Project description:InvF, an AraC-type transcriptional activator, regulated the expression of genes that encoded the secreted effector molecules SipABCD, SigD, SptP, and SopE in Salmonella typhimurium. However, it seems that almost all effector homologs were lost in P. fluorescens 2P24. To identify the InvF regulon in strain 2P24, the invF deficient mutant 2P24ΔinvF was constructed, and we implemented transcriptome sequencing (RNA-seq). Both of strains 2P24 and 2P24ΔinvF were incubated in mannitol-glutamate (MG) minimal medium at 28℃ for 6 h and 12 h. The cell fractions were separated by centrifugation at 10, 000 rpm for 5 min at 4°C. Total RNA was isolated using a E.Z.N.A.® Bacterial RNA Kit (Omega Bio‐tek, USA) as described by the manufacturer for RNA-seq. mRNA profiles of strains 2P24 and 2P24ΔinvF were generated by deep sequencing, in triplicate, using Illumina Hiseq. A total of 127 significantly differentially expressed genes (DEGs) were obtained by comparing the transcriptional level of strain 2P24ΔinvF with 2P24 at 6 h and 12 h [Fold change ≥ 1.5; p value ≤ 0.05]. Fifty-two down-regulated genes were regarded as InvF regulon candidates. Among the InvF regulon candidates, 39 genes were screened based on their gene functional annotation for qRT-PCR verification. Finally, eight genes were confirmed to be regulated positively by InvF. They encoded dihydrolipoyl dehydrogenase, toxin-activating lysine-acyltransferase, phage infection protein, AsnC family protein, two hypothetical proteins, NAD(P)H dehydrogenase, and protein IolH, respectively.
Project description:DNA microarray technology was used to survey changes in gene expression in P. fluorescens after mitomycin C (MMC) treatment. As expected, genes associated with the SOS response were upregulated. These include genes coding the recombination involved protein RecA, DNA repair protein RecN, excinuclease ABC subunit A UvrA, and the LexA repressor protein. The expression profile was similar to that which had been shown for E. coli after MMC treatment. Interestingly, expression of 33 bacteriophage-like genes was upregulated two hours after MMC treatment. Those genes are clustered in the chromosome. This result suggests that MMC may induce a prophage resident in the P. fluorescens genome. However, no phage particles were detected in a preparation of P. fluorescens strain DC454 that had been treated with MMC using transmission electron microscopy, and the same preparation failed to produce phage plaques on lawns of any of 10 different Pseudomonas strains tested, suggesting that the 33 bacteriophage-like gene cluster represents a defective prophage. Keywords: time course, stress response
Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.
Project description:Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon Mutants used in this study are further described in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679 A four chip study using total RNA recovered from two independent wild-type cultures of wild type strain Pseudomonas fluorescens Pf0-1 and two independent cultures of Pseudomonas fluorescens Pf0-1 delta pst mutant (deletion of the pstSCAB operon). Each chip measures the expression level of 5733 open reading frames (ORFs) genes from Pseudomonas fluorescens Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene, with three-fold technical redundancy.
