Browsing by Author "Rainey PB"

Now showing 1 - 7 of 7
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    Bistability in a metabolic network underpins the De Novo evolution of colony switching in Pseudomonas fluorescens
    (PUBLIC LIBRARY SCIENCE, 12/03/2015) Gallie J; Libby E; Bertels F; Remigi P; Jendresen CB; Ferguson GC; Desprat N; Buffing MF; Sauer U; Beaumont HJE; Martinussen J; Kilstrup M; Rainey PB
    © 2015 Gallie et al. Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution.
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    Characterising the drinking water microbiome on campgrounds in New Zealand
    (23/10/2012) Phiri BJ; Biggs PJ; Prattley DJ; Stevenson MA; Rainey PB; French NP
    Whole-genome, 16S and 18S ribosomal RNA (rRNA) analyses combined with conventional isolation techniques are being applied to profile microbial community DNA associated with drinking water on campgrounds. The current study has a serial cross-sectional design and is being conducted on 15 campgrounds that are situated across New Zealand (Figure 1) and are managed by the Department of Conservation (DOC). Preliminary results generally show low Escherichia coli counts in water, suggesting minimal faecal contamination, and a low proportion of faecal samples were positive for Campylobacter and Giardia.
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    Exploring the sociobiology of pyoverdin-producing Pseudomonas.
    (WILEY-BLACKWELL, 2013-11) Zhang X-X; Rainey PB
    The idea that bacteria are social is a popular concept with implications for understanding the ecology and evolution of microbes. The view arises predominately from reasoning regarding extracellular products, which, it has been argued, can be considered "public goods." Among the best studied is pyoverdin-a diffusible iron-chelating agent produced by bacteria of the genus Pseudomonas. Here we report the de novo evolution of pyoverdin nonproducing mutants, genetically characterize these types and then test the appropriateness of the sociobiology framework by performing growth and fitness assays in the same environment in which the nonproducing mutants evolved. Our data draw attention to discordance in the fit between social evolution theory and biological reality. We show that pyoverdin-defective genotypes can gain advantage by avoiding the cost of production under conditions where the molecule is not required; in some environments pyoverdin is personalized. By exploring the fitness consequences of nonproducing types under a range of conditions, we show complex genotype-by-environment interactions with outcomes that range from social to asocial. Together these findings give reason to question the generality of the conclusion that pyoverdin is a social trait.
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    Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    (BIOMED CENTRAL LTD, 2009) Silby MW; Cerdeno-Tarraga AM; Vernikos GS; Giddens SR; Jackson RW; Preston GM; Zhang XX; Moon CD; Gehrig SM; Godfrey SAC; Knight CG; Malone JG; Robinson Z; Spiers AJ; Harris S; Challis GL; Yaxley AM; Harris D; Seeger K; Murphy L; Rutter S; Squares R; Quail MA; Saunders E; Mavromatis K; Brettin TS; Bentley SD; Hothersall J; Stephens E; Thomas CM; Parkhill J; Levy SB; Rainey PB; Thomson NR
    BACKGROUND: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
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    In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella
    (Oxford University Press on behalf of Genetics Society of America, 2021-01) Paulson AR; O'Callaghan M; Zhang X-X; Rainey PB; Hurst MRH; Oliver B
    The function of microbes can be inferred from knowledge of genes specifically expressed in natural environments. Here, we report the in vivo transcriptome of the entomopathogenic bacterium Yersinia entomophaga MH96, captured during initial, septicemic, and pre-cadaveric stages of intrahemocoelic infection in Galleria mellonella. A total of 1285 genes were significantly upregulated by MH96 during infection; 829 genes responded to in vivo conditions during at least one stage of infection, 289 responded during two stages of infection, and 167 transcripts responded throughout all three stages of infection compared to in vitro conditions at equivalent cell densities. Genes upregulated during the earliest infection stage included components of the insecticidal toxin complex Yen-TC (chi1, chi2, and yenC1), genes for rearrangement hotspot element containing protein yenC3, cytolethal distending toxin cdtAB, and vegetative insecticidal toxin vip2. Genes more highly expressed throughout the infection cycle included the putative heat-stable enterotoxin yenT and three adhesins (usher-chaperone fimbria, filamentous hemagglutinin, and an AidA-like secreted adhesin). Clustering and functional enrichment of gene expression data also revealed expression of genes encoding type III and VI secretion system-associated effectors. Together these data provide insight into the pathobiology of MH96 and serve as an important resource supporting efforts to identify novel insecticidal agents.
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    Origin and evolution of the kiwifruit canker pandemic
    (Oxford University Press, 1/04/2017) McCann HC; Li L; Liu Y; Li D; Pan H; Zhong C; Rikkerink EHA; Templeton MD; Straub C; Colombi E; Rainey PB; Huang H
    Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of eighty sequenced Psa genomes we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbour strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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    Water quality, metagenomics and the microbial community in DOC campground water
    Phiri BJ; French NP; Rainey PB; Stevenson MA; Prattley DJ; Biggs PJ