0000000001047057
AUTHOR
Guillermo Rodrigo
showing 23 related works from this author
Viral fitness correlates with the magnitude and direction of the perturbation induced in the host’s transcriptome: the tobacco etch Potyvirus—tobacco…
2018
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyv…
Molecular signatures of silencing suppression degeneracy from a complex RNA virus
2021
As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA sil…
Robust dynamical pattern formation from a multifunctional minimal genetic circuit.
2010
Abstract Background A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle. Results We propose a new mechanism to generate developmental patterns and oscillations using a minimal number of genes. For this, we design a synthetic gene circuit with an antagonistic self-regulation to study the spatio-temporal control of protein expression. He…
Nonequilibrium thermodynamics of the RNA-RNA interaction underlying a genetic transposition program
2021
Thermodynamic descriptions are powerful tools to formally study complex gene expression programs evolved in living cells on the basis of macromolecular interactions. While transcriptional regulations are often modeled in the equilibrium, other interactions that occur in the cell follow a more complex pattern. Here, we adopt a nonequilibrium thermodynamic scheme to explain the RNA-RNA interaction underlying IS10 transposition. We determine the energy landscape associated with such an interaction at the base-pair resolution, and we present an original scaling law for expression prediction that depends on different free energies characterizing that landscape. Then, we show that massive experim…
Virus-host interactome: Putting the accent on how it changes
2017
[EN] Viral infections are extremely complex processes that could only be well understood by precisely characterizing the interaction networks between the virus and the host components. In recent years, much effort has gone in this directionwith the aimof unveiling themolecular basis of viral pathology. These networks are mostly formed by viral and host proteins, and are expected to be dynamic bothwith time and space (i.e., with the progression of infection, as well as with the virus and host genotypes; what we call plastodynamic). This largely overlooked spatio-temporal evolution urgently calls for a change both in the conceptual paradigms and experimental techniques used so far to characte…
Empirical modeling of material composition and size in MOFs prepared with ligand mixtures
2019
Systematic analyses of the composition and size of metal-organic frameworks built with Zn4O and terephthalic/amino-terephthalic acid mixtures, together with a kinetic assay, reveal how these ligands behave differently, which reveals the complexity of crystal growth in these frameworks and the ability to tune it on purpose.
CRISPR-mediated strand displacement logic circuits with toehold-free DNA
2021
DNA nanotechnology, and DNA computing in particular, has grown extensively over the past decade to end with a variety of functional stable structures and dynamic circuits. However, the use as designer elements of regular DNA pieces, perfectly complementary double strands, has remained elusive. Here, we report the exploitation of CRISPR-Cas systems to engineer logic circuits based on isothermal strand displacement that perform with toehold-free double-stranded DNA. We designed and implemented molecular converters for signal detection and amplification, showing good interoperability between enzymatic and nonenzymatic processes. Overall, these results contribute to enlarge the repertoire of su…
Post-transcriptional bursting in genes regulated by small RNA molecules
2018
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules. We exploit this framework to compare transcriptional and post-transcriptional bursting and also…
Suprathreshold stochastic resonance behind cancer
2018
Noise in gene expression is pervasive and, in some cases, even fulfills a functional role. Cancer cell populations exploit noise to increase heterogeneity as a defense against therapies. What lies behind this picture is a phenomenon of stochastic resonance led by the collective, rather than by individual cells.
Abscisic Acid Connects Phytohormone Signaling with RNA Metabolic Pathways and Promotes an Antiviral Response that Is Evaded by a Self-Controlled RNA …
2020
© 2020 The Authors.
Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
2009
46 pages, 4 tables, 6 figures, 3 additinoal files.
CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation
2021
The novel respiratory virus SARS-CoV-2 is rapidly evolving across the world with the potential of increasing its transmission and the induced disease. Here, we applied the CRISPR-Cas12a system to detect, without the need of sequencing, SARS-CoV-2 genomes harboring the E484K mutation, first identified in the Beta variant and catalogued as an escape mutation. The E484K mutation creates a canonical protospacer adjacent motif for Cas12a recognition in the resulting DNA amplicon, which was exploited to obtain a differential readout. We analyzed a series of fecal samples from hospitalized patients in Valencia (Spain), finding one infection with SARS-CoV-2 harboring the E484K mutation, which was t…
Vanillin cell sensor
2007
Our project for iGEM 2006 consisted of designing a cellular vanillin biosensor. We used an EnvZ -E. coli strain as a chassis, and constructed two different devices: a sensor and an actuator, assembled using OmpR-P as a standardised mediator. The sensor device contained a computation- ally designed vanillin receptor and a synthetic two-component signal transduction protein (Trz). The receptor protein was based on a ribose-binding protein as scaffold. The Trz was built by fusion of the periplasmic and transmembrane domains of a Trg protein with an EnvZ kinase domain. When the receptor complex binds Trg, an allosteric motion is propagated to the cyto- plasmic EnvZ kinase domain, resulting in a…
Engineering a Circular Riboregulator in Escherichia coli
2020
RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli . We showed that the resulting riboregulator can trans -activate gene expression by interacting with a cis -repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled thi…
Evolutionary impact of copy number variation rates.
2017
[Objective]: Copy number variation is now recognized as one of the major sources of genetic variation among individuals in natural populations of any species. However, the relevance of these unexpected observations goes beyond diagnosing high diversity. [Results]: Here, it is argued that the molecular rates of copy number variation, mainly the deletion rate upon variation, determine the evolutionary road of the genome regarding size. Genetic drift will govern this process only if the efective population size is lower than the inverse of the deletion rate. Otherwise, natural selection will do.
Boolean computation in plants using post-translational genetic control and a visual output signal
2018
[EN] Due to autotrophic growing capacity and extremely rich secondary metabolism, plants should be preferred targets of synthetic biology. However, developments in plants usually run below those in other taxonomic groups. In this work we engineered genetic circuits capable of logic YES, OR and AND Boolean computation in plant tissues with a visual output signal. The circuits, which are deployed by means of Agrobacterium tumefaciens, perform with the conditional activity of the MYB transcription factor Roseal from Antirrhinum majus inducing the accumulation of anthocyanins, plant endogenous pigments that are directly visible to the naked eye or accurately quantifiable by spectrophotometric a…
Model-based design of RNA hybridization networks implemented in living cells
2017
[EN] Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs. These networks are ultimately coupled to the control of gene expression. We relied on a thermo-dynamic model of the different stable…
Modulation of Intracellular O-2 Concentration in Escherichia coli Strains Using Oxygen Consuming Devices
2018
International audience; The use of cell factories for the production of bulk and value-added compounds is nowadays an advantageous alternative to the traditional petrochemical methods. Nevertheless, the efficiency and productivity of several of these processes can improve with the implementation of micro-oxic or anoxic conditions. In the industrial setting, laccases are appealing catalysts that can oxidize a wide range of substrates and reduce O-2 to H2O. In this work, several laccase-based devices were designed and constructed to modulate the intracellular oxygen concentration in bacterial chassis. These oxygen consuming devices (OCDs) included Escherichia coil's native laccase (CueO) and …
Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time
2020
Synthetic biology aims at engineering gene regulatory circuits to end with cells (re)programmed on purpose to implement novel functions or discover natural behaviors. However, one overlooked question is whether the resulting circuits perform as intended in variety of environments or with time. Here, we considered a recently engineered genetic system that allows programming the cell to work as a minimal computer (arithmetic logic unit) in order to analyze its operability regime. This system involves transcriptional and post-transcriptional regulations. In particular, we studied the analog behavior of the system, the effect of physicochemical changes in the environment, the impact on cell gro…
Additional file 2 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular chan…
2020
Additional file 2: Fig. S2. Evolutionary stability of a control system (E. coli transformed with plasmid pRHA27). Continuous fluorescence monitoring of four biological replicates (A-D) over one week.
Additional file 1 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular chan…
2020
Additional file 1: Fig. S1. Environmental robustness assessment of a control system (E. coli transformed with plasmid pRHA27; this system just expresses sfGFP under the control of the lac promoter). Fluorescence monitoring (normalized green fluorescence) when the culture medium changes (pH and temperature variation). Error bars correspond to standard errors over four biological replicates.
Additional file 3 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular chan…
2020
Additional file 3: Fig. S3. Schematics of the plasmids pRHA40, pRHA12, and pRHA1240.
Additional file 4 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular chan…
2020
Additional file 4: Dataset S1. Experimental and theoretical data of the half adder behavior. The Excel file contains an implementation of the mathematical model.