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

Alexander V. Yakhnin, Mikhail Bubunenko, Zachary F. Mandell, Lucyna Lubkowska, Sara Husher, Paul Babitzke, Mikhail Kashlev

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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 Escherichia coli. 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 E. coli 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 E. coli.

Original languageEnglish (US)
Article numbere2221114120
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number24
StatePublished - 2023

All Science Journal Classification (ASJC) codes

  • General

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