Biology subjects

Hockett, K. L.

Publications and source records attributed to Hockett, K. L..

8 recordsLinked to original sources

bioRxiv2024

Genomic evidence for widespread reciprocal recognition and killing among Pseudomonas syringae strains

Community assembly dynamics are in part driven by competition between community members. Diverse bacteria antagonize competitors through the production of toxic compounds, such as bacteriophage-derived tailocins. These toxins are highly specific in their targeting, which is determined by interactions between the tailocins tail fiber and competitors lipopolysaccharide O-antigen moieties. Tailocins play a pivotal role in mediating microbial interactions among the economically significant plant pathogens within the Pseudomonas syringae species complex, with the potential to alter community structure and disease progression in host plants. Previous work looking at 45 P. syringae strains has demonstrated that at least two phylogenetic clades of tail fibers are encoded in the conserved tailocin region across the species complex, which roughly corresponds to two clusters of targeting activity. To better understand the full diversity of tail fibers associated with tailocins in the species complex, we screened 2,161 publicly available genomes for their tailocin tail fiber content, predicted protein structures that represent the diversity of fibers, and investigated forces possibly driving the distribution of fibers throughout the species complex. Here we present evidence that while the two previously described tail fiber clades are indeed widespread among virulent P. syringae strains, their distribution is largely uncorrelated with phylogeny. Instead, we found that the presence of one tail fiber or the other is strongly correlated with the allelic diversity of another gene, associated with lipopolysaccharide O-antigen structure, dTDP-4-dehydrorhamnose reductase. Our findings suggest the presence of two reciprocally targeting groups of strains distributed throughout the P. syringae species complex that transcend phylogenetic relationships.

genomics↗

bioRxiv2022

SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization

The Pseudomonas syringae species complex (PSSC) is a diverse group of plant pathogens with a collective host range encompassing almost every food crop grown throughout the world. As a threat to global food security, rapid detection and characterization of epidemic and emerging pathogenic lineages is essential. However, phylogenetic identification and prediction of virulence is often complicated by an unclarified taxonomy and the diversity of virulence factor repertoires carried by PSSC isolates. To address these issues, we have built SYRINGAE (www.syringae.org), a web-based phylogenetic placement and functional inference pipeline for PSSC. SYRINGAE contains a comprehensive phylogeny of 2,161 quality-checked genome assemblies annotated with 120 virulence genes. From this dataset, naive Baye classification models trained from life identification numbers (LINs) and common marker gene sequences can be used for accurate identification of isolates. SYRINGAE efficiently articulates taxonomical and functional data generated over the last several decades on PSSC and constitutes a unique tool tailored towards the rapid characterization of PSSC emerging strains of concern.

microbiology↗

bioRxiv2022

Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex

The Pseudomonas syringae species complex is comprised of several closely related species of bacterial plant pathogens. Here, we use in-silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluate their in-silico amplification rate in 2,161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity (ANI), and we train naive Bayes classification models to quantify classification resolution. Further, we show the potential for using single amplicon sequence data to predict an important determinant of host specificity and range, type III effector protein repertoires.

microbiology↗

bioRxiv2021

Transcriptional profiles of a foliar fungal endophyte (Pestalotiopsis, Ascomycota) and its endohyphal bacterium (Luteibacter, Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation

Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. We developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in co-culture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in co-culture was greater than in axenic culture, but the opposite was true for the Pestalotiopsis sp. Dual RNA-seq data demonstrate that growing in co-culture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. TWEETWhen in co-culture, Luteibacter downregulates motility and upregulates a T6SS. Gene expression changes in its host, Pestalotiopsis, suggest the bacterium impacts fungal cell structure and methionine availability. IMPORTANCEInteractions between microbes and their hosts have important outcomes for host- and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together vs. separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.

microbiology↗

bioRxiv2020

Prophylactic Application of Tailocins Prevents Infection by Pseudomonas syringae

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our group has recently categorized and characterized tailocins produced by and tailocin sensitivities of the phytopathogen Pseudomonas syringae, and here we extend these experiments to test whether prophylactic tailocin application can prevent infection of Nicotiana benthamiana by P. syringae pv. syringae B728a. Specifically, we demonstrate that multiple strains can produce tailocins that prevent infection by strain B728a and engineer a deletion mutant to prove that tailocin targeting is responsible for this protective effect. Lastly, we provide evidence that heritable resistance mutations do not explain the minority of cases where tailocins fail to prevent infection. Our results extend previous reports of prophylactic use of tailocins against phytopathogens, and establish a model system with which to test and optimize tailocin application for prophylactic treatment to prevent phytopathogen infection.

microbiology↗

bioRxiv2019

Evidence of Tailocin Persistence and Resistance in Pseudomonas

Phage tail-like bacteriocins (tailocins) are bacterially-produced protein toxins that can mediate competitive interactions between co-colonizing bacteria. Both theoretical and empirical research has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive, sensitive outcompete resistant, and resistant outcompete producers. These so-called rock-paper-scissor dynamics explain how all three populations can be maintained in the same environment, without one genotype driving the others extinct. Using Pseudomonas syringae as a model system, we demonstrate that otherwise sensitive bacterial cells have the ability to survive bacteriocin exposure through a physiological mechanism. This mechanism is similar to the persister phenotype that allows cells to survive antibiotic exposure, without acquiring antibiotic resistance. We show that a significant fraction of the target cells that survive a lethal dose of tailocin did not exhibit any detectable increase in survival in subsequent exposure (i.e. they survived through a persistence-like mechanism). Tailocin persister cells were more prevelant in stationary rather than log phase cultures. Of the fraction of cells that gained detectable tailocin resistance, there was a range of resistance from complete (insensitive) to incomplete (partially sensitive). By genomic sequencing and genetic engineering we showed that a mutation in a hypothetical gene containing 8-10 transmembrane domains causes tailocin high-persistence and genes of various glycosyl transferases cause incomplete and complete tailocin resistance. Importantly, of the several classes of mutations, only those causing complete tailocin resistance compromised host fitness. This result, combined with previous research, indicates that bacteria likely utilize persistence as a means to survive bacteriocin-mediated killing without suffering the costs associated with resistance. This research provides important insight into how bacteria can escape the trap of fitness trade-offs associated with gaining de novo tailocin resistance, and expands our understanding of how sensistive bacterial populations can persist in the presence of lethal competitors.

microbiology↗

bioRxiv2018

FleN contributes to heterogeneous swimming at high temperatures in Pseudomonas syringae

Motility is generally conserved among many animal and plant pathogens. Environmental conditions, however, significantly impact expression of the motile phenotype. In this study, we describe a novel heterogeneous motility phenotype in Pseudomonas syringae, where under normally suppressive incubation conditions (30{degrees}C) punctate colonies arise that are spatially isolated from the point of inoculation, giving rise to a motility pattern we term constellation swimming (CS). We demonstrate that this phenotype is reproducible, reversible, and dependent on a functioning flagellum. Mirroring the heterogeneous motility phenotype, we demonstrate the existence of a sub-population of cells under non-permissive conditions that express flagellin (fliC) at levels similar to cells incubated under permissive conditions using both quantitative single cell microscopy and flow cytometry. To understand the genetics underlying the CS phenotype, we selected for naturally arising mutants that exhibited a normal swimming phenotype at the warmer incubation temperature. Sequencing these mutants recovered several independent non-synonymous mutations within FleN (also known as FlhG) as well as mutations within the promoter region of FleQ, the master flagellum regulator in Pseudomonas. We further show that nutrient depletion is the likely underlying cause of CS, as reduced nutrients will stimulate both fliC expression and a normal swimming phenotype at 30 {degrees}C.

microbiology↗

bioRxiv2017

Conditionally Redundant Bacteriocin Targeting by Pseudomonas syringae

The widespread use of antimicrobials under clinical and agricultural settings has resulted in the evolution of resistance to these compounds. To combat the emergence of resistance, current research efforts are focusing on designing treatments to exploit combinations of antimicrobials, where the evolution of resistance confers sensitivity to alternative compounds. In this work we demonstrate that strains of Pseudomonas syringae possess a natural analogue to this strategy. Specifically, we demonstrate that a single strain produces multiple bacteriocins that can target another strain, but antimicrobial activity of the second bacteriocin is manifest only after resistance to the first emerges. The evolution of resistance also sensitizes the target strain to bacteriocins from a variety of other strains. Strains of P. syringae therefore encode multiple bacteriocins that can act in a conditionally redundant manner. It is possible that combinations of bacteriocins could be applied as a cocktail or sequentially, to potentially achieve durable pathogen control.

microbiology↗