Biology subjects

Jackson, R.

Publications and source records attributed to Jackson, R..

At least 19 recordsLinked to original sources

bioRxiv2025

Developmental Progression and Single-Cell Heterogeneity of Orientia tsutsugamushi during Intracellular Infection

Orientia tsutsugamushi, the causative agent of human scrub typhus disease, is an obligate intracellular bacterium transmitted by mites. It replicates exclusively within eukaryotic cells, inhabiting a range of host cell types in mammals and mites. Previously, we demonstrated that its extracellular, non-replicative form is developmentally distinct from the intracellular replicative form. In this study, we investigated spatial and temporal heterogeneity within the intracellular bacterial population. By quantifying bacterial DNA replication, protein synthesis, cell division, and subcellular localization, we defined four distinct intracellular growth stages: pre-active, lag, log, and maturation. Using microscopy-based single-cell analysis of selected transcripts and proteins, we further revealed transcriptional and translational heterogeneity within microcolonies. These findings highlight the complex, asynchronous nature of intracellular O. tsutsugamushi growth and underscore the importance of single-cell analysis in understanding its pathobiology. ImportanceScrub typhus is a serious, sometimes life-threatening disease caused by the bacterium Orientia tsutsugamushi, which is spread by the bites of tiny mites and is common in many rural parts of Asia. This bacterium can only survive and grow inside living cells, where hundreds of individual bacteria may infect a single host cell. Until now, it was unclear whether all the bacteria inside a cell behaved the same way or if they existed in different stages of growth. In this study, we show that O. tsutsugamushi goes through several distinct stages while growing inside host cells and that not all bacteria are at the same stage at the same time. Even within a single infected cell, some bacteria are actively dividing, while others are preparing to leave the cell. Understanding these stages provides a new framework for exploring how the bacterium develops, spreads, and causes disease -- insights that could help guide future research and improve ways to control or treat scrub typhus.

microbiology↗

bioRxiv2025

Assessing the Potential of Switchgrass (Panicum virgatum L.) for Storing Carbon Belowground: Insights from a Multi-Site US Study

Agricultural intensification depletes belowground carbon (C) stocks, partly due to the exclusion of deep-rooted perennial species from landscapes where they were once dominant. Reintroducing deep-rooted perennials to cultivated land may help to mitigate SOC loss and restore ecosystem function. We quantified the effect of replacing shallow-rooted annual crops with a deep-rooted perennial grass, switchgrass (Panicum virgatum L.), by comparing 10 to 30 year-old switchgrass stands with paired annual row crop fields across the central and eastern USA. We hypothesized that switchgrass would store more root C and SOC than neighboring shallow-rooted annual crops, and that these effects would extend deeper than 30 cm. We also evaluated whether switchgrass stimulates decomposition of SOC at depth using radiocarbon (14C) to quantify replacement of slow cycling isotopically depleted SOC. Finally, we explored whether the effect of switchgrass on SOC is moderated by soil chemical and physical properties. While the effect of switchgrass on SOC in the surface 100 cm was positive at most sites, the average effect was highly uncertain and statistically indistinguishable from zero (mean difference in SOC = 0.6 kg C m-2 [95% CI -0.8 to +1.9 kg C m-2]). By contrast, we found that root biomass C was consistently more deeply distributed and more abundant under switchgrass, yielding an estimated additional 0.6 kg C m-2 in the surface 100 cm of soil under switchgrass [95% CI +0.5 to +0.7 kg C m-2]. 14C measurements suggested that root C inputs were adding to existing SOC without stimulating decomposition. The effect of switchgrass on belowground C was not strongly related to any of the environmental factors that we evaluated. Our observations show that root biomass C can contribute substantially to belowground C stocks when deep-rooted perennial grasses replace shallow-rooted annual crops.

ecology↗

bioRxiv2025

The maternal inflammatory proteome during pregnancy and its role in predicting the risk of spontaneous preterm birth

BackgroundSpontaneous preterm birth (sPTB) is a significant adverse outcome of pregnancy. Being able to identify and improve the management of those who may be at risk requires robust screening methods. The use of circulating molecular markers provides a promising and non-invasive solution to this problem to allow necessary and successful intervention. The role of inflammation has been continuously demonstrated to play a key role in the onset of sPTB with intrauterine inflammation being a key driver. Here we sought out to explore the inflammatory proteome using a nested case-control approach using samples from pregnant participants in the INSIGHT cohort. ObjectivesTo explore the maternal blood proteome in the second trimester using the Olink Explore panel to identify inflammatory proteins associated with sPTB and assess their predictive value, both independently and in combination with cell-free RNA (cfRNA). Study DesignWe conducted a nested case-control study to investigate inflammatory protein profiles during the second trimester of pregnancy. A total of 138 maternal blood plasma samples were analysed using a targeted proteomic assay quantifying 384 inflammation-related proteins. Differential expression analysis and a LASSO-logistic regression model with Leave-One-Out Cross-Validation (LOOCV) were applied to evaluate the association between inflammatory biomarkers and spontaneous preterm birth (sPTB) outcomes. ResultsUsing predictive modelling of the maternal blood proteome, 16 inflammation-related proteins were identified as key discriminators of sPTB risk, with proteins such as PGF, COL9A1, CST7, CXCL6 and GALNT3 emerging as major contributors for predicting sPTB risk. Using inflammation-related maternal proteins alone to predict sPTB (<35 weeks) achieved an area under the receiver operating characteristic curve (AUC-ROC) of 0.76 (95% CI: 0.66-0.84). The incorporation of both cfRNA and proteomic data into an integrated model, improved the area under the curve to 0.85 (95% CI: 0.78-0.92). The integrated model highlighted inflammatory biomarkers that are not only implicated in preterm birth but also in essential physiological mechanisms such as placental function, tissue remodelling, and extracellular matrix composition, which are critical to maintaining pregnancy and preventing premature labour. ConclusionsThese findings demonstrate that an integrated approach using both cfRNA and proteomic signatures of the second trimester maternal blood plasma yields a more comprehensive biomarker profile for predicting preterm birth risk. This multimodal strategy not only enhances the predictive accuracy but also captures a broader array of biological signals across multiple organ systems. Compared to relying solely on inflammatory proteome markers, this multiomic method offers a deeper molecular characterisation of preterm birth risk in the maternal blood plasma.

systems biology↗

bioRxiv2025

Venom vesicles from the parasitoid Ganaspis hookeri facilitate venom protein entry into host immune cells

The parasitoid wasp Ganaspis hookeri infects Drosophila melanogaster larvae, laying an egg and injecting venom directly into the host body cavity. While infected hosts mount an immune response in an attempt to eliminate the parasitoid egg, parasitoid venom proteins act to inhibit these host immune responses and manipulate host physiology to ensure infection success. A key immune suppressive venom protein in G. hookeri is a venom- specific isoform of the SERCA (Sarco/endoplasmic reticulum Ca2+-ATPase) calcium pump. However, SERCA is a large hydrophobic protein, and the mechanism by which it and other venom proteins are transported into the host is not well understood. We used a variety of biophysical, biochemical, and cell biological approaches to assess the properties of G. hookeri venom. Electronic microscopy and nanoparticle tracking analysis revealed the presence of venom vesicles as a putative transport mechanism. We used tunable resistive pulse sensing (TRPS) to biophysically characterize these vesicles, and our TRPS data suggest G. hookeri venom is composed of multiple vesicle types that are distinguishable by size, zeta potential, and density. Finally, we fluorescently labeled venom vesicles to test for entry into host immune cells. We observed that these vesicles interact with immune cells membranes and are internalized into the cell. Our data support a model in which G. hookeri venom proteins, including SERCA, are packaged into an array of venom vesicles, and transported into host cells for immune suppression.

biochemistry↗

bioRxiv2024

Imaging of live bacterial whole-cell biosensors illuminates spatial sialic acid availability within the inflamed mammalian gut

Host mucin-derived sialic acids are key drivers of microbial colonisation, growth and pathogenicity within the mammalian gut. However, their study is hindered by complex spatiotemporal dynamics: Many gut metabolites, including sialic acids, are rapidly consumed, transformed or absorbed by the microbiota or host, meaning that conventional measurements of faeces or bulk digesta often fail to capture their true local availability. In contrast, engineered bacterial-whole cell biosensors provide an in situ read-out of metabolite exposure at the point and time of use, before these molecules are depleted. Here, we demonstrate increases in the bioavailability of sialic acid in the inflamed mouse gut using an engineered Escherichia coli biosensor that reports on sialic acid exposure via NanR-regulated transcriptional circuit. The biosensor robustly colonises the mouse gut and remains functional for at least six weeks. Through organ-scale imaging at single bacterial resolution we observe strong correlations between disease status and biosensor response in two inflammation models. Profiling along the length of the gut uncovers regional variations between the maximal sialic acid sensing and the peak inflammatory response within host tissues in a murine colitis model. Simultaneous tracking of host and microbial markers of inflammation informs the therapeutic response to sialidase inhibition, which accelerates disease recovery. Together, these data illuminate the complex spatial dynamics involved in shared host-microbiome metabolism and demonstrate the broader power of using engineered bacterial biosensors to monitor in situ bioavailability of rapidly turned-over metabolites within the gut.

synthetic biology↗

bioRxiv2024

PRMT1 Modulates Alternative Splicing to Enhance HPV18 mRNA Stability and Promote the Establishment of Infection

Only persistent HPV infections lead to the development of cancer. Thus, understanding the virus-host interplay that influences the establishment of viral infection has important implications for HPV biology and human cancers. The ability of papillomaviruses to establish in cells requires the strict temporal regulation of viral gene expression in sync with cellular differentiation. This control primarily happens at the level of RNA splicing and polyadenylation. However, the details of how this spatio-temporal regulation is achieved still need to be fully understood. Until recently, it has been challenging to study the early events of the HPV lifecycle following infection. We used a single-cell genomics approach to identify cellular factors involved in viral infection and establishment. We identify protein arginine N-methyltransferase 1 (PRMT1) as an important factor in viral infection of primary human cervical cells. PRMT1 is the main cellular enzyme responsible for asymmetric dimethylation of cellular proteins. PRMT1 is an enzyme responsible for catalyzing the methylation of arginine residues on various proteins, which influences processes such as RNA processing, transcriptional regulation, and signal transduction. In this study, we show that HPV18 infection leads to increased PRMT1 levels across the viral lifecycle. PRMT1 is critical for the establishment of a persistent infection in primary cells. Mechanistically, PRMT1 inhibition leads to a highly dysregulated viral splicing pattern. Specifically, reduced PRMT1 activity leads to intron retention and a change in the E6 and E7 expression ratio. In the absence of PRMT1, viral transcripts are destabilized and subject to degradation via the nonsense-mediated decay (NMD) pathway. These findings highlight PRMT1 as a critical regulator of the HPV18 lifecycle, particularly in RNA processing, and position it as a potential therapeutic target for persistent HPV18 infections.

microbiology↗

bioRxiv2024

The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis

Our knowledge about the meningeal immune system has recently burgeoned, particularly our understanding of how innate and adaptive effector cells are mobilized to meet brain challenges. However, information on how meningeal immunocytes guard brain homeostasis in healthy individuals remains sparse. This study highlights the heterogeneous and polyfunctional regulatory-T (Treg) cell compartment in the meninges. A Treg subtype specialized in controlling Th1-cell responses and another known to control responses in B-cell follicles were substantial components of this compartment, foretelling that punctual Treg-cell ablation rapidly unleashed interferon-gamma production by meningeal lymphocytes, unlocked their access to the brain parenchyma, and altered meningeal B-cell profiles. Distally, the hippocampus assumed a reactive state, with morphological and transcriptional changes in multiple glial-cell types; within the dentate gyrus, neural stem cells showed exacerbated death and desisted from further differentiation, associated with inhibition of spatial-reference memory. Thus, meningeal Treg cells are a multifaceted bulwark to brain homeostasis at steady-state. One sentence summaryA distinct population of regulatory T cells in the murine meninges safeguards homeostasis by keeping local interferon-{gamma}-producing lymphocytes in check, thereby preventing their invasion of the parenchyma, activation of hippocampal glial cells, death of neural stem cells, and memory decay.

immunology↗

bioRxiv2024

Excitatory and inhibitory synapses form a tight subcellular balance along dendrites that decorrelates over development

A balance between excitation and inhibition is crucial for neurotypical brain function. Indeed, disruptions in this relationship are frequently associated with the pathophysiology of neurodevelopmental disorders. Nevertheless, how this balance is established during the dynamic period of neurodevelopment remains unexplored. Using multiple techniques, including in utero electroporation, electron microscopy and electrophysiology, we reveal a tight correlation in the distribution of excitatory and inhibitory synapses along dendrites of developing CA1 hippocampal neurons. This balance was present within short dendritic stretches (<20{micro}m), and surprisingly, was most pronounced during early development, sharply declining with maturity. The tight matching between excitation and inhibition was unexpected, as inhibitory synapses lacked an active zone when formed and exhibited compromised evoked release. We propose that inhibitory synapses form as a stabilising scaffold, to counterbalance growing excitation levels. This relationship diminishes over time, suggesting a critical role for a subcellular balance in early neuronal function and circuit formation.

neuroscience↗

bioRxiv2023

Point mutations in Arf1 reveal cooperative effects of the N-terminal region and myristate for GTPase-activating protein catalytic activity

The ADP-ribosylation factors (Arfs) constitute a family of small GTPases within the Ras superfamily, with a distinguishing structural feature of a hypervariable N-terminal extension of the G domain modified with myristate. Arf proteins, including Arf1, have roles in membrane trafficking and cytoskeletal dynamics. While screening for Arf1:small molecule co-crystals, we serendipitously solved the crystal structure of the non-myristoylated engineered mutation [L8K]Arf1 in complex with a GDP analogue. Like wild-type (WT) non-myristoylated Arf1*GDP, we observed that [L8K]Arf1 exhibited an N-terminal helix that occludes the hydrophobic cavity that is occupied by the myristoyl group in the GDP-bound state of the native protein. However, the helices were offset from one another due to the L8K mutation, with a significant change in position of the hinge region connecting the N-terminus to the G domain. Hypothesizing that the observed effects on behavior of the N-terminus affects interaction with regulatory proteins, we mutated two hydrophobic residues to examine the role of the N-terminal extension for interaction with guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs). Different than previous studies, all mutations were examined in the context of myristoylated Arf. Mutations had little or no effect on spontaneous or GEF-catalyzed guanine nucleotide exchange but did affect interaction with GAPs. [F13A]myrArf1 was less than 1/2500, 1/1500, and 1/200 efficient as substrate for the GAPs ASAP1, ARAP1 and AGAP1; however, [L8A/F13A]myrArf1 was similar to WT myrArf1. We hypothesized that the myristate moiety associates with the N-terminal extension to alter its structure, thereby affecting its function. Using molecular dynamics simulations, the effect of the mutations on forming alpha helices was examined, yet no differences were detected. The results indicate that lipid modifications of GTPases and consequent anchoring to a membrane influences protein function beyond simple membrane localization. Hypothetical mechanisms are discussed.

biochemistry↗

bioRxiv2023

Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae

1.The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealands only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand we aimed to characterise the viromes of New Zealands bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environmental-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what is possibly the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealands only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.

microbiology↗

bioRxiv2023

Peripheral serotonergic neurons regulate anxiety-like behavior and intestinal barrier immunity

Serotonergic circuits in the central nervous system play important roles in regulating mood and behavior, yet the functions of peripheral serotonergic neurons are less understood. Here, we engineered mice lacking the serotonin-producing enzyme Tph2 in peripheral neurons but with intact Tph2 in central neurons. In contrast to mice lacking Tph2 in all neurons, mice lacking Tph2 in peripheral serotonergic neurons did not exhibit increased territorial aggression. However, similar to the total body Tph2 KO mice, the conditional KO animals, exhibited reduced gut motility and decreased anxiety-like behavior. These observations reveal that peripheral serotonergic neurons contribute to control of intestinal motility and anxiety-like behavior and suggest that therapeutics targeting this subset of peripheral neurons could be beneficial.

immunology↗

bioRxiv2023

Graded functional changes in ATL reflect both semantic content and process.

Recent work has focussed on how patterns of functional change within the temporal lobe relate to whole-brain dimensions of intrinsic connectivity variation (Margulies et al., 2016). We examined two such connectivity gradients reflecting the separation of (i) unimodal versus heteromodal and (ii) visual versus auditory-motor cortex, examining visually presented verbal associative and feature judgments, plus picture-based context and emotion generation. Functional responses along the first dimension sometimes showed graded change between modality-tuned and heteromodal cortex (in the verbal matching task), and other times showed sharp functional transitions, with deactivation at the extremes and activation in the middle of this gradient (internal generation). The second gradient revealed more visual than auditory-motor activation, regardless of content (associative, feature, context, emotion) or task process (matching/generation). We also uncovered subtle differences across each gradient for content type, which predominantly manifested as differences in relative magnitude of activation or deactivation.

neuroscience↗

bioRxiv2023

Targeted proteomic quantitation of NRF2 signaling and predictive biomarkers in HNSCC

The NFE2L2/NRF2 oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry (MS)-based targeted proteomics assay based on internal standard triggered parallel reaction monitoring (IS-PRM) to quantify 69 NRF2 pathway components and targets as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved the existing IS-PRM acquisition algorithm, called SureQuant, to increase throughput, sensitivity, and precision. Testing the optimized platform on 27 lung and upper aerodigestive cancer cell models revealed 35 NRF2 responsive proteins. In formalin-fixed paraffin-embedded (FFPE) HNSCCs, NRF2 signaling intensity positively correlated with NRF2 activating mutations and with SOX2 protein expression. PD-L2/CD273 and protein markers of T-cell infiltration correlated positively with one another and with human papilloma virus (HPV) infection status. p16/CDKN2A protein expression positively correlated with the HPV oncogenic E7 protein, and confirmed the presence of translationally active virus. This work establishes a clinically actionable HNSCC protein biomarker assay capable of quantifying over 600 peptides from frozen or FFPE archived tissues in under 90 minutes.

cancer biology↗

bioRxiv2023

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e., cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data (https://viz.datascience.arizona.edu/3DEpiEx/).

cell biology↗

bioRxiv2023

Evidence of phylosymbiosis in Formica ants

Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes. To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing. We reveal that Formica species and clades harbour highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e. phylosymbiosis, in that related hosts harbour more similar microbial communities. Our analysis also revealed significant correlations between microbe co-occurrences, which suggests that synergistic and antagonistic interactions may contribute to the phylosymbiotic signal. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localisation within the host.

evolutionary biology↗

bioRxiv2023

Identifying nonlinear Functional Connectivity with EEG/MEG using Nonlinear Time-Lagged Multidimensional Pattern Connectivity (nTL-MDPC)

Investigating task- and stimulus-dependent connectivity is key to understanding how brain regions interact to perform complex cognitive processes. Most existing connectivity analysis methods reduce activity within brain regions to unidimensional measures, resulting in a loss of information. While recent studies have introduced new functional connectivity methods that exploit multidimensional information, i.e., pattern-to-pattern relationships across regions, they have so far mostly been applied to fMRI data and therefore lack temporal information. We recently developed Time-Lagged Multidimensional Pattern Connectivity for EEG/MEG data, which detects linear dependencies between patterns for pairs of brain regions and latencies in event-related experimental designs (Rahimi et al., 2022b). Due to the linearity of this method, it may miss important nonlinear relationships between activity patterns. Thus, we here introduce nonlinear Time-Lagged Multidimensional Pattern Connectivity (nTL-MDPC) as a novel bivariate functional connectivity metric for event-related EEG/MEG applications. nTL-MDPC describes how well patterns in ROI X at time point tx can predict patterns of ROI Y at time point ty using artificial neural networks (ANNs). We evaluated this method on simulated data as well as on an existing EEG/MEG dataset of semantic word processing, and compared it to its linear counterpart (TL-MDPC). We found that nTL-MDPC indeed detected nonlinear relationships more reliably than TL-MDPC in simulations with moderate to high numbers of trials. However, in real brain data the differences were subtle, with identification of some connections over greater time lags but no change in the connections identified. The simulations and EEG/MEG results demonstrate that differences between the two methods are not dramatic, i.e. the linear method can approximate linear and nonlinear dependencies well. HighlightsO_LInTL-MDPC is a bivariate functional connectivity method for event-related EEG/MEG C_LIO_LInTL-MDPC detects linear and nonlinear connectivity at zero and non-zero lags C_LIO_LInTL-MDPC revealed connectivity between ATL hub and semantic control regions C_LIO_LIDifferences between linear and nonlinear TL-MDPC were small C_LI

neuroscience↗

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↗