Biology subjects

Villarreal, F.

Publications and source records attributed to Villarreal, F..

5 recordsLinked to original sources

bioRxiv2023

De novo assembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Black flounder (Paralichthys orbignyanus) is an economically important ma-rine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina sequencing technology. We started with two independent libraries (from one female and one pool of females; each with 150 bp paired-end reads, a mean insert length of 350 bp, and >35 X-fold coverage). Each library was assembled separately using SOAPdenovo2 and the resulting contigs were scaffolded with SSPACE3 before gaps were filled with GapCloser. In vertebrates, including teleosts, the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to test whether the small genome size of Pleuronectiformes is related to the size of their introns and exons. The assemblies re-sulted in a genome size of [~]538 Mbp (41.35% GC content, 0.11% undetermined bases). Analysis of the assemblies at the core genes level (subset of the 458 universally ex-pressed KOG families) revealed that more than 98% of core genes are present, with more than 78% of them having more than 50% coverage. This indicates a fairly complete and accurate genome at the coding sequence level. Prediction of genes based on statistical predictors (geneid) and sequence-based predictors (Exonerate, using a closely related species, Paralichthys olivaceus, as a reference) was performed. This revealed 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types (including a complete set of spliceosomes and several types of snoRNA and miRNA). As a result, this study concluded that the reduced genome size of flounders is related to a reduction in transcript size, mainly through a reduction in exon number, but also through a reduction in large introns. Thus, both components seem to be involved in the strategy of genome reduction in Pleuronectiformes.

genomics↗

bioRxiv2023

Comprehensive characterization of the complex BAHD acyltransferase family from 218 land plants species: phylogenomic analysis and identification of specificity determinant positions

Chemodiversity is a fundamental trait acquired by plants during their lands colonization. This resulted from an evolutionary process leading to the increase in the number of homologues from a distinct set of protein superfamilies, many of them associated to the specialized metabolism, which allowed the expansion of the chemical space to cope with several environmental cues. BAHD acyltransferases are among these important superfamilies, catalyzing a reaction leading to the acylation of acceptor metabolites with Coenzyme A-activated donors. BAHD acyltransferases can use a wide variety of substrates and they often times display substrate permissiveness towards a wide variety of substrates. Together, these factors complicates the reliable identification and functional annotation of BAHD homologues, also due to the (relatively) limited amount of biochemical data on BAHD acyltransferases. In this work, we take a phylogenomics and computational approach to study the BAHD superfamily in land plants. Using a clustered training set with 27 proteomes, followed by the classification of additional 191 proteomes, we obtained a final BAHDome with 15607 homologues. The training set was clustered in 16 groups, that, together with the identification of cluster of orthologues from the complete BAHDome, were partially assigned functionally to different families guided by the characterized activities (in terms of metabolites used) present in each group. However, the function assignation was not direct in several cases, due to large sequence number, taxonomical distribution on the group, and high sequence variability intra-group. Finally, we used the different families (and functional subfamilies) identified to detect specificity determining positions (SDPs), that may account to explain the functional diversity by finding key positions in, for example, substrate interaction. However, only a handful of the SDPs identified in this work are linked to the substrate binding pocket. Together, these results allow to partially annotate functional BAHD families, which have evolved in a complex pattern of taxonomical and functional signals to allow interaction with multiple substrates, more likely associated to protein dynamics rather than direct substrate interaction.

genomics↗

bioRxiv2022

Seqrutinator: Non-Functional Homologue Sequence Scrutiny for the Generation of large Datatsets for Protein Superfamily Analysis

BackgroundIn recent years protein bioinformatics has resulted in many good algorithms for multiple sequence alignment (MSA) and phylogeny. Little attention has been paid to sequence selection whereas notably recently published complete proteomes often have many sequences that are partial or derive from pseudogenes. Not only do these sequences add noise to the MSA, phylogeny and other downstream computational analyses, they also instigate many errors in the processing of the MSAs and downstream analyses, including the phylogeny. ObjectiveThis work aims to provide and test an objective, automated but flexible pipeline for the scrutiny of sequence sets from large, complex, eukaryotic protein superfamilies. The pipeline should classify sequences with high precision and recall as either functional or non-functional. The pipeline should classify no or only a few SwissProt sequences as non-functional (high precision) and sequences from other related superfamilies as non-functional (high recall) and result in a demonstrably much improved MSA (high performance). ResultsSeqrutinator is a pipeline that consists of five modules written in Python3 that identify and remove sequences that are likely Non-Functional Homologues (NFH). Here we tested the pipeline using three complex plant superfamilies (BAHD, CYP and UGT) that act in specialized metabolism, using the complete proteomes of 16 plant species as input and SwissProt as a control. Only 1.94% of SwissProt sequences with wetlab evidence were identified as NFH and all sequences from other related superfamilies were removed. Most NFH sequences are partial but, interestingly, their removal results in highly improved MSAs. a few but significant sequences that instigate large gaps were found. The five modules show similar behaviour when applied to the 16 sequence sets of the three analysed superfamilies. Pipelines with different module orders result in similar classifications and, moreover, show that different modules often detect the same sequences. Conclusion and perspectiveSeqrutinator forms a consistent pipeline for sequence scrutiny that does result in sequence sets that generate high fidelity MSAs. Recovery analyses show the method has high precision and recall.

bioinformatics↗

bioRxiv2021

Comprehensive multi-omics study of the molecular perturbations induced by simulated diabetes on coronary artery endothelial cells

Coronary artery endothelial cells (CAEC) exert an important role in the development of cardiovascular disease. Dysfunction of CAEC is associated with cardiovascular disease in subjects with type 2 diabetes mellitus (T2DM). However, comprehensive studies of the effects that a diabetic environment exerts on this cellular type scarce. The present study characterized the molecular perturbations occurring on cultured bovine CAEC subjected to a prolonged diabetic environment (high glucose [HG] and high insulin [HI]). Changes at the metabolite and peptide level were assessed by untargeted metabolomics and chemoinformatics, and the results were integrated with proteomics data using published SWATH-based proteomics on the same in vitro model. Our findings were consistent with reports on other endothelial cell types, but also identified novel signatures of DNA/RNA, aminoacid, peptide, and lipid metabolism in cells under a diabetic environment. Manual data inspection revealed disturbances on tryptophan catabolism and biosynthesis of phenylalanine-based, glutathione-based, and proline-based peptide metabolites. Fluorescence microscopy detected an increase in binucleation in cells under treatment that also occurred when human CAEC were used. This multi-omics study identified particular molecular perturbations in an induced diabetic environment that could help unravel the mechanisms underlying the development of cardiovascular disease in subjects with T2DM.

biochemistry↗

bioRxiv2019

Formation of multinucleated variant endothelial cells with altered mitochondrial function in cultured coronary endothelium under simulated diabetes

Coronary endothelial dysfunction is associated with atherosclerosis and myocardial infarction in subjects with type 2 diabetes mellitus (T2DM). Vascular endothelial cells are referred to as small and polygonal mononuclear cells. However, multi-nucleated and large endothelial cells (named as multinucleated variant endothelial cells [MVECs]) have been reported in the aorta, wherein their abundance correlates with atherosclerosis severity. The role of MVECs in coronary endothelium remains obscure. We hypothesized that simulated diabetic conditions increase the number of MVECs and affect their mitochondrial structure/function in cultured coronary endothelium. The in vitro model of diabetes consisted in the treatment of bovine coronary artery endothelial cells (BCAECs) with high-insulin (100 nmol/L, HI) for three days followed by high-glucose (20 mmol/L, HG) and HI for nine additional days. Simulated diabetic conditions increased the abundance of MVECs compared to normal glucose (NG, 5.5 mM). MVECs had a higher nucleic acid content (7.2-Fold), cell diameter (2.2-Fold), and cell area (11.4-Fold) than mononuclear cells. Immunodetection of von-Willebrand factor (endothelial cell marker) in MVECs was positive. The mitochondrial mass was reduced, and mitochondrial membrane potential increased in mononuclear cells cultured in HG+HI compared to mononuclear cells grown in NG. However, the opposite mitochondrial findings were noted in MVECs compared to mononuclear cells. Mass spectrometry-based quantitative proteomic and gene ontology analysis suggested augmented mitochondrial autophagy, apoptosis, and inflammation suppression in cells cultured under HG+HI compared to NG conditions. These findings show that simulated diabetes increases the abundance of MVECs, and that mitochondrial structure and function are differentially affected between MVECs and mononuclear cells.

cell biology↗