The mechanism of pRNA-mediated release of RNA polymerase from Bacillus subtilis 6S-1 RNA

Adaptation of the transcriptome to nutrient limitation and resupply is a fundamental process in bacteria, particularly in natural habitats. Bacterial 6S RNA, an ubiquitous and growth phasedependent regulator of transcription, binds to RNA polymerase (RNAP) and inhibits transcription during stati...

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Bibliographic Details
Main Author: Beckmann, Benedikt
Contributors: Hartmann, Roland (Prof. Dr.) (Thesis advisor)
Format: Dissertation
Language:English
Published: Philipps-Universität Marburg 2010
Pharmazeutische Chemie
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Summary:Adaptation of the transcriptome to nutrient limitation and resupply is a fundamental process in bacteria, particularly in natural habitats. Bacterial 6S RNA, an ubiquitous and growth phasedependent regulator of transcription, binds to RNA polymerase (RNAP) and inhibits transcription during stationary growth. Upon nutrient resupply, RNAP acts as an RNA-dependent RNA polymerase by transcribing large amounts of short RNAs (pRNAs) from 6S RNA as template, leading to dissociation of 6S RNARNAP complexes. Whereas the majority of bacteria express a single 6S RNA species, Bacillus subtilis encodes two 6S RNAs (6S-1 and 6S-2) of similar secondary structure, but with different expression profiles. In this work, we investigated the two 6S RNAs of B. subtilis, focusing on pRNA synthesis and its role for the function of 6S RNA. Concurrently, we identified pRNA transcription from 6S-1 RNA in vivo using high-troughput sequencing techniques and we developed a novel Northern hybridization protocol for detection of pRNAs in bacterial total cellular extracts. Our results show that the release of RNAP from 6S-1 RNA, the functional homolog of the well investigated E. coli 6S RNA, is regulated by stable pRNA binding. Additionally, we found structural changes of 6S-1 RNA, induced by differences in pRNA length in different growth phases. This specific structural change of 6S RNA seems to be conserved among bacteria. Furthermore, we are able to show that the two processes of RNAP release and 6S-1 RNA degradation are coupled in vivo. Taken together, our results expand the current understanding of 6S RNA function and provide insight into the mechanism of RNAP release from 6S RNA in bacteria. iii
DOI:https://doi.org/10.17192/z2010.0758