Biology subjects

Pereto, J.

Publications and source records attributed to Pereto, J..

4 recordsLinked to original sources

bioRxiv2018

Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential

Microbial communities from harsh environments hold great promise as sources of biotechnologically-relevant strains. In the present work, we have deeply characterized the microorganisms from three different rocky locations of the Mediterranean coast, an environment characterised by being subjected to harsh conditions such as high levels of irradiation and large temperature and salinity fluctuations. Through culture-dependent and culture-independent techniques, we have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. A culture-independent approach through high-throughput 16S rRNA amplicon sequencing revealed that all three locations display very similar microbial communities, suggesting that there is a stable community associated to the sampled region, with Stanieria cyanosphaera, Rubrobacter sp. and the families Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa. Furthermore, shotgun metagenomic sequencing results were in concordance with the high-thoughput 16S rRNA, and allowed a description of the eukaryotic and archaeal members of the community, which were abundant in Ascomycota and halotolerant archaea, respectively. The culture-dependent approach yielded a collection of 100 isolates (mainly pigmented), out of which 12 displayed high antioxidant activities, as proved with two in vitro (hydrogen peroxide and DPPH) and an in vivo (model organism C. elegans) assays.

microbiology↗

bioRxiv2018

Bioprospecting the solar panel microbiome: high-throughput screening for antioxidant bacteria in a Caenorhabditis elegans model

Microbial communities that are exposed to sunlight typically share a series of adaptations to deal with the radiation they are exposed to, including efficient DNA repair systems, pigment production and protection against oxidative stress, which makes these environments good candidates for the search of novel antioxidant microorganisms. In this research project, we isolated potential antioxidant pigmented bacteria from a dry and highly-irradiated extreme environment: solar panels. High-throughput in vivo assays using Caenorhabiditis elegans as an experimental model demonstrated the high antioxidant and ultraviolet-protection properties of these bacterial isolates that proved to be rich in carotenoids. Our results suggest that solar panels harbor a microbial community that includes strains with potential applications as antioxidants.

microbiology↗

bioRxiv2018

Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways during the divergence of primates and rodents. Then, we related those selective pressures to the functional and topological characteristics of the pathways. We have used DNA sequences of all enzymes (956) of the metabolic pathways comprised in the HumanCyc database, using genome data for humans and five other mammalian species.\n\nWe have found that the evolution of metabolic genes is primarily constrained by the layer of the metabolism in which the genes participate: while genes encoding enzymes of the inner core of metabolism are much conserved, those encoding enzymes participating in the outer layer, mediating the interaction with the environment, are evolutionarily less constrained and more plastic, having experienced faster functional evolution. Genes that have been targeted by adaptive selection are endowed by higher out-degree centralities than non-adaptive genes, while genes with high in-degree centralities are under stronger purifying selection. When the position along the pathway is considered, a funnel-like distribution of the strength of the purifying selection is found. Genes at bottom positions are highly preserved by purifying selection, whereas genes at top positions, catalyzing the first steps, are open to evolutionary changes.\n\nThese results show how functional and topological characteristics of metabolic pathways contribute to shape the patterns of evolutionary pressures driven by natural selection and how pathway network structure matters in the evolutionary process that shapes the evolution of the system.

systems biology↗

bioRxiv2017

A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid

Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism -which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome scale metabolic network (GEM) for the bacterial consortium from the cedar aphid iBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e. tryptophan and biotin biosynthesis) and the proposal of a hitherto unnoticed event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate. In silico knock-out experiments with iBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is more significant than previously thought.

systems biology↗