Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.
Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.
Institute of Systems and Synthetic Biology, Université d'Évry-Val-d'Essonne, CNRS, F-91000 Évry, France.
Shensi
S
Shen
Institute of Systems and Synthetic Biology, Université d'Évry-Val-d'Essonne, CNRS, F-91000 Évry, France.
Guillermo
G
Rodrigo
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
Satya
S
Prakash
Instituto de Biología Molecular y Celular de Plantas, CSIC - Universidad Politécnica de Valencia, 46022 Valencia, Spain.
Eszter
E
Majer
Institute of Systems and Synthetic Biology, Université d'Évry-Val-d'Essonne, CNRS, F-91000 Évry, France.
Thomas E
TE
Landrain
Institute of Systems and Synthetic Biology, Université d'Évry-Val-d'Essonne, CNRS, F-91000 Évry, France.
Boris
B
Kirov
Instituto de Biología Molecular y Celular de Plantas, CSIC - Universidad Politécnica de Valencia, 46022 Valencia, Spain.
José-Antonio
JA
Daròs
Institute of Systems and Synthetic Biology, Université d'Évry-Val-d'Essonne, CNRS, F-91000 Évry, France School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK Alfonso.Jaramillo@gmail.com.
Alfonso
A
Jaramillo
D019295:Computational Biology / Q000379:methods; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D016337:RNA, Catalytic / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000378:metabolism*; D015398:Signal Transduction; D059010:Single-Cell Analysis
D016337:RNA, Catalytic; D058727:RNA, Small Untranslated