Biology subjects

Santos, M. A. S.

Publications and source records attributed to Santos, M. A. S..

4 recordsLinked to original sources

bioRxiv2023

A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans.

Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals, but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37{degrees}C, the ability to switch between yeast and hyphal forms and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. The latter leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex proteomic samples. To address this question, we have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying low-level amino acid misincorporation events at the proteome level. We have also analysed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our MS/MS data. The data show that C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG sites, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins. The study also demonstrates that increasing misincorporation of Leucine at CUG sites does not alter the translational fidelity of the other codons. These findings advance existing knowledge on amino acid misincorporations in C. albicans and add a new dimension to the remarkable capacity of this fungus to diversify its proteome.

microbiology↗

bioRxiv2023

tRNASer overexpression induces adaptive mutations in NSCLC tumors

tRNAs are a driving force of genome evolution in Yeast and Bacteria. Their deregulation is frequently observed in tumors with Serine tRNAs being often overexpressed. This has important functional consequences, such as increased metabolism and tumor growth. In yeast, time and chemical stimulus boost alterations in the genome driven by tRNA deregulation. Therefore, we hypothesized that tRNA deregulation may contribute to the increased genome instability observed in tumors. To study the effect of tRNA deregulation in tumors, we overexpressed tRNA-Ser-AGA-2-1 in a NSCLC cell line, H460. This cell line and a Mock (control) were xenografted in nude mice and collected at 3 timepoints: T1-Naive; T2-Treated once with cisplatin/vehicle and; T3) treated twice with cisplatin/vehicle. These tumors were characterized by WES, RNAseq and Mass Spectrometry and the data obtained was integrated. The tumor mutation burden was increased in T3 tRNASerOE tumors, regardless of treatment. Although in T1 Mock and tRNASer tumors have a similar number of variants, in T2&3, tRNASerOE tumors display two times more variants than Mock tumors regardless of treatment. Interestingly, tRNASerOE exclusive variants favor proliferation and therapy resistance, which is in line with the phenotypes observed and supported by RNAseq and proteomics data. In conclusion, tRNASerOE increases the tumor mutation burden and the variants detected favor tumor growth, proving tRNA deregulation is enough to induce adaptive mutations in the genome.

cancer biology↗

bioRxiv2021

Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

Gene expression alterations occur in all mouse tissues during aging, but recent works highlight minor rather than major dysregulation amplitude for most genes, questioning whether differentially expressed genes on their own provide deep insight into aging biology. To clarify this issue, we have combined differential gene expression with weighted gene correlation network analysis (WGCNA) to identify expression signatures accounting for the pairwise relations between gene expression profiles and the cumulative effect of genes with small fold- changes during aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice. Functional enrichment analysis of the overlap of genes identified in both approaches showed that immunity-related responses, mitochondrial energy metabolism, tissue regeneration and detoxification are prominently altered in the brain, heart, muscle, and liver, respectively, reflecting an age-related global loss of tissue function. While data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, particularly proteostasis-related pathways, which we highlight as important features of murine tissue physiological aging.

genetics↗

bioRxiv2020

tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast

Abstract/SummaryProtein synthesis rate and accuracy are essential for bona fide protein synthesis and proteome homeostasis (proteostasis), however the mRNA translation elongation factors that prevent protein mistranslation, misfolding and aggregation are poorly understood. To address this question, we evaluated the role of 70 yeast tRNA modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated and mistranslated proteins. We show that the mitochondrial tRNA-modifying enzyme Slm3 thiolates the cytoplasmic tRNAs at position 34 and that decreased levels of mcm5s2U34 in SLM3 mutants are compensated by increasing mcm5U34, ncm5U34 and ncm5Um34 levels. In the tRNA gene knockout strains, stress response proteins are overrepresented in protein aggregates and their genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications. Increased rates of amino acid misincorporation were detected in the yeast ELP1, SLM3 and TRM9 gene knockout mutants at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, misfolding and cellular proteotoxic stress.

molecular biology↗