Biology subjects

Guillermo Rodrigo

Publications and source records attributed to Guillermo Rodrigo.

6 recordsLinked to original sources

bioRxiv2016

Genetic redundancies enhance information transfer in noisy regulatory circuits

Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of multiple circuit copies. The result is due to the contribution of noise to the generation of autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors that correlate the responses of the redundant units (extrinsic noise or regulatory cross-talk) contribute to reduce fidelity, while those that further uncouple them (heterogeneity within the copies) can lead to stronger information gain. Overall, our study emphasizes how the interplay of signal thresholding, redundancy, and noise influences the accuracy of cellular decision making. Understanding this interplay provides a basis to explain collective cell signaling mechanisms, and to engineer robust decisions with noisy genetic circuits.

Systems Biology↗

bioRxiv2015

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.

Synthetic Biology↗

bioRxiv2014

Cooperative riboregulation in living cells through allosteric programming of toehold activation

Living cells rely on small non-coding RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. Contrary to most protein-based activators of transcription, all known riboregulators do not exploit cooperative binding mechanisms to activate gene expression. We conceived a general strategy to design cooperative riboregulation by programming a hierarchical toehold activation cascade, which we implemented into a de novo sequence design algorithm. We engineered different riboregulatory systems relying on the conditional formation of a heterotrimeric species. We characterized the specificity of each RNA-RNA interaction in vitro and the cooperative activation of gene expression in Escherichia coli. As we only rely on a biochemical model to compute allosteric regulation, our strategy could be applied to reach more complex RNA-based nanostructures regulating gene expression for synthetic biology applications.

Synthetic Biology↗

bioRxiv2014

Engineering a circular riboregulator in Escherichia coli

Circular RNAs have recently been shown to be important gene expression regulators in mammalian cells. However, their role in prokaryotes remains elusive. Here, we engineered a synthetic riboregulator that self-splice to produce a circular molecule, exploiting group I permuted intron-exon (PIE) sequences. We demonstrated that the resulting circular riboregulator can activate gene expression, showing increased dynamic range compared to the linear form. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker. Thanks to the increased regulatory activity by higher stability, isolation due to self-splicing, and modularity of PIE, we envisage engineered circular riboregulators in further synthetic biology applications.

Synthetic Biology↗

bioRxiv2014

Dual autogenous control of the multiple antibiotic resistance phenotype in Escherichia coli

Bacteria can defend against diverse antibiotics by mounting a multiple antibiotic resistance (mar) phenotype. The resistance is linked to a chromosomal locus that encodes an activator and a repressor regulating their own expression. Here, we investigated how this dual autogenous control determines the dynamics of the response. We found that the regulatory architecture provides a mechanism to enable rapid induction, generate pulses of activation, and increase the range of sensing. The response is also graded and homogeneous across the population. Moreover, the interaction of a third regulator with the core module fine tunes the previous features, while limiting the cross-talk with metabolic signals. A minimal model accurately anticipates these properties, and emphasizes how specific attributes of the circuit components constrain the appearance of other potential behaviors associated to the regulatory design. Our results integrate both molecular and circuit-level characteristics to fully elucidate the dynamic emergence of the mar phenotype.

Systems Biology↗

bioRxiv2014

Regulatory RNA design through evolutionary computation and strand displacement

The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.

Synthetic Biology↗