Biology subjects

Green, A. E.

Publications and source records attributed to Green, A. E..

8 recordsLinked to original sources

bioRxiv2026

Niche-specific contribution of the branched-chain amino acid biosynthesis protein IlvD in Streptococcus pneumoniae infection

Systemic pneumococcal infections are a major cause of morbidity and mortality. Pneumococci isolated from bacteraemia lack clear genetic signatures distinguishing them from isolates recovered from other disease sites. The bloodstream is an evolutionary dead end, providing no means of onward transmission, and acute bacteraemic events offer limited opportunity for within-host evolution. Nonetheless, we reasoned that it might be possible to identify genetic determinants of virulence in blood through genomic comparison of matched lung and blood isolates from individual infections. Using samples from a mouse invasive pneumonia model, we observed frequent occurrence of low population frequency mutations in ilvD - encoding a branched-chain amino acid (BCAA) biosynthesis protein - in bloodstream isolates. These mutations were absent from the lung-resident bacterial population. The single-nucleotide polymorphisms in ilvD clustered in a short stretch of nucleotides that are highly conserved across bacteria, suggesting they might disrupt protein function. Deletion of ilvD in pneumococcal strain D39 conferred competitive advantages in both in vitro environments mimicking the bloodstream and in mouse and Drosophila systemic infection models. Improved survival of ilvD mutants within phagocytic cells was dependent on iron availability. Conversely, disruption of ilvD reduced fitness in the nasopharynx, suggesting BCAA biosynthesis is required for upper airway colonisation but is a liability in the context of systemic infection. Nasopharyngeal colonisation defects could be rescued by administering intranasal BCAA to infected mice, suggesting loss of capacity for de novo BCAA synthesis in ilvD mutants accounted for reduced upper airway fitness. In support of a critical role for BCAA biosynthesis in the primary commensal lifestyle of pneumococcus, genomic analysis of clinical isolates demonstrated that ilvD is under purifying selection. Collectively, these findings highlight the context-specific role of IlvD and BCAA biosynthesis in infection, with a requirement for protein function in the BCAA-restricted environment of nasopharynx, but fitness benefits deriving from loss of IlvD and its associated iron-sulfur cluster, in the BCAA-rich conditions of blood.

microbiology↗

bioRxiv2024

Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits

The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.

evolutionary biology↗

bioRxiv2023

Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans

Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n = 58 genomes) and lineage 2 (n = 221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49-novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes: ghrB_1 in lineage 1, and glnM_2 in lineage 2, and diagnostic PCRs targeting them successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable variance with the majority of isolates tested being motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.

microbiology↗

bioRxiv2022

Reducing mitochondrial ribosomal gene expression does not alter metabolic health or lifespan in mice

Maintaining mitochondrial function is critical to an improved health span and lifespan. Introducing mild stress by inhibiting mitochondrial translation invokes the mitochondrial unfolded protein response (UPRmt) and increases lifespan in several animal models. Notably, lower mitochondrial ribosomal protein (MRP) expression also correlates with increased lifespan in a reference population of mice. In this study, we tested whether partially reducing the expression of a critical MRP, Mrpl54, reduced mitochondrial DNA-encoded protein content, induced the UPRmt, and affected lifespan or metabolic health using germline heterozygous Mrpl54 mice. Despite reduced Mrpl54 expression in multiple organs and a reduction in mitochondrial-encoded protein expression in myoblasts, we identified few significant differences between male or female Mrpl54+/- and wild type mice in initial body composition, respiratory parameters, energy intake and expenditure, or ambulatory motion. We also observed no differences in glucose or insulin tolerance, treadmill endurance, cold tolerance, heart rate, or blood pressure. There were no differences in median life expectancy or maximum lifespan. Overall, we demonstrate that genetic manipulation of Mrpl54 expression reduces mitochondrial-encoded protein content but is not sufficient to improve healthspan in otherwise healthy and unstressed mice.

cell biology↗

bioRxiv2022

Exploring Functional Brain Network Modularity in Educational Contexts

The brains modular functional organization facilitates adaptability. Modularity has been linked with a wide range of cognitive abilities such as intelligence, memory, and learning. However, much of this work has (1) considered modularity while a participant is at rest rather than during tasks conditions and/or (2) relied primarily on lab-based cognitive assessments. Thus, the extent to which modularity can provide information about real-word behavior remains largely unknown. Here, we investigated whether functional modularity during resting-state and task-based fMRI was associated with academic learning (measured by GPA) and ability (measured by PSAT) in a large sample of high school students. Additional questions concerned the extent to which modularity differs between rest and task conditions, and across spatial scales. Results indicated that whole-brain modularity during task conditions was significantly associated with academic learning. In contrast to prior work, no such associations were observed for resting-state modularity. We further showed that differences in modularity between task conditions and resting-state varied across spatial scales. Taken together, the present findings inform how functional brain network modularity - during task conditions and while at rest - relate to a range of cognitive abilities.

neuroscience↗

bioRxiv2021

GCN5 Maintains Muscle Integrity by Acetylating YY1 to Promote Dystrophin Expression

This work identifies a novel role for the acetyltransferase GCN5 in regulating muscle integrity through inhibition of DNA binding activity of the transcriptional repressor YY1. Here we report that in mice a muscle-specific knockout of GCN5 (Gcn5skm-/-) reduces the expression of key structural muscle proteins, including dystrophin, resulting in myopathy. Supporting our observation, a meta-analysis between the differential transcriptome of Gcn5skm-/- muscle and all available open-access data sets identified top correlations with musculoskeletal diseases in humans. GCN5 was found to acetylate YY1 at two residues (K392 and K393), which disrupts the interaction between the YY1 zinc-finger region and DNA. De/acetylation mimics for these YY1 post-translational modifications modulated muscle structural gene expression and DNA binding. Analysis of human GTEx data also found positive and negative correlations between fiber diameter and GCN5 and YY1 respectively. Collectively, our results demonstrate that GCN5 acetyltransferase activity regulates YY1 DNA binding and expression of dystrophin to modulate muscle integrity.

cell biology↗

bioRxiv2020

Identification of colonisation and virulence determinants of Streptococcus pneumoniae via experimental evolution in mouse infection models

Streptococcus pneumoniae is a commensal of the human nasopharynx and a major cause of respiratory and invasive disease. Pneumococcus stimulates upper respiratory tract inflammation that promotes shedding from mucosal surfaces and transmission to new hosts. Colonisation and transmission are partially antagonistic processes. Adhesion to surfaces and evasion of host responses favours the former, whilst detachment, promoted by inflammation, is necessary for the latter. We sought to determine how adaptation and evolution of pneumococcus within its nasopharyngeal niche might progress when selective pressures associated with transmission were removed. This was achieved by serial passage of pneumococci in mouse models of nasopharyngeal carriage, manually transferring bacteria between mice. To assess the role of host environmental factors on pneumococcal evolution, we also performed analogous experimental evolution in a mouse pneumonia model, passaging pneumococci through lungs. Nasopharynx-passaged pneumococci became more effective colonisers, whilst those evolved within lungs showed reduced virulence. We observed selection of mutations in genes associated with cell wall biogenesis and metabolism in both nasopharynx and lung lineages, but identified prominent examples of parallel evolution that were niche specific. We focussed on gpsA, a gene in which the same single nucleotide polymorphism arose in two independently evolved nasopharynx-passaged lineages. We identified a single nucleotide change conferring resistance to oxidative stress and enhanced nasopharyngeal colonisation potential. We show that gpsA is also a frequent target of mutation during human colonisation. These findings highlight the role played by the host environment in determining trajectories of bacterial evolution and the potential of experimental evolution in animal infection models for identification of novel pathogen virulence and colonisation factors.

microbiology↗

bioRxiv2020

Structural insights into loss of function of a pore forming toxin and its role in pneumococcal adaptation to an intracellular lifestyle

The opportunistic pathogen Streptococcus pneumoniae has dual lifestyles: one of an asymptomatic colonizer in the human nasopharynx and the other of a deadly pathogen invading sterile host compartments. The latter triggers an overwhelming inflammatory response, partly driven via pore forming activity of the cholesterol dependent cytolysin (CDC), pneumolysin. Although pneumolysin-induced inflammation drives person-to-person transmission from nasopharynx, the primary reservoir for pneumococcus, it also contributes to high mortality rates, creating a bottleneck that hampers widespread bacterial dissemination, thus acting as a double-edged sword. Serotype 1 ST306, a widespread pneumococcal clone, harbours a non-hemolytic variant of pneumolysin (Ply-NH). Performing crystal structure analysis of Ply-NH, we identified Y150H and T172I as key substitutions responsible for loss of its pore forming activity. We uncovered a novel inter-molecular cation-{pi} interaction, governing formation of the transmembrane {beta}-hairpins (TMH) in the pore state of Ply, which can be extended to other CDCs. H150 in Ply-NH disrupts this interaction, while I172 provides structural rigidity to domain-3, through hydrophobic interactions, inhibiting TMH formation. Loss of pore forming activity enabled improved cellular invasion and autophagy evasion, promoting an atypical intracellular lifestyle for pneumococcus, a finding that was corroborated in in vivo infection models. Attenuation of inflammatory responses and tissue damage promoted tolerance of Ply-NH-expressing pneumococcus in the lower respiratory tract. Adoption of this altered lifestyle may be necessary for ST306 due to its limited nasopharyngeal carriage, with loss of pore forming ability of Ply facilitating a benign association of SPN in an alternative, intracellular host niche. AUTHOR SUMMARYStreptococcus pneumoniae, the main causative agent of pneumonia, triggers inflammation and tissue damage by expressing a pore-forming toxin, pneumolysin (Ply). Ply-induced inflammation drives pneumococcal transmission from nasopharynx (its primary reservoir), but also contributes to host mortality, limiting its occupiable habitats. Here, we uncovered the structural basis for loss of pore-forming activity of a Ply variant, present in Serotype 1 ST306, and observed that this enabled adoption of an intracellular lifestyle, attenuating inflammatory responses and prolonging host tolerance of pneumococcus in the lower airways. This commensal-like lifestyle, resembling that of members of the mitis group of Streptococci, might have evolved within ST306 by loss of function ply mutations, compensating for limited nasopharyngeal carriage capacity by facilitating adaptation to an alternate niche.

microbiology↗