Biology subjects

Garces, R.

Publications and source records attributed to Garces, R..

5 recordsLinked to original sources

bioRxiv2026

When do bacterial mechanosensitive channels get activated?

Bacterial cell envelopes are complex multilayer structures that combine mechanical protection with a multitude of transport and sensory functions. Bacteria maintain substantial turgor pressures which is needed to withstand external forces, grow and maintain shape. An osmotic downshock can create fatal pressure levels. To survive, bacteria rapidly release osmolytes, mainly ions and small metabolites, through mechanosensitive channels (Mscs). Mscs are embedded in the plasma membrane (PM) and act as pressure/tension-activated valves, reducing pressure and preserving cell integrity. It is not well understood, however, how overall stresses are distributed among the layers of the cell envelope, and, in particular, when tension would be borne by the PM and felt by the channels. In this study, we numerically and analytically examine stress distributions within a two-layer model of the cell envelope under varying turgor pressure. We use experimentally determined parameters for PM and peptidoglycan (PG) elasticities, and include enzyme/antibiotic induced weakening of the PG. We introduce, as a critical parameter, a PM reservoir, without which an observed substantial area increase during the shock would not be possible without PM rupture. We used finite-element simulations to model cell swelling assuming linear elasticity of the envelope components, and analytical calculations to model nonlinear PG strain hardening. We analyzed tension sharing between PG and PM with varying PM reservoir sizes during osmotic downshocks. We estimate that an envelope area increase of slightly more than 50% would occur at a turgor pressure of ~11 atm and would be sufficient to fully unfold a 50% PM reservoir and also generate sufficient PM tension to activate mechanosensitive channels. A softening of the PG layer with lysozyme or {beta}-lactam antibiotics is predicted to increase cell expansion at a given turgor pressure and trigger earlier activation of mechanosensitive channels, leading to increased, deleterious metabolite loss.

biophysics↗

bioRxiv2025

Nonlinear continuum description of the E. coli cell wall under high turgor pressure

The principal stress-bearing component of bacterial cell walls is the tough, covalently linked peptidoglycan network. It is an active material that maintains shape and integrity of bacterial cells in the presence of high turgor pressures while constantly growing. It is not well understood how its extremal material properties derive from its molecular structure. The large stress in the cell wall demands a description going beyond small-strain approximations, an approach that has not been taken in the biomaterials community. We here derive a continuum elastic model of E. coli peptidoglycan (PG) in two steps: We first reduce the complex microscopic structure of the PG layer to the spring elements of a 2D hyperelastic triangular network, and then interpret those results in the context of finite-strain continuum theory. We present a self-contained formalism to study stress-strain relationships for large deformations and arbitrary anisotropies. We obtain the minimal model compatible with the available data on E. coli morphology and mechanics. We show that the strain hardening of PG leads to a stiffness matrix that is linearly proportional to the turgor pressure of the cell.

biophysics↗

bioRxiv2024

High Throughput Screening with a Primary Human Mucociliary Airway Model Identifies a Small Molecule with Anti-SARS-CoV-2 Activity

Respiratory viruses (e.g. influenza, RSV, SARS etc.) attack the proximal airway and cause a wide spectrum of diseases for which we have limited therapies. To date, a few primary human stem cell-based models of the proximal airway have been reported for drug discovery but scaling them up to a higher throughput platform remains a significant challenge. Here we present a microscale, primary human stem cell-based proximal airway model of SARS-CoV-2 infection, which is amenable to moderate-to-high throughput drug screening. The model recapitulates the heterogeneity of infection seen among different patients and with different SARS-CoV-2 variants. We applied this model to screen 2100 compounds from targeted drug libraries using an image-based quantification method. While there were heterogeneous responses across variants for host factor targeting compounds, the direct acting antivirals showed a consistent response and we characterized a new antiviral drug that is effective against both the parental strain and the Omicron variant.

cell biology↗

bioRxiv2022

The sunflower WRINKLED1 transcription factor regulates fatty acid biosynthesis genes through an AW box binding sequence with a particular base bias

Sunflower (Helianthus annuus L.) is an important oilseed crop in which the biochemical pathways leading to seed oil synthesis and accumulation have been widely studied. However, how these pathways are regulated is less well understood. The WRINKLED1 (WRI1) transcription factor is considered a master regulator in the transcriptional control of triacylglycerol biosynthesis, acting through the AW box binding element (CNTNG(N)7CG) that resides in the promoter of target genes. Here, we identified the sunflower WRI1 gene and characterized its activity in electrophoretic mobility shift assays. We studied its role as a co-regulator of sunflower genes involved in plastidial fatty acid synthesis, identifying genes bound by this transcription factor. Sunflower WRI1-targets included genes encoding all subunits of the pyruvate dehydrogenase complex, the -CT and BCCP genes of the acetyl-CoA carboxylase complex, genes encoding acyl carrier proteins and key genes of the fatty acid synthase complex (KASIII, KASI and KAR), together with the FATA1 gene. As such, sunflower WRI1 regulates seed plastid fatty acid biosynthesis in a coordinated manner, establishing a WRI1 push and pull strategy that drives oleic acid synthesis for its export into the cytosol. We also analyzed the sequence of the functional sunflower AW box, determining the base bias at the N positions in the active sunflower AW box motif. Accordingly, we conclude that the sunflower AW box is sequence-sensitive at the non-conserved positions, enabling WRI1-binding. Moreover, we found that sunflower WRI1 could bind to a non-canonical AW-box motif, opening the possibility of searching for new target genes.

plant biology↗

bioRxiv2019

Drebrin-like protein regulates body bending of C. elegans via suppression of NCA cationleak channels

Drebrin-like protein (DBN-1) in C. elegans is an adaptor protein that connects different cellular pathways to the actin cytoskeleton. Using a CRISPR-Cas9 system, we generated a new dbn-1 allele, which lacks 80% of C-terminal part of DBN-1. The mutant displays a striking hyper-bending locomotion phenotype and body posture with two times stronger curvature than wild type. We show by atomic force microscopy that the muscle tone of the mutant remains unaffected. Aiming to track down the cause of hyper-bending, we performed genetic epistasis experiments. We found that mutations in the Rho-specific guanine-nucleotide exchange factor (GEF) domain of UNC-73 (Trio), pan-neuronal expression of dominant negative RHO-1 and mutations in NCA (NALCN) cation leak channels all suppressed hyper-bending in the dbn-1 mutant. These data indicate that DBN-1 negatively regulates the activity of both NCA-1 and NCA-2 channels, opposing RHO-1 in the non-canonical Gq pathway. We conclude that DBN-1 is an important component of the neuronal signaling cascade that controls the degree of C. elegans body bending during locomotion.

genetics↗