Biology subjects

Navarro, R.

Publications and source records attributed to Navarro, R..

3 recordsLinked to original sources

bioRxiv2021

Integrated Proteomic and Metabolomic Analyses of the Mitochondrial Neurodegenerative Disease MELAS

MELAS (mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes) is a progressive neurodegenerative disease caused by pathogenic mitochondrial DNA variants. The pathogenic mechanism of MELAS remains enigmatic due to the exceptional clinical heterogeneity and the obscure genotype-phenotype correlation among MELAS patients. To gain insights into the pathogenic signature of MELAS, we designed a comprehensive strategy integrating proteomics and metabolomics in patient-derived dermal fibroblasts harboring the ultra-rare MELAS pathogenic variant m.14453G>A, specifically affecting the mitochondrial respiratory Complex I. Global proteomics was achieved by data-dependent acquisition (DDA) and verified by data-independent acquisition (DIA) using both Spectronaut and the recently launched MaxDIA platforms. Comprehensive metabolite coverage was achieved for both polar and nonpolar metabolites in both reverse phase and HILIC LC-MS/MS analyses. Our proof-of-principle MELAS study with multi-omics integration revealed OXPHOS dysregulation with a predominant deficiency of Complex I subunits, as well as alterations in key bioenergetic pathways, glycolysis, tricarboxylic acid cycle, and fatty acid {beta}-oxidation. The most clinically relevant discovery is the downregulation of the arginine biosynthesis pathway, likely due to blocked argininosuccinate synthase, which is congruent with the MELAS cardinal symptom of stroke-like episodes and its current treatment by arginine infusion. In conclusion, we demonstrated an integrated proteomic and metabolomic strategy for patient-derived fibroblasts, which has great clinical potential to discover therapeutic targets and design personalized interventions after validation with a larger patient cohort in the future. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/473301v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1f59135org.highwire.dtl.DTLVardef@110451forg.highwire.dtl.DTLVardef@129f9d8org.highwire.dtl.DTLVardef@d1f347_HPS_FORMAT_FIGEXP M_FIG Graphic Abstract: Integrated proteomics and metabolomics of patient fibroblasts revealed dysregulations in arginine biosynthesis, OXPHOS complexes, and bioenergetic pathways in MELAS, a mitochondrial neurodegenerative disease caused by mitochondrial DNA mutations. C_FIG

systems biology↗

bioRxiv2020

Defects in plant immunity modulate the rates and patterns of RNA virus evolution

It is assumed that host genetic variability for susceptibility to infection necessarily conditions virus evolution. Differences in host susceptibility can either drive the virus to diversify into strains that track different defense alleles (e.g., antigenic diversity) or to infect only the most susceptible genotypes. To clarify these processes and their effect on virulence, we have studied how variability in host defense responses determine the evolutionary fate of viruses. To accomplish this, we performed evolution experiments with Turnip mosaic potyvirus in Arabidopsis thaliana mutants. Mutant plants had disruptions in infection-response signaling pathways or in genes whose products are essential for potyvirus infection. Genotypes were classified into five phenogroups according to their response to infection. In order to disentangle how host susceptibility affects virus adaptation, independent viral lineages were evolved in selected plant genotypes. Evaluating disease-related traits of the evolved lineages, we found that evolution proceeded faster in the most resistant hosts than in the most permissive ones, as expected for adaptation to a harsh environment. By sequencing the genomes of the evolved viral lineages, we found that the multifunctional protein VPg turned out to be the target of selection in most host genotypes. When all evolved viral lineages were tested for fitness in all plant genotypes used in the experiments, we found compelling evidences that generalist viruses were selected by the most restrictive plant genotypes, while permissive genotypes selected for specialist viruses. Overall, this work illustrates how different host defense signaling pathways constrain not only disease-related traits but virus evolution.

evolutionary biology↗

bioRxiv2017

Diminishing returns of inoculum size on the rate of a plant RNA virus evolution

Understanding how genetic drift, mutation and selection interplay in determining the evolutionary fate of populations is one of the central questions of Evolutionary Biology. Theory predicts that by increasing the number of coexisting beneficial alleles in a population beyond some point does not necessarily translates into an acceleration in the rate of evolution. This diminishing-returns effect of beneficial genetic variability in microbial asexual populations is known as clonal interference. Clonal interference has been shown to operate in experimental populations of animal RNA viruses replicating in cell cultures. Here we carried out experiments to test whether a similar diminishing-returns of population size on the rate of adaptation exists for a plant RNA virus infecting real multicellular hosts. We have performed evolution experiments with tobacco etch potyvirus in two hosts, the natural and a novel one, at different inoculation sizes and estimated the rates of evolution for two phenotypic fitness-related traits. Firstly, we found that evolution proceeds faster in the novel than in the original host. Secondly, we found the predicted diminishing-returns effect of inoculum size on the rate of evolution for one of the fitness traits, but not for the other, which suggests that selection operates differently on each trait.

evolutionary biology↗