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  A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs

Brueck, M., Koebel, T. S., Dittmar, S., Ramírez Rojas, A. A., Georg, J., Berghoff, B. A., et al. (2024). A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. bioRxiv: the preprint server for biology, 2024.04.24.590872.

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 Creators:
Brueck, Michel1, 2, Author
Koebel, Tania S.2, Author
Dittmar, Sophie1, Author
Ramírez Rojas, Adán Andrés2, Author           
Georg, Jens1, Author
Berghoff, Bork A.1, Author
Schindler, Daniel2, Author                 
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1external, ou_persistent22              
2Core Facility MPG MAXGenesys DNAfoundry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266268              

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 Abstract: All organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) are an important aspect of the regulation network underlying the adaptation to such changes. sRNAs base-pair with their target mRNAs, allowing rapid modulation of the proteome. This post-transcriptional regulation is usually facilitated by RNA chaperones, such as Hfq. sRNAs have a potential as synthetic regulators that can be modulated by rational design. In this study, we use a library-based approach and an oxacillin susceptibility assays to investigate the importance of the seed region length for synthetic sRNAs based on RybB and SgrS scaffolds in Escherichia coli. In the presence of Hfq we show that 12 nucleotides are sufficient for regulation. Furthermore, we observe a scaffold-specific Hfq-dependency and processing by RNase E. Our results provide information for design considerations of synthetic sRNAs in basic and applied research.Competing Interest StatementThe authors have declared no competing interest.

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Language(s): eng - English
 Dates: 2024-04-24
 Publication Status: Issued
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 Rev. Type: No review
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Title: bioRxiv : the preprint server for biology
  Abbreviation : bioRxiv
Source Genre: Journal
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Pages: - Volume / Issue: - Sequence Number: 2024.04.24.590872 Start / End Page: - Identifier: ZDB: 2766415-6
CoNE: https://pure.mpg.de/cone/journals/resource/2766415-6