Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription
| Autor: | Zakia Morichaud, Konstantin Brodolin |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Transcription Genetic LDT long duplex template Biochemistry RNAP RNA polymerase Abortive initiation chemistry.chemical_compound RbpA Bacterial transcription Transcription (biology) RNA:DNA hybrid stability RNA polymerase Promoter Regions Genetic abortive transcription Polymerase AsiA General transcription factor biology ITC initially transcribing complex DNA-Directed RNA Polymerases transcription initiation factor CRE core recognition element Cell biology NTP nucleoside triphosphate Research Article initial-transcription pausing Sigma Factor 03 medical and health sciences NAC nucleotide addition cycle Escherichia coli RNA synthesis Molecular Biology SDT short duplex template 030102 biochemistry & molecular biology RNA Mycobacterium tuberculosis DNA Cell Biology bacterial transcription WT wild-type enzymes and coenzymes (carbohydrates) 030104 developmental biology chemistry health occupations biology.protein bacteria Holoenzymes |
| Zdroj: | The Journal of Biological Chemistry |
| ISSN: | 0021-9258 |
| Popis: | All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The nucleotide at the RNA 3' end determines the pause lifetime. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The anti-pausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This "RNAP boosting" activity of the initiation factor is shaped by the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP. |
| Databáze: | OpenAIRE |
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