Biology subjects

Puigbo, P.

Publications and source records attributed to Puigbo, P..

3 recordsLinked to original sources

bioRxiv2020

Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (EPSPS) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in autotrophs. Our results reveal that bacteria easily become resistant to glyphosate through changes in the EPSPS active site. This indicates the importance of examining how glyphosate affects microbe-mediated ecosystem functions and human microbiomes.

microbiology↗

bioRxiv2020

Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase)

Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from >90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.

bioinformatics↗

bioRxiv2020

An unsupervised algorithm for host identification in flaviviruses

Early characterization is essential to control the spread of emerging viruses, such as the Zika Virus outbreak in 2014. A major challenge is the identification of potential hosts for novel viruses. We introduce an algorithm to identify the host range of a virus from its raw genome sequence that will be a useful tool to understand host-virus relationships.

bioinformatics↗