Biology subjects

de Koster, C. G.

Publications and source records attributed to de Koster, C. G..

3 recordsLinked to original sources

bioRxiv2025

A mathematical kinetic model of memory in Bacillus subtilis spore germination

Dormant Bacillus subtilis spores germinate through interaction of germinants with germinant receptors (GRs). Subsequently, the activated GR signal is transduced to SpoVA proteins that constitute transport channels. The opening of the SpoVA channel then leads to calcium dipicolinic acid (CaDPA) release and then completion of spore germination. Spores are known to exhibit memory in germination, as spores given an initial short germinant pulse respond more readily to a second pulse. We have developed a mathematical model to identify a minimal reconstructed molecular network that is crucial for germination kinetics leading to memory of germinant exposure; the model reproduces experimental double germinant pulse germination curves. Analysis of the reconstructed network indicates that a minimal set of inactive and active GRs and a SpoVA channel in three states - closed inactive, closed active and open - is needed to reproduce memory. Spore germination memory is introduced in the network by the activation and deactivation rates of GRs, and by the interplay between activation of closed SpoVA channels and their rate of opening and closing. Author summaryDormant bacterial spores return to life in germination when exposed to germinants which are recognized by germinant receptors (GRs). Spores have memory of germinant exposure, such that more spores germinate after a 2nd germinant pulse than after the 1st one, if intervals between pulses are short. In this work, a mathematical model has been developed that reproduces experimental memory behavior. Computer simulations of the model reveal the crucial factors in spore memory of germinant exposure as: i) active and inactive GR states and ii) a membrane channel for a major spore core molecule, Ca-dipicolinic acid (CaDPA), with the channel existing in closed inactive, closed active and open states, all of which are indispensable for spore memory. The model will be part of an iterative cycle of modelling of network dynamics and generating hypotheses for further experimentation.

microbiology↗

bioRxiv2019

Vegetative Cell and Spore Proteomes of Peptoclostridium difficile show finite differences and reveal potential biomarkers.

Clostridioides difficile-associated infection (CDI) is a health-care-associated infection mainly transmitted via highly resistant endospores from one person to the other. In vivo, the spores need to germinate in to cells prior to establishing an infection. Bile acids and glycine, both available in sufficient amounts inside the human host intestinal tract, serve as efficient germinants for the spores. It is therefore, for better understanding of Clostridioides difficile virulence, crucial to study both the cell and spore states with respect to their genetic, metabolic and proteomic composition. In the present study, mass spectrometric relative protein quantification, based on the 14N/15N peptide isotopic ratios, has led to quantification of over 700 proteins from combined spore and cell samples. The analysis has revealed that the proteome turnover between a vegetative cell and a spore for this organism is moderate. Additionally, specific cell and spore surface proteins, vegetative cell proteins CD1228, CD3301 and spore proteins CD2487, CD2434 and CD0684 are identified as potential protein markers for C. difficile infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/598045v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@c5969aorg.highwire.dtl.DTLVardef@228704org.highwire.dtl.DTLVardef@ce49f1org.highwire.dtl.DTLVardef@158928e_HPS_FORMAT_FIGEXP M_FIG Abstract graphic For Table of Contents Only\n\nC_FIG

microbiology↗

bioRxiv2016

In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at peptide level

Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the {delta} and {beta}' subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how {delta} might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.

biochemistry↗