Structure/Function of CAZYmes from extreme environments
CAZymes (Carbohydrate-active enzymes) from extreme environments are studied for their hyperstability and ability to degrade novel carbohydrates under harsh conditions, leading to potential applications in industries like biofuels and biorefining. We investigate the structure-activity relationships of these enzymes by identifying specific CAZymes using genomic and metagenomic approaches, determining their 3D structures, and understanding how their active sites are adapted to function in extreme conditions like high heat, salt, or pH. Our research involves diverse target environments, including hot springs and deep-sea trenches, to discover unique CAZymes with specific substrate specificities, such as those targeting lignocellulose or other complex plant polymers.
We are interested to understand how these enzymes are adapted degrading polysaccharides at high pH (alkaliphiles), high (thermophiles) or even low temperatures (psychrophiles). Understanding the molecular adaptations at these environments, we can exploit them for biofuel production, biorefining of biomass, and other industrial processes that require enzymes active under harsh conditions.
To achieve this, we use a multidisciplinary approach employing (meta)genomics and enzyme mining, classic enzymology, but also structural biology and protein engineering to manipulate the structure improving their stability and/or activity.
Enzymology of the Human Gut Microbiota
The human gut microbiota is a complex microbial community that plays a central role in digestion, metabolism, and health. A key feature of these microbes is their ability to produce enzymes that degrade, transform, and synthesize biomolecules otherwise inaccessible to humans. The human genome encodes relatively few carbohydrate-active enzymes (CAZymes), but the gut microbiota compensates by contributing a large, diverse enzymatic repertoire.
In our group, we are interested to understand how Bacteroides species encode Polysaccharide Utilization Loci (PULs) which are genomic clusters containing glycoside hydrolases, carbohydrate esterases, and binding proteins that enable degradation of diverse glycans.Thurough these systems, Bacteroides is able to process complex polymers from the diet, such as arabinogalactan proteins (AGP) or b-glucans from cereals or fungal cell walls, producing short-chain fatty acids (SCFAs) as a final product.
Protein Engineering of Laccases and other plastic degrading enzymes
Plastics such as polyethylene terephthalate (PET), polyethylene (PE), polyurethane (PU), and polystyrene (PS) are highly resistant to degradation due to their hydrophobicity, crystallinity, and stable chemical bonds. Recently, enzymatic plastic degradation has emerged as a sustainable solution, with enzymes like laccases, cutinases, PET hydrolases, esterases, and peroxidases showing promise. However, natural enzymes often suffer from low activity, poor thermostability, narrow substrate scope, and low tolerance to harsh conditions.
To overcome these limitations, protein engineering approaches—including rational design, directed evolution, and computational methods—have been applied to improve enzyme performance for plastic degradation.
In our lab, we are committed to improve the function and activity of laccases and PET hydrolases that are targeting PE and PET, respectively. In addition to the mining of novel enzymes using a (meta)genomic approach, we are interested to dissect the intriguing mechanism of these enzymes and generate tools to improve their activity through AI and Machine Learning.
Cell signalling and cross-talk between bacterial members
Bacteria use cell-to-cell communication to coordinate group behaviours. The most common system is quorum sensing (QS), where bacteria produce, release, and detect signalling molecules (autoinducers). When the concentration of these molecules reaches a threshold (indicating a high population density), gene expression is activated collectively. This regulates traits such as biofilm formation, bioluminiscence or even sporulation.
In our lab, we are interested to understand how bacteria members "cross-talk" each other within a community. If we understand these interactions, we could develop strategies to enrich the content of a specific member within that community.
We have projects where we are trying to dissect how different bacterial members in the human gut, including Bacteroidota and Bacillota, share nutrients and what metabolic pathways are activated during this process. We are specially keen to decipher the oligosaccharides that are "shared" between different members but also other stratagies such as "pirating" sugars from the host.