Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

RBP-RNA interactions in the 5’ UTR lead to structural changes that alter translation

Noa Katz, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, Roee Amit
doi: https://doi.org/10.1101/174888
Noa Katz
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roni Cohen
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Oz Solomon
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
3School of Computer Science, Interdisciplinary Center, Herzeliya 46150, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Beate Kaufmann
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Orna Atar
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zohar Yakhini
2Department of Computer Science, Technion - Israel Institute of Technology, Haifa 32000, Israel.
3School of Computer Science, Interdisciplinary Center, Herzeliya 46150, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah Goldberg
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roee Amit
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
4Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: roeeamit@technion.ac.il
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

We study translational regulation by a 5’ UTR sequence encoding the binding site of an RNA-binding protein (RBP) in bacteria, using a reporter assay and Selective 2’-hydroxyl acylation analysed by primer extension sequencing (SHAPE-Seq). We tested constructs containing a single hairpin, based on the binding sites of the coat RBPs of bacteriophages GA, MS2, PP7, and Qβ, positioned in the 5’ UTR of a reporter gene. With specifically-bound RBP present, either weak repression or up-regulation is observed, depending on the binding site and its flanking sequence. SHAPE-Seq data for a representative construct exhibiting up-regulation, indicates a partially-folded hairpin and non-reactive upstream and downstream flanking region, which we attribute to intermediate structures that apparently blocks translation. RBP binding stabilizes the fully-folded hairpin state and thus facilitates translation, suggesting that the up-regulating constructs are RBP-sensing riboswitches. This finding is further supported by lengthening the binding-site stem, which in turn destabilizes the translationally-inactive state, and abolishes the up-regulating behavior. Finally, we found that the combination of two binding sites, positioned in the 5’ UTR and gene-header of the same transcript, can yield a cooperative regulatory response. Together, we show that the interaction of an RBP with its RNA target facilitates structural changes in the RNA, which is reflected by a controllable range of binding affinities and dose response behaviors. Thus, demonstrating that RNA-RBP interactions can provide a platform for constructing gene regulatory networks that are based on translational, rather than transcriptional, regulation.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted April 13, 2018.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
RBP-RNA interactions in the 5’ UTR lead to structural changes that alter translation
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
RBP-RNA interactions in the 5’ UTR lead to structural changes that alter translation
Noa Katz, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, Roee Amit
bioRxiv 174888; doi: https://doi.org/10.1101/174888
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
RBP-RNA interactions in the 5’ UTR lead to structural changes that alter translation
Noa Katz, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, Roee Amit
bioRxiv 174888; doi: https://doi.org/10.1101/174888

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Synthetic Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4234)
  • Biochemistry (9128)
  • Bioengineering (6774)
  • Bioinformatics (23989)
  • Biophysics (12117)
  • Cancer Biology (9523)
  • Cell Biology (13773)
  • Clinical Trials (138)
  • Developmental Biology (7627)
  • Ecology (11686)
  • Epidemiology (2066)
  • Evolutionary Biology (15506)
  • Genetics (10638)
  • Genomics (14322)
  • Immunology (9479)
  • Microbiology (22832)
  • Molecular Biology (9089)
  • Neuroscience (48987)
  • Paleontology (355)
  • Pathology (1480)
  • Pharmacology and Toxicology (2568)
  • Physiology (3844)
  • Plant Biology (8327)
  • Scientific Communication and Education (1471)
  • Synthetic Biology (2296)
  • Systems Biology (6187)
  • Zoology (1300)