Biology subjects

Boddy, C. N.

Publications and source records attributed to Boddy, C. N..

4 recordsLinked to original sources

bioRxiv2025

Heteropentameric architecture predisposes functional inequivalence of acetylcholine receptor agonist sites

Muscle-type acetylcholine receptors are heteropen-tameric ion channels composed of four different but evolutionarily related subunits. These subunits assemble with a precise stoichiometry and arrangement, such that two distinct agonist-binding sites are formed at interfaces between a principal -subunit and a complementary {delta} or {varepsilon}/{gamma}-subunit. Chemical differences between the two complementary subunits are presumed to confer functional inequivalence to the two agonist sites. This interpretation, however, overlooks the asymmetric architecture of the acetylcholine receptor, which places each subunit, and therefore each agonist site, at unique positions within the heteropentamer. The extent to which functional inequivalence of the agonist sites stems from this structural asymmetry, as opposed to chemical differences, remains unexplored. Here, we reconstruct an ancestral subunit capable of substituting for both complementary subunits, thereby engineering hybrid ancestral/human acetylcholine receptors with chemically identical agonist sites. Despite being chemically identical, these agonist sites remain functionally inequivalent. We show that this functional inequivalence stems from distinct intersubunit interactions dictated by the receptors heteropentameric architecture, which also underlie the subunit-dependent effects of a human disease-causing mutation. Thus, structural asymmetry emerges as a fundamental determinant of receptor function, capable of imposing functional inequivalence even in chemically identical sites, with implications for both the evolution of heteromeric protein complexes and the molecular basis of disease.

biophysics↗

bioRxiv2025

A Suite of Stains: Characterization of four fluorophores as complementary tools for visualizing neutral lipids in an extremophilic green alga

Understanding lipid metabolism in algae is critical to advancing our knowledge on fundamental algal physiology and for harnessing these organisms as platforms for the sustainable production of high-energy lipids. BODIPY is the most prevalently used fluorescent dye for the visualization of lipid droplets (LDs) in algae; however, its limitations warrant exploration of alternatives. Here we evaluate and compare four lipophilic fluorophores (BODIPY, DAF, Cou, DPAS) for their effectiveness in staining LDs in the extremophilic green alga Chlamydomonas priscui. We assess each dyes photophysical properties, synthetic accessibility, LD specificity, cellular toxicity, and suitability for microscopy and flow cytometry. All four dyes successfully stain LDs, but their performance diverges under different experimental conditions. BODIPY permits long-term incubation allowing quantification in time-course studies but exhibits poor LD specificity and high susceptibility to photobleaching. DAF enables polarity-sensitive staining but is highly toxic on prolonged exposure or during cellular stress. Cou and DPAS yield strong LD-specific signals with low cytotoxicity, making them ideal for studies involving environmental stress. However, DPAS requires room-temperature incubation, pointing toward greater potential utility for non-extremophilic algae. These results expand the toolbox for lipid biotechnology research in extremophiles and underscore the importance of tailoring dye selection and experimental conditions to algal physiology.

plant biology↗

bioRxiv2024

The ATP-dependent protease ClpYQ degrades cell division proteins DivIVA and Mbl in Bacillus subtilis

ATP-dependent proteases play key roles in bacterial protein quality control and regulation of cellular processes. ClpYQ and ClpXP are ATP-dependent proteases in the Gram-positive bacteria Bacillus subtilis. To date, no substrate proteins of B. subtilis ClpYQ have been characterized. The protease component encoded by clpQ is synthetically lethal with clpP and the two genes are non-essential individually, suggesting potentially redundant roles for ClpYQ and ClpXP. Previous quantitative proteomic data predicted that B. subtilis proteins DivIVA and Mbl, components of the divisome and elongasome respectively, are potential substrates of ClpYQ. The role of DivIVA and Mbl in cell division and elongation suggests a significant role of ClpYQ in regulating cell division through targeted degradation of key divisome and elongasome proteins. Here we confirm that DivIVA and Mbl are degraded by ClpYQ both in vitro and in vivo, and thus identify the first two substrates of ClpYQ in B. subtilis.

biochemistry↗

bioRxiv2022

A comparison of hard and soft direct methods for DNA extraction from soil

Nucleic acid extraction is the first step in molecular biology studies of soil bacterial communities. The most common used soil DNA extraction method is the direct, hard extraction Mobio method, which uses bead beating to lyse bacteria. In this study we compared the Mobio method with a soft, enzymatic lysis extraction method. Next generation sequencing (Illumina and Pyrosequencing) of amplicons generated from four 16S primer pairs and DNA from 12 soils and 3 composts was used to compare the two extraction methods. Four bacterial orders, the delta proteobacterial Desulfuromonadales and gamma proteobacterial Pseudomonadales, Enterobacteriales, and Alteromonadales were more common in amplicons from soft extracted DNA, sometimes by two orders of magnitude. These groups can be a significant fraction of the bacterial population. For example the Pseudomonadales made up to 16 % and Enterobacteriales 10% of amplicons from Soft extracted DNA. The JG30-KF-CM45 order was under extracted by the enzymatic lysis extraction method. Results differed more by primer choice than extraction method and the phylogenetic resolution of differences between extraction methods changed with primer choice. Given how often Mobio extraction is used, these proteobacterial orders are probably under-represented in the studies of soil bacteria that use nucleic acid methods. Further improvements in soil DNA extraction are needed. Amplicons sequencing studies should use a range of different primers to confirm the phylogenetic resolution of their results. ImportanceSeveral large scale studies of soil bacteria that compare thousands of soil samples across continents have used the Mobio method for DNA extraction. Large scale studies like these are increasing with the recent establishment of the Global Soil Biodiversity Observation Network (Soil BON), which also uses the Mobio method. The results of this work will be used to make policy decisions about how to manage the soil and may be a guide for bioprospectors. As the Mobio method is so widely used, it is important to know its limitations. Studies that use the Mobio method underestimate the fraction of several proteobacterial groups. Most notably the Enterobacteria and Pseudomonas can be under extracted by 10-100 fold. The degree of under extraction varies with different soils.

microbiology↗