Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The effect of zinc limitation on transcriptome expression in Pseudomonas fluorescens Pf-5

ABSTRACT: Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing zinc-limited culture against zinc-amended culture in M9 minimal media Two-condition experiment, non-zinc treated culture versus zinc sulphate supplemented culture. 3 biological replicates including 3 technical replicates for one of the biological replicate and 2 technical replicates for another biological replicate. Swap-dye experiments were performed

ORGANISM(S): Pseudomonas fluorescens

SUBMITTER: Chee Kent Lim

PROVIDER: E-GEOD-32921 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Pf-5 is an important biocontrol strain of Pseudomonas fluorsecens, that improves plant growth, mainly via the production of secondary metabolites and growth/colonisation competition. Copper is a broad-spectrum antimicrobial that is effective against bacteria, fungi and even viruses in soluble forms such as copper sulfate and to a lesser extent in solid form, such as copper surfaces. Copper sulfate is commonly sprayed on food crops to increase yield and is becoming more routinely used due to the increasing problem of resistance to standard pesticides. Thus, an obvious question that remains is: what effect is this introduced copper having on these important biocontrol strains? First, the phenotypic effects of copper on carbon utilisation and pH tolerance was tested using Biolog. Interestingly, the ability of Pf-5 to utilise amino acids as a sole carbon source was largely unaltered, but the presence of copper completely eliminated the utilisation of carbohydrates or fatty acids, and diminished the use of carboxylic acids and amines. This could be explained by copper-mediated disruptions of enzymes in metabolic pathways, such as the TCA cycle. The effect on gene expression was examined using reverse transcriptomics, which established molecular bases for the phenotypic results, and confirmed some known mechanisms for copper resistance, efflux and transporter proteins, and highlighted the delicate interplay with cellular control of iron, as well as uncovered the interesting relationship between integrated bacteriophage and copper as a molecular switch. The integrated phage, Prophage 01, was downregulated in the presence of copper and when this phage was activated with Mitomycin C, the copper appeared to stop the phage from going into lytic cycle and protected lysis of the cells. Prophage 01 is integrated between the housekeeping genes mutS and cinA and is conserved throughout many Pseudomonas. However, only Pf-5, out of the 10 strains tested seemed to be protected from cell lysis by copper, indicating that Prophage 01 in Pf-5 has unique features that interact with Cu. Two-condition experiment, where normal culture in rich medium versus cell treated with CuSO4. 3 biological replicates including 3 technical replicates for one of the biological replicates and 2 technical replicates for another of biological replicates. Swap-dye experiments were performed.

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The effect of zinc limitation on transcriptome expression in Pseudomonas fluorescens Pf-5

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