Biology subjects

Souza, S.

Publications and source records attributed to Souza, S..

3 recordsLinked to original sources

bioRxiv2026

Carbohydrate-active enzymes of giant viruses: Molecular and biochemical characterization of glycosyl hydrolases from algae-infecting chloroviruses

Microbial hydrolases are considered to be promising enzymes for pathogen control. Bacterial and viral chitinases of the glycosyl hydrolase (GH) 18 family are important biological macromolecules with antifungal and anti-insect activity. Chloroviruses, nucleocytoplasmic large DNA viruses (NCLDVs) that infect unicellular green algae have a considerable number of genes involved in carbohydrate metabolism, including the chitinase GH18 family. In this study, we investigated the abundance and diversity of chitinases in chlorovirus genomes using a combination of silico and in vitro strategies, and characterized these enzymes at a molecular and biochemical level. Different enzymatic profiles were observed in Chlorovirus subgenera revealing the different viral machinery related to host species. We performed a comprehensive biochemical characterization of three heterologous expressed GH18 domains, which revealed their endo and exochitinase activity and thermostability. Crystallographic analysis of the GH18 domain by X-ray diffraction yielded a structure at 1.0 [A] resolution, representing the highest-resolution structure reported to date for a giant viral protein and showing lower predominancy of residue coevolution compared GH18 chitinases from other organisms. Additionally, our binding site characterization predicted high conservation in betachloroviruses and gammachloroviruses, and less so in alphachloroviruses. Lastly, these enzymes did not inhibit fungal growth of medical and agricultural importance species in vitro but exhibited high inhibitory activity against different algae at nanogram/mL range. Together, our experimental and computational data show that evolutionary events may contribute to maintaining viral chitinases enzymatic activity and specificity. These findings highlight the potential of virus-derived enzymes as promising new biotechnological tools for microbial control against different algal strains.

microbiology↗

bioRxiv2024

Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16

Osteogenic differentiation is essential for bone development, metabolism, and repair; however, the underlying regulatory relationships among genes remain poorly understood. To elucidate the transcriptomic changes and identify novel regulatory genes involved in osteogenic differentiation, we differentiated mesenchymal stem cells (MSCs) derived from 20 human iPSC lines into preosteoblasts (preOBs) and osteoblasts (OBs). We then performed transcriptome profiling of MSCs, preOBs and OBs. The iPSC-derived MSCs and OBs showed similar transcriptome profiles to those of primary human MSCs and OBs, respectively. Differential gene expression analysis revealed global changes in the transcriptomes from MSCs to preOBs, and then to OBs, including the differential expression of 840 genes encoding transcription factors (TFs). TF regulatory network analysis uncovered a network comprising 451 TFs, organized into five interactive modules. Multiscale embedded gene co-expression network analysis (MEGENA) identified gene co-expression modules and key network regulators (KNRs). From these analyses, KLF16 emerged as an important TF in osteogenic differentiation. We demonstrate that overexpression of Klf16 in vitro inhibited osteogenic differentiation and mineralization, while Klf16+/- mice exhibited increased bone mineral density, trabecular number, and cortical bone area. Our study underscores the complexity of osteogenic differentiation and identifies novel regulatory genes such as KLF16, which plays an inhibitory role in osteogenic differentiation both in vitro and in vivo.

molecular biology↗

bioRxiv2023

A non-canonical mechanism of GPCR activation

The goal of designing safer, more effective drugs has led to tremendous interest in molecular mechanisms through which ligands can precisely manipulate signaling of G-protein-coupled receptors (GPCRs), the largest class of drug targets. Decades of research have led to the widely accepted view that all agonists--ligands that trigger GPCR activation--function by causing rearrangement of the GPCRs transmembrane helices, opening an intracellular pocket for binding of transducer proteins. Here we demonstrate that certain agonists instead trigger activation of free fatty acid receptor 1 by directly rearranging an intracellular loop that interacts with transducers. We validate the predictions of our atomic-level simulations by targeted mutagenesis; specific mutations which disrupt interactions with the intracellular loop convert these agonists into inverse agonists. Further analysis suggests that allosteric ligands could regulate signaling of many other GPCRs via a similar mechanism, offering rich possibilities for precise control of pharmaceutically important targets.

molecular biology↗