Biology subjects

O'Brien, S.

Publications and source records attributed to O'Brien, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Massively scaled variant effect mapping across the MAPK pathway reveals the importance of molecular and cellular context

Variation alters inherent protein properties like thermodynamic stability and catalytic activity, and these intrinsic effects are shaped by the complex cellular environment. Signaling cascades typify this complexity, with tens or hundreds of proteins acting in concert through regulated states and interactions to transduce signals. Here, we measure the effect of 186,676 variants across 17 proteins in the RAS-MAPK pathway on protein abundance and pathway activity in human cells under diverse conditions, for a total of 503,099 variant effect measurements. We discovered 14,412 dominant negative variants across 12 proteins, nearly all previously unknown, that disrupt specific domains or interaction interfaces while leaving other functions intact and that are depleted from the human population. Measuring the abundance of 106,642 variants across 10 proteins under HSP90 inhibition showed that HSP90 shapes the effect of 67% of missense variants across the pathway, buffering destabilizing variants in both strong and weak clients. Our variant effect data, collected in the context of an intact proteome, enabled us to assess the functional importance of 395 experimentally and computationally modeled MAPK protein interactions. Using additional mutational scans, we resolved how the promiscuous switch II helix binding surface of KRAS accommodates overlapping interactions with LZTR1 and SOS1, revealing distinct allosteric networks that support each interaction. Thus, we establish a framework for measuring variant effects at unprecedented scale in human cells, illuminating fundamental MAPK pathway signaling mechanisms and demonstrating that cellular context profoundly shapes the effect of most variants.

genomics↗

bioRxiv2026

Transcriptional adaptation influences buffering among essential paralog gene families

Buffering among paralogous genes is a well-described phenomenon in which genetic redundancy provides genetic robustness. Shared function among paralogs allows for a compensation effect when one or more paralog family genes are inactivated. Considering the role of transcriptional adaptation in influencing gene expression among highly homologous genes, we sought to identify whether transcriptional adaptation has a role in paralog buffering. We performed Perturb-seq of 110 paralog gene knockouts and assessed compensatory gene expression effects among paralogs as well as at the whole transcriptome level. This analysis identified six paralog pairs that undergo a transcriptional adaptation following CRISPR-mediated loss of one paralog in the pair. Further, we found that the upregulation of TIA1 following paralog TIAL1 loss requires nonsense-mediated decay, and active nuclear import via the importin IPO8. These data provide a comprehensive evaluation of transcriptional adaptation and show that transcriptional adaptation is recurrent but not pervasive among paralogous human genes.

genetics↗

bioRxiv2026

Hidden State Genomics: Graph-Based Analysis of Sparse Auto-Encoder Feature Activity in Genomic Language Models

Pre-trained genomic language model (gLM) representations have been anticipated to enable enhanced deep learning predictions on several genomics tasks, but current benchmarking has led to questions over what they actually encode. We studied this with mechanistic interpretability on InstaDeeps Nucleotide Transformer v2 (500M), training sparse autoencoders across all 24 encoder layers to probe latent features. Correlation-based annotation against reference regulatory tracks was inconsistent across layers and insufficient for causal interpretation. We therefore built typed sequence-to-feature knowledge graphs to explore the SAE feature space and compared cisplatin-binding versus non-binding genomic DNA sequence communities by PageRank centrality, validating candidate features with decoder-based interventions and a CNN binding classifier. Interventions showed asymmetric effects: suppressive features could collapse predictive signal, while binding-associated features shifted predictions cumulatively with the presence of other binding-associated signals. Dependency maps further indicated strong local feature sensitivity within sequences. Together, these results provide evidence that gLM representations encode highly granular sequence syntax and conservation patterns, aligning more strongly with tightly coupled molecular interactions and local biophysical constraints than with complex, distributed regulatory logic. Within the scope of our intervention setting, this pattern is consistent with stronger performance on selected molecular tasks and weaker performance on broader regulatory inference, motivating scalable methods for causal feature annotation.

bioinformatics↗

bioRxiv2026

Fungicide drives de novo evolution of multidrug resistance in the plant growth promoting rhizobacterium, Pseudomonas fluorescens

Plant growth-promoting rhizobacteria (PGPR) are key members of soil microbial communities, supporting nutrient cycling, plant health, and productivity. In agricultural soils, these beneficial bacteria are often exposed to multiple stressors simultaneously, including fungicides, antibiotics, and rising temperatures. Despite their ecological importance, little is known about how PGPR respond evolutionarily to such combined stressors. Here, we investigated how the model PGPR Pseudomonas fluorescens SBW25 evolves resistance to the fungicide formulation Fubol Gold (metalaxyl-M + mancozeb), under ambient or warming soil conditions. Using a 16-week experimental evolution in soil microcosms with a fully factorial design (fungicide {+/-} warming), we assessed the evolution of fungicide resistance via phenotypic assays and whole-genome sequencing. Fungicide exposure rapidly selected for increased fungicide resistance, detectable as early as week 4, and co-selected for multidrug resistance, likely through mutations in a mexS ortholog that cause efflux pump overexpression. Warming did not alter the evolution of fungicide resistance; however, populations subjected to both fungicide and warming stress went extinct more rapidly, indicating that population evolutionary rescue was less effective under dual stress. Our findings show that fungicides alone can drive multidrug resistance in beneficial soil bacteria, suggesting that strategies to tackle AMR in agriculture should also consider non-antibiotic drivers of resistance.

microbiology↗

bioRxiv2026

Fungicide and warming interact to reduce soil ecosystem functioning

Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bioremediation. However, intensively managed environments such as agricultural soils are increasingly challenged with multiple harsh environmental stressors from the compounding effects of climate change and conventional agricultural practices. Understanding how soil communities will respond to environmental stress along multiple axes is key for predicting how environmental change will impact terrestrial soil ecosystems. We combine experimental evolution with community phenotyping, 16s rRNA metabarcoding, fungicide resistance assays and plant experiments, to show that fungicide and warming temperatures together drive a synergistic reduction in soil community respiration rates, metabolic capacity and plant growth promotion (Hordeum vulgare), which would have been missed by looking at stressor effects independently. Dual stressors caused widespread loss of metabolic activity, particularly for carbohydrates and carboxylic acids, highlighting impairment of community function. Fungicide-evolved soil isolates had a 16-fold increase in fungicide resistance, but only in the absence of warming - suggesting that the dual stressor treatment constrained fungicide adaptation. Together, our findings suggest that the number of stressors (rather than the nuances of individual stressors) may be key for predicting soil microbial community responses to environmental change across multiple axes.

ecology↗

bioRxiv2025

AI-Enhanced Marker-Assisted Selection Concept for The Multifunctional Honey Bee (Hymenoptera: Apidea) Protein Vitellogenin (Vg)

Managed honey bees (Hymenoptera: Apidae: Apis mellifera L) have experienced unsustainably high rates of annual loss driven by several interacting factors, most notably pests, pathogens, pesticides, and poor nutrition. Breeding bee stocks that can cope with these challenges is a priority. Advanced molecular methods (marker-assisted selection, MAS) have enhanced the breeding efficiency of domesticated animals in recent years, but have not contributed strongly to honey bee stock improvements. This is largely because desirable traits of bees usually emerge from collective phenotypes of workers (sterile females) instead of from the breeding individuals (queens and male drones). For collective phenotypes, single genes typically have small, additive effects, so identifying impactful MAS targets is challenging. Here, we provide proof of concept for a new approach to honey bee breeding through MAS using the multifunctional protein Vitellogenin (Vg), a protein known to interact with and mitigate the primary drivers of colony loss. Our pipeline leverages cutting-edge, artificial intelligence (AI)-driven protein structure modeling algorithms to predict the effects of genetic variants of Vg on relevant molecular functions including lipid, zinc, and DNA binding. Following the AI-powered Vg variant selection step, we use a combination of standard apicultural techniques and DNA sequencing validation to breed honey bee queens homozygous for the desirable Vg allele. Our protocol can kick-start a new area of modernized bee breeding: an AI-enhanced MAS system that allows cost-effective and nimble development of stocks to meet urgent and long-term needs of stakeholders.

genetics↗

bioRxiv2025

Co-infection with Streptococcus and Rothia spp. drives prophage dynamics in Pseudomonas aeruginosa in an artificial sputum model

ObjectivesChronic bacterial lung infections with Pseudomonas aeruginosa are common in people with cystic fibrosis (CF) but interactions with other commonly seen members of the CF lung community, such as Streptococcus and Rothia spp., are not well understood. The aim of this study was to determine the impact of other species on P. aeruginosa using an artificial sputum medium (ASM) model designed to mimic the conditions in the CF lung. MethodsP. aeruginosa LESB58, representing a CF epidemic strain, was inoculated into ASM either alone or in co-culture with Streptococcus anginosus, Streptococcus vestibularis, Rothia mucilaginosa or Rothia dentocariosa. Gene expression was assessed using RNAseq at 72 and 96 h timepoints. Free phage numbers were assessed by plaque assay and qPCR. ResultsDifferential expression of P. aeruginosa genes, including those related to virulence factors such as prophage, type III secretion, exopolysaccharides and pyochelin production, was seen in co-culture conditions compared with single-species culture. In particular, at 72 h, there was lower expression of most LES prophage genes under co-culture conditions, and this corresponded with lower overall free phage at the same timepoint. Specifically, during co culture, there was a reduction in the levels of a D3112-like transposable phage, previously shown to have the ability to drive CF-like adaptations in an experimental evolution model, and an increase in levels of Pf1-like filamentous phage, associated with altered biofilm formation and immune responses. ConclusionGene expression changes during co-culture with Streptococcus and Rothia spp. were identified affecting key P. aeruginosa virulence factors including phage. Further work indicated changes to free phage levels of two important P. aeruginosa LESB58 prophage with the potential to affect P. aeruginosa adaptation, antibiotic resistance and host immune response in the CF lung. This study emphasises the importance of understanding the influence of lung commensals on focal pathogens in a complex microbiome.

microbiology↗

bioRxiv2024

Mechanisms driving epigenetic and transcriptional responses of microglia in a neurodegenerative lysosomal storage disorder model

Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders (LSDs) and is associated with various age-related neurodegenerative diseases1,2, but there is limited understanding of the mechanisms by which altered lysosomal function leads to changes in gene expression that drive pathogenic cellular phenotypes. To investigate this question, we performed systematic imaging, transcriptomic, and epigenetic studies of major brain cell types in Sgsh null (KO) mice, a preclinical mouse model for Sanfilippo syndrome (Mucopolysaccharidosis Type IIIA, MPS-IIIA)3,4. MPS-IIIA is a neurodegenerative LSD caused by homozygous loss-of-function (LoF) mutations in SGSH which results in severe early-onset developmental, behavioral, and neurocognitive impairment5-15. Electron microscopy, immunohistochemistry, and single-nucleus RNA-sequencing analysis revealed microglia as the cell type exhibiting the most dramatic phenotypic alterations in Sgsh KO mice. Further temporal analysis of microglia gene expression showed dysregulation of genes associated with lysosomal function and immune signaling pathways beginning early in the course of the disease. Sgsh deficiency similarly resulted in increases in open chromatin and histone acetylation at thousands of putative microglia-specific enhancers associated with upregulated genes but had much less impact on the epigenetic landscapes of neurons or oligodendrocytes. We provide evidence for dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with PU.1/ETS and C/EBP transcription factors. Lastly, we show that features of the transcriptomic and epigenetic alterations observed in murine Sgsh deficiency are also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimers disease patients, revealing common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.

neuroscience↗

bioRxiv2024

Mutant RIT1 cooperates with YAP to drive an EMT-like lung cancer state

The discovery of oncogene addiction in cancer has led to the development of over a dozen FDA-approved biomarker-driven therapies in lung adenocarcinoma. Somatic mutations of the "Ras-like in all tissues" (RIT1) gene are non-canonical driver events in lung cancer, occurring in [~]2% of lung adenocarcinomas in a mutually exclusive fashion with KRAS and EGFR mutations. Patients with RIT1-mutant lung cancer lack targeted therapy treatment options, and a lack of pre-clinical models has hindered the development of therapeutic strategies for RIT1-mutant lung cancer. Here we report a new mouse model of RIT1-driven lung cancer in which the human RIT1M90I variant can be induced in a Cre-regulated manner. We show that autochthonous expression of RIT1M90I in the lung weakly promotes cancer alone or in combination with loss of the p53 tumor suppressor. However, potent synergy between RIT1M90I and inactivation of Nf2 drives an aggressive epithelial-to-mesenchymal (EMT) lung cancer with 100% penetrance and short latency. We show this oncogenic cooperation is driven by synergistic activation of cJUN, a component of the AP-1 complex. Therapeutic inhibition of MEK and YAP/TEAD suppressed RIT1-driven lung cancer in vivo. These data identify YAP/TEAD as an important mediator of RIT1s oncogenic potential and nominate TEAD as an important drug target in RIT1-mutant lung cancer. HIGHLIGHTSO_LIWe report a new RIT1M90I-mutant autochthonous lung tumor model C_LIO_LIThe most common oncogenic variant of RIT1, RIT1M90I, weakly promotes lung tumor development C_LIO_LIRIT1M90I drives the formation of lethal lung tumors in cooperation with p53 and Nf2 tumor suppressor gene loss C_LIO_LIRIT1M90I and YAP cooperatively regulate cJUN expression C_LIO_LITherapeutic MEK and TEAD targeting suppresses RIT1M90I-driven tumorigenesis C_LI

cancer biology↗

bioRxiv2024

Temporal and spatial variability in availability bias has consequences for marine bird abundance estimates during the non-breeding season

O_LITo effectively monitor how marine ecosystems are being reshaped by anthropogenic pressures, we require understanding of species abundances and distributions. Due to their socio-economic and ecological value, predatory species are often at the forefront of survey efforts. However, survey data are only valuable if they can reliably be converted into estimates of underlying distributions. C_LIO_LIWe consider at-sea surveys of marine predators that often inform ecological impact assessments of offshore windfarms. These surveys are subject to a form of detection bias called availability bias whereby individuals which are submerged below the surface are consequently unavailable for detection. Although correction factors are commonly used in these surveys, they are currently based on limited data that may not be species-, time-, or area-specific. Here, we use time-depth-recorder data to investigate variation in marine bird availability bias. C_LIO_LIWe found that the proportion of diving marine birds submerged below the sea surface during daylight hours, and therefore unavailable to be counted during surveys, varied by species, month, and area. For three of our focal species wintering around northwest Europe (Atlantic puffin, common guillemot, razorbill) our results were different to comparable values previously used to correct for the availability bias, whereas no correction factors are regularly used for the fourth species (red-throated diver). We now present availability bias correction factors that are species- and month-specific to the areas the study populations use during their non-breeding seasons: the North Sea, the north and west coasts of the UK, the Baltic Sea, and Icelandic coastal waters. C_LIO_LISynthesis and applications: Variation in the proportion of daylight hours that marine birds spent submerged lead to differences in availability bias correction factors, thereby impacting estimations of their abundances. We encourage use of correction factors that use data from the species, marine area, and month during which surveys are conducted to provide more accurate abundance estimates. Using more relevant correction factors will result in increasingly accurate abundance and distribution estimates of diving marine birds, with relevance for a range of applications including planning for offshore windfarm developments, the designation and monitoring of protected areas, and understanding environmental change. C_LI

ecology↗

bioRxiv2023

Spatial refuges and nutrient acquisition predict the outcome of evolutionary rescue in evolving microbial populations

Microbial populations are often exposed to environmental stressors that impact their survival and evolution. Eco-evolutionary theory suggests microbial populations may be able to survive a stressor through "spatial refuges" - i.e., areas of low or reduced stress such as within biofilms. However, spatial refuges reduce a populations access to nutrients, so may be detrimental depending on the severity of the stressor they are sheltering from. Using predictions from a general mathematical model, and the experimental evolution of the bacterium Pseudomonas fluorescens SBW25 under salinity stress and varying opportunities to form spatial refuges (i.e., agitated or non-agitated culture conditions), we show that spatial refuges can rescue a population from stressors only when nutrient levels are high. In the surviving high-salinity evolved populations (i.e., non-agitated culture conditions and high-nutrients), clones had an increased salinity resistance, indicating that spatial refuges can facilitate evolutionary rescue. Though whole genome resequencing did not reveal a single specific mutation associated with salt resistance, we found that clones evolved under control conditions (lower salt, high-nutrients, and no agitation) acquired mutations in a putative chemotaxis gene and showed increased motility. This indicates that spatial refuges under high salinity may also constrain adaptations to other environmental factors. Together, our combination of theory, laboratory experiment, and genome re-sequencing demonstrate the value and limits of spatial refuges in alleviating environmental stress within microbial populations.

microbiology↗

bioRxiv2023

CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality

A major impediment to the characterization of mtDNA repair mechanisms, in comparison to nuclear DNA repair mechanisms, is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of a mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox) we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted Dox screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentially of our top hit - WRNIP1 - observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.

biochemistry↗

bioRxiv2022

Public goods exploitation is reduced in species-rich microbial communities

Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e. interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence select for increased intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2-15 species. We find, contrary to our prediction, that siderophore exploitation is reduced in high diversity communities, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. Our results suggest that maintaining a healthy soil microbiota could contribute to the maintenance of siderophore production in natural communities.

microbiology↗

bioRxiv2022

SCF-FBXW7 regulates G2-M progression through control of CCNL1 ubiquitination

FBXW7, which encodes a substrate specific receptor of an SCF E3 ligase complex, is a frequently mutated human tumor suppressor gene known to regulate the post-translational stability of various proteins involved in cellular proliferation. Here, using genome-wide CRISPR screens we report a novel synthetic lethal genetic interaction between FBXW7 and CCNL1 and describe CCNL1 as a new substrate of the SCF-FBXW7 E3 ligase. Further analysis showed that the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle since defective CCNL1 accumulation, resulting from FBXW7 mutation, leads to shorter mitotic time. Cells harboring FBXW7 loss-of-function mutations are hypersensitive to treatment with a CDK11 inhibitor, highlighting a genetic vulnerability that could be leveraged for cancer treatment.

cancer biology↗

bioRxiv2020

Gene functional networks and autism spectrum characteristics in young people with intellectual disability

BackgroundGenes associated with Intellectual disability (ID) can be grouped into networks according to gene function. This study asked whether individuals with ID show differences in autism spectrum characteristics (ASC), depending on the functional network membership of their rare, pathogenic de novo genetic variants. MethodsChildren and young people with ID of known genetic origin were allocated to two broad functional network groups: synaptic physiology (n=29) or chromatin regulation (n=23). We applied principle components analysis to the Social Responsiveness Scale to map the structure of ASC in this population, and identified three components - Inflexibility, Social Understanding and Social Motivation. We then used Akaike Information Criterion (AIC) to test the best fitting models for predicting ASC components, including demographic factors (age, gender), non-ASC behavioural factors (global adaptive function, anxiety, hyperactivity, inattention) and gene functional networks. ResultsWe found that, when other factors are accounted for, the chromatin regulation group showed higher levels of Inflexibility. We also observed contrasting predictors of ASC within each network group. Within the chromatin regulation group, Social Understanding was associated with inattention, and Social Motivation was predicted by hyperactivity. Within the synaptic group, Social Understanding was associated with hyperactivity, and Social Motivation was linked to anxiety. ConclusionWe report that gene functional networks can predict Inflexibility, but not other ASC dimensions. Contrasting behavioural associations within each group suggests network-specific developmental pathways from genomic variation to autism. Simple classification of neurodevelopmental disorder genes as high risk or low risk for autism is unlikely to be valid or useful.

genetics↗

bioRxiv2019

Interspecific social interactions shape public goods production in natural microbial communities

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic non-ferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same - intermediate siderophore levels were favored - and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members. SignificanceBacterial communities possess remarkable taxonomic and metabolic diversity and play a key role in nearly every biogeochemical process on Earth. Rapid evolution (occurring over ecological time scales) can in principle shape these processes, yet we have little understanding of its importance in natural communities. Here, we quantified how the production of metal-detoxifying siderophores is driven by species compositional changes and evolution in a compost community in response to copper stress. We found that siderophore production converged at intermediate levels, with evolutionary and ecological changes occurring at similar rates. Understanding how ecological and evolutionary processes contribute to shaping trait distributions will improve our ability to predict ecosystem responses to global change, and aid in the engineering of microbial consortia.

evolutionary biology↗

bioRxiv2019

The C. elegans 3’UTRome V2: an updated genomic resource to study 3’UTR biology

3-Untranslated Regions (3-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3-UTRome, which we named 3-UTRome v2. This resource contains high-quality 3-UTR data mapped at single base ultra-resolution for 23,084 3-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3-UTRome v2 represents the most comprehensive and high-resolution 3-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3-UTR biology and miRNA targeting in a living organism.

genomics↗

bioRxiv2019

Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations

Transposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Here we show, using experimental evolution of Pseudomonas aeruginosa in iron-limited and iron-rich environments causing differential expression of siderophore cooperation, that transposable phages promoted divergence into extreme siderophore production phenotypes in iron-limited populations. Iron-limited populations with transposable phages evolved siderophore over-producing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations in pvd genes, encoding pyoverdine biosynthesis, and pqs genes, encoding quinolone signaling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.

evolutionary biology↗