Biology subjects

Santos, M. D.

Publications and source records attributed to Santos, M. D..

3 recordsLinked to original sources

bioRxiv2023

In silico characterization, homology modeling and structure-based functional annotation of Nile Tilapia (Oreochromis niloticus) Hsp70 and Hsc70 proteins

BackgroundThe molecular chaperones known as heat shock proteins 70 (Hsp70) and heat shock cognate protein 70 (Hsc70) are vital for maintaining cellular integrity and controlling stress. MethodologyThe On-Hsp70 and On-Hsc70 proteins from Nile tilapia (Oreochromis niloticus) have been thoroughly examined in this study using in silico analysis, homology modeling, and functional annotation. Homology modeling was carried out using the SWISS- MODEL program, and the proposed model was assessed for its high reliability through analyses including ProSA, Verify 3D, PROVE, ERRAT, and Ramachandran plot. ResultsThe essential features of the On-Hsp70 and On-Hsc70 proteins encompass amino acid lengths (640 and 645), molecular weights (70,233.48 and 70,773.17 Da), theoretical isoelectric points (pI = 5.63 and 5.28), and the overall counts of negatively and positively charged residues (95 and 86; 95 and 81). Furthermore, the instability index (II) values were 35.27 (On-Hsp70) and 38.85 (On-Hsc70). Similarly, the aliphatic index (AI) exhibited high values for both proteins, reaching 84.58 (On-Hsp70) and 82.85 (On-Hsc70). On-Hsp70 and On-Hsc70 were both shown to contain an MreB/Mbl domain. DiscussionThe authors found that On-Hsp70 and On-Hsc70 share key characteristics, including an acidic nature, high stability, and conserved domains. Protein-protein interaction analysis identified the co-chaperone Stip1 as a primary functional partner. Comparative modeling yielded highly reliable 3D models, revealing structural similarity to known proteins and predicted binding sites. Furthermore, the primary subcellular localization of both proteins is the cytoplasm. Functional analysis predicted an AMP-PNP binding site for On-Hsp70 and ATP binding site for On-Hsc70. ConclusionThe discoveries deepen our understanding of Hsc70 and Hsp70 in Nile tilapia, highlighting their importance in fish physiology and positioning them as crucial study topics moving forward. This study adds to our understanding of the actions of these proteins in cellular processes and stress responses, which could impact fish health and resilience.

bioinformatics↗

bioRxiv2021

Multiple genes in cis mediate the effects of a single chromatin accessibility variant on aberrant synaptic development and function in human neurons

Despite hundreds of risk loci from genome-wide association studies of neuropsychiatric disorders, causal variants/genes remain largely unknown. Here, in NEUROG2-induced human neurons, we identified 31 risk SNPs in 26 schizophrenia (SZ) risk loci that displayed allele-specific open chromatin (ASoC) and were likely to be functional. Editing the strongest ASoC SNP rs2027349 near vacuolar protein sorting 45 homolog (VPS45) altered the expression of VPS45, lncRNA AC244033.2, and a distal gene, C1orf54, in human neurons. Notably, the global gene expression changes in neurons were enriched for SZ risk and correlated with post-mortem brain gene expression signatures of neuropsychiatric disorders. Neurons carrying the risk allele exhibited increased dendritic complexity, synaptic puncta density, and hyperactivity, which were reversed by knocking-down distinct cis-regulated genes (VPS45, AC244033.2, or C1orf54), suggesting a phenotypic contribution from all three genes. Interestingly, transcriptomic analysis of knockdown cells suggested a non-additive effects of these genes. Our study reveals a compound effect of multiple genes at a single SZ locus on synaptic development and function, providing a mechanistic link between a non-coding SZ risk variant and disease-related cellular phenotypes.

genetics↗

bioRxiv2021

Compound- and fiber type-selective requirement of AMPKγ3 for insulin-independent glucose uptake in skeletal muscle

Objective: The metabolic master-switch AMP-activated protein kinase (AMPK) mediates insulin-independent glucose uptake in muscle and regulates the metabolic activity of brown and beige adipose tissue (BAT). The regulatory AMPK{gamma}3 isoform is uniquely expressed in skeletal muscle and also potentially in BAT. Here, we investigated the role that AMPK{gamma}3 plays in mediating skeletal muscle glucose uptake and whole-body glucose clearance in response to small-molecule activators that act on AMPK via distinct mechanisms. We also assessed if {gamma}3 plays a role in adipose thermogenesis and browning. Methods: Global AMPK{gamma}3 knockout (KO) mice were generated. A systematic whole-body, tissue and molecular phenotyping linked to glucose homeostasis was performed in {gamma}3 KO and wild type (WT) mice. Glucose uptake in glycolytic and oxidative skeletal muscle ex vivo, as well as blood glucose clearance in response to small molecule AMPK activators that target nucleotide-binding domain of {gamma} subunit (AICAR) and allosteric drug and metabolite (ADaM) site located at the interface of the and {beta} subunit (991, MK-8722) were assessed. Oxygen consumption, thermography, and molecular phenotyping with a {beta}3-adrenergic receptor agonist (CL-316,243) treatment were performed to assess BAT thermogenesis, characteristics and function. Results: Genetic ablation of {gamma}3 did not affect body weight, body composition, physical activity, and parameters associated with glucose homeostasis under chow or high fat diet. {gamma}3 deficiency had no effect on fiber-type composition, mitochondrial content and components, or insulin-stimulated glucose uptake in skeletal muscle. Glycolytic muscles in {gamma}3 KO mice showed a partial loss of AMPK2 activity, which was associated with reduced levels of AMPK2 and {beta}2 subunit isoforms. Notably, {gamma}3 deficiency resulted in a selective loss of AICAR-, but not MK-8722-induced blood glucose-lowering in vivo and glucose uptake specifically in glycolytic muscle ex vivo. We detected {gamma}3 in BAT and found that it preferentially interacts with 2 and {beta}2. We observed no differences in oxygen consumption, thermogenesis, morphology of BAT and inguinal white adipose tissue (iWAT), or markers of BAT activity between WT and {gamma}3 KO mice. Conclusions: These results demonstrate that {gamma}3 plays a key role in mediating AICAR- but not ADaM site binding drug-stimulated blood glucose clearance and glucose uptake specifically in glycolytic skeletal muscle. We also showed that {gamma}3 is dispensable for thermogenesis and browning of iWAT.

physiology↗