We are interested in a broad range of topics in basic and applied microbiology. We use a number of methodologies, from molecular to computational, to refactor biological systems with the intention of learning from its fundamental properties.

The main research topics are described below. In all our projects we aim to keep a balance between the deep questions and the applications, not forgetting about tool and technology development if needed.

Cell economics

Cells contain limited amounts of resources available for gene expression. The way these resources are allocated determines cell viability and survival in changing environments. Resource allocation has an impact too in the expression of exogenous genes, typically in synthetic circuits, that generate an extra burden to the cell and fail to behave according to their design specifications.  The analysis of how scarce resources are distributed is, in essence, an economics problem.

A simple genetic circuit expressing a constitutive GFP and an inducible RFP is used to monitor couplings in the expression of the two due to the competition for ribosomes. The couplings are captured by a linear relationship termed ‘isocost line’.

We are trying to understand how resources, mainly the transcriptional and translational machinery, are allocated in microbial cells. Unraveling molecular determinants of this process will greatly help to optimize the design of synthetic circuits as well as the cellular physiology. We are currently developing applications of this research in Escherichia coli, Clostridium and Pseudomonas putida for the expression of complex modular genetic circuits, the production of commodity chemicals and biodegradable plastic materials such as PHA (P4SB)

Population dynamics in structured environments

Microbes do not live in isolation. Interactions in communities are of great importance for environmental processes and also affect – and are affected by – our lifestyle as illustrated for example by the spread of antimicrobial resistance genes.

Microbes in nature grow in colonies forming large aggregates called biofilms. We study the assembly of these colonies looking at their formation under the microscope and also on plates. In complex populations, limited cell mobility together with limited diffusion of nutrients and other shared molecules, have as a consequence the formation of distinct habitats with differential species composition. The evolution that microbes undergo in this niches is greatly conditioned by surrounding species and their capability to adapt, giving rise to even more complex dynamics and interactions.

colonies

Effect of genetic drift on conjugation on agar plates. Two populations of cells tagged with different colours are allowed to demix and form genotypic identical sectors from the centre of a plate. If one of these populations carries a transferable plasmids it is possible to quantify conjugation challenging the colony with a circular filter soaked in an antibiotic (right picture)

We are interested in analyzing these properties related to the ability of antibiotic resistance gene transfer through conjugation as well as in the potential of using bacteriophages as a tool that could replace current antibiotic treatments.

Fitness landscapes

We use fitness landscapes as a metaphor to understand evolution. A fitness landscape is a collection of genotypes performing a particular function. We use the landscape analogy to understand how new functions emerge. For instance, using a combination of selection and high-throughput sequencing we have investigated the ability of a pool of all possible 24mer RNA sequences to bind to a ligand. This pool is composed by 1014 unique sequences each represented 1,000 times.

landscape

Detail of a two-dimensional representation of a fitness landscapes for short RNAs that bing to GTP. The picture shows the evolutionary paths connecting three distinct families clustered in peaks with high activity

The complete experimental coverage of a landscape is only possible for very short molecules with a reduced alphabet, such as the one mentioned. In the case of proteins, it is impossible to completely cover the astronomically large space of sequences. It is still possible, however, to use fitness landscapes to narrow down the search area and find evolutionary paths leading to new functional sequences. We are building on this knowledge to look for bacteriophages and antibodies with evolved specificity for a number of applications, including the development of new biosensors and antibiotics.

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