Biology subjects

Little, R.

Publications and source records attributed to Little, R..

6 recordsLinked to original sources

bioRxiv2026

CoEVFold suite: user friendly pipelines to visually represent protein coevolution

Multiple sequence alignment (MSA) data underlies current principles in protein folding and protein-protein interaction prediction, from which large language models (LLMs) in tandem with protein datasets, can predict protein structure. However, what is missing are user-friendly tools that enable researchers to predict and demonstrate coevolution - the principal input which these MSAs infer. Here we present tools to identify and visualize coevolution, through a pipeline (CoEVFold) that uses basic direct coupling algorithms derived from GREMLIN and alignment of sequences from MMSEQs2. The pipeline generates a visual representation of coevolution for a single protein but can also represent coevolution of homomeric or heteromeric protein complexes, as well as coevolution within protein networks. The input for this pipeline can be an amino acid sequence, or user input protein structures from Alphafold their own files or the PDB database. In validation of CoEVFolds capabilities, and utilising proteins from known prokaryotic and eukaryotic model systems (Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae), as well as phage proteins, CoEVFold predicts coevolution between proteins known to interact, proteins known to oligomerise, and coevolution in proteins known to be part of a protein complex. Collectively, these suite of tools, named CoEVFold suite, have broad applicability and provide a useful toolkit to those interested in dissecting protein-protein interactions and networks. AvailabilityThe code is available online at https://colab.research.google.com/drive/1MSSvNTq7KZ4Lr0XTz89vUuK-J3xOTzwS?usp=sharing and Github. https://github.com/MishterBluesky/CoEVFold Supplementary informationSupplementary data is available via Figshare and supplementary materials.

microbiology↗

bioRxiv2025

Loss of circulating glucocorticoid rhythm disrupts the circadian transcriptome and vascular reactivity in the mouse renal artery

AimsMolecular clocks in the vasculature contribute to the normal circadian blood pressure (BP) rhythm. Glucocorticoids are known to synchronise molecular clocks within peripheral tissues. Disruption of the endogenous glucocorticoid rhythm causes "non-dipping", a BP pattern associated with elevated cardiovascular risk. The mechanisms for this are unclear but vascular changes likely contribute. We examined the effect of impaired glucocorticoid rhythmicity on the time-of-day dependent vascular function and define the circadian transcriptome under control conditions and under arrhythmic glucocorticoids. Methods and ResultsMale C57BL6J mice kept on a 12:12 hour light/dark cycle were implanted with a subcutaneous slow-release pellet containing vehicle or corticosterone ([~]3.7mg/kg/day), which flattened the endogenous glucocorticoid rhythm. After 7 days, renal arteries were isolated at 7am and 7pm to measure vasoreactivity using wire myography. Other arteries were taken 2-hourly over a 48-hour period for RNA sequencing. In control arteries, endothelium-dependent and independent vasodilation was elevated at wake-phase compared to the sleep-phase. This temporal variation was absent in the renal arteries from corticosterone treated mice. Using CircaCompare and LimoRhyde, we found circadian rhythms in 459 of the 14 225 protein-coding transcripts in control arteries. Following corticosterone treatment, 156 genes lost their rhythm, including canonical clock genes, genes involved in "peroxide homeostasis" such as Nox4 and "TNF signalling" like Mmp14. Paradoxically 492 genes gained a rhythm and were predominantly mitochondrial-related. ConclusionsThis study expands the molecular landscape for understanding circadian vascular physiology and emphasises the impact of glucocorticoid rhythm on temporal changes in gene expression and vascular function. This is clinically relevant to the pathogenesis of vascular dysfunction associated with perturbed glucocorticoid signalling for e.g. in metabolic syndrome and chronic stress. TRANSLATIONAL PERSPECTIVEDisruption of the normal circadian rhythm of plasma glucocorticoid levels causes non-dipping blood pressure, a profile associated with enhanced cardiovascular risk. The role of vascular dysfunction in this context is unknown. We report that arrhythmic plasma glucocorticoid levels impair time-dependent vasoreactivity and alters the circadian transcriptome of the renal artery. We provide a molecular framework for investigations into glucocorticoid-induced vascular dysfunction across the 24-hour day. Clinically, this is relevant for patients on chronic glucocorticoid therapy but could have generalisable implications for the underlying mechanisms of blood pressure rhythm. Targeting rhythm-sensitive vascular pathways may offer novel avenues to improve blood pressure rhythms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/650449v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1c988b8org.highwire.dtl.DTLVardef@2f0ee7org.highwire.dtl.DTLVardef@17b6e25org.highwire.dtl.DTLVardef@7c6afb_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2022

Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities

Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their natural environmental niche.

microbiology↗

bioRxiv2022

Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk

Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator controlling the host proteome through direct interaction with host mRNAs and interference with the hosts translational regulatory network. This mRNA interference leads to largescale proteomic changes in metabolic genes, key regulators and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle. Significance StatementPlasmids are recognised for their important role in bacterial evolution as drivers of horizontal gene transfer. Less well understood are the effects of plasmids upon bacterial behaviours by manipulating the expression of key bacterial phenotypes. Until now, examples of plasmid manipulation of their bacterial hosts were limited to highly targeted transcriptional control of a few related traits. In contrast, here we describe the first plasmid global translational regulator evolved to control the bacterial behavioural switch from a motile to a sessile lifestyle and bacterial metabolism, mediated through manipulation of the bacterial proteome. Moreover, this global translational regulator is common across divergent plasmids in a wide range of bacterial host taxa, suggesting that plasmids may commonly control bacterial lifestyle in the clinic, agricultural fields, and beyond.

microbiology↗

bioRxiv2021

Potassium effects on NCC are attenuated during inhibition of Cullin E3-ubiquitin ligases

The thiazide sensitive sodium-chloride co-transporter (NCC) plays a vital role in maintaining sodium (Na+) and potassium (K+) homeostasis. NCC activity is modulated by the with-no-lysine kinases 1 and 4 (WNK1 and WNK4), the abundance of which are controlled by the RING-type E3 ligase Cullin 3 (Cul3) and its substrate adapter Kelch-like protein 3. Dietary K+ intake has an inverse correlation with NCC activity, but the mechanism underlying this phenomenon remains to be fully elucidated. Here, we investigated the involvement of other members of the Cullin family in mediating K+ effects on NCC phosphorylation (active form) and abundance. In kidneys from mice fed diets varying in K+ content, there were negative correlations between NCC (phosphorylated and total) and active (neddylated) forms of Cullins (Cul1, 3, 4 and 5). High dietary K+ effects on phosphorylated NCC were attenuated in Cul3 mutant mice (CUL3-Het/{Delta}9). Short-term (30 min) and long-term (24 h) alterations in the extracellular K+ concentration did not affect Cullin neddylation levels in ex vivo renal tubules. Short-term, the ability of high extracellular K+ to decrease NCC phosphorylation was preserved in the presence of MLN4924 (pan Cullin inhibitor), but the response to low extracellular K+ was absent. Long-term, MLN4924 attenuated the effects of high extracellular K+ on NCC phosphorylation and responses to low extracellular K+ were absent. Our data suggest that in addition to Cul3, other Cullins are involved in mediating the effects of K+ on NCC phosphorylation and abundance.

physiology↗

bioRxiv2020

Mechanistic understanding enables the rational design of salicylanilide combination therapies for Gram-negative infections

One avenue to combat multidrug-resistant Gram-negative bacteria is the co-administration of multiple drugs (combination therapy), which can be particularly promising if drugs synergize. The identification of synergistic drug combinations, however, is challenging. Detailed understanding of antibiotic mechanisms can address this issue by facilitating the rational design of improved combination therapies. Here, using diverse biochemical and genetic assays, we reveal the molecular mechanisms of niclosamide, a clinically-approved salicylanilide compound, and demonstrate its potential for Gram-negative combination therapies. We discovered that Gram-negative bacteria possess two innate resistance mechanisms that reduce their niclosamide susceptibility: a primary mechanism mediated by multidrug efflux pumps and a secondary mechanism of nitroreduction. When efflux was compromised, niclosamide became a potent antibiotic, dissipating the proton motive force (PMF), increasing oxidative stress and reducing ATP production to cause cell death. These insights guided the identification of diverse compounds that synergized with salicylanilides when co-administered (efflux inhibitors, membrane permeabilizers, and antibiotics that are expelled by PMF-dependent efflux), thus suggesting that salicylanilide compounds may have broad utility in combination therapies. We validate these findings in vivo using a murine abscess model, where we show that niclosamide synergizes with the membrane permeabilizing antibiotic colistin against high-density infections of multidrug-resistant Gram-negative clinical isolates. We further demonstrate that enhanced nitroreductase activity is a potential route to adaptive niclosamide resistance but show that this causes collateral susceptibility to clinical nitro-prodrug antibiotics. Thus, we highlight how mechanistic understanding of mode of action, innate/adaptive resistance, and synergy can rationally guide the discovery, development and stewardship of novel combination therapies. ImportanceThere is a critical need for more effective treatments to combat multidrug-resistant Gram-negative infections. Combination therapies are a promising strategy, especially when these enable existing clinical drugs to be repurposed as antibiotics. We reveal the mechanisms of action and basis of innate Gram-negative resistance for the anthelmintic drug niclosamide, and subsequently exploit this information to demonstrate that niclosamide and analogs kill Gram-negative bacteria when combined with antibiotics that inhibit drug efflux or permeabilize membranes. We confirm the synergistic potential of niclosamide in vitro against a diverse range of recalcitrant Gram-negative clinical isolates, and in vivo in a mouse abscess model. We also demonstrate that nitroreductases can confer resistance to niclosamide, but show that evolution of these enzymes for enhanced niclosamide resistance confers a collateral sensitivity to other clinical antibiotics. Our results highlight how detailed mechanistic understanding can accelerate the evaluation and implementation of new combination therapies.

microbiology↗