal RNA operons, an essential antipausing factor, and a transcription-translation coupling factor in . We employed RNET-seq for genome-wide mapping of RNAP pause sites in wild-type and NusG-depleted cells. We demonstrate that NusG is a major antipausing factor that suppresses thousands of backtracked and nonbacktracked pauses across the genome. The NusG-suppressed pauses were enriched immediately downstream from the translation start codon but were also abundant elsewhere in open reading frames, small RNA genes, and antisense transcription units. This finding revealed a strong similarity of NusG to Spt5, which stimulates the elongation rate of many eukaryotic genes. We propose a model in which promoting forward translocation and/or stabilization of RNAP in the posttranslocation register by NusG results in suppression of pausing in .