Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

Abstract

BackgroundPhytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory shows biocontrol potential against various plant pathogens. To characterize the effect of LBUM223 on the transcriptome of P. infestans, we conducted an in vitro time-course study. Confrontational assay was performed using P. infestans inoculated alone (control) or with LBUM223, its phzC- isogenic mutant (not producing PCA), or exogenically applied PCA. Destructive sampling was performed at 6, 9 and 12 days and the transcriptome of P. infestans was analysed using RNA-Seq. The expression of a subset of differentially expressed genes was validated by RT-qPCR.ResultsBoth LBUM223 and exogenically applied PCA significantly repressed P. infestans’ growth at all times. Compared to the control treatment, transcriptomic analyses showed that the percentages of all P. infestans’ genes significantly altered by LBUM223 and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%, respectively. When applying an absolute cut-off value of 3 fold change or more for all three harvesting times, 207 genes were found significantly differentially expressed by PCA, either produced by LBUM223 or exogenically applied. Gene ontology analysis revealed that both treatments altered the expression of key functional genes involved in major functions like phosphorylation mechanisms, transmembrane transport and oxidoreduction activities. Interestingly, even though no host plant tissue was present in the in vitro system, PCA also led to the overexpression of several genes encoding effectors. The mutant only slightly repressed P. infestans’ growth and barely altered its transcriptome.ConclusionsOur study suggests that PCA is involved in P. infestans’ growth repression and led to important transcriptomic changes by both up- and down-regulating gene expression in P. infestans over time. Different metabolic functions were altered and many effectors were found to be upregulated, suggesting their implication in biocontrol.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4852-1) contains supplementary material, which is available to authorized users.

Transcriptomic, Biochemical, and Morphological Study Reveals the Mechanism of Inhibition of Pseudopestalotiopsis camelliae-sinensis by Phenazine-1-Carboxylic Acid

“…Transcriptome indicated that DEGs were significantly enriched in oxidoreductase activity (acting on paired donors, with incorporation or reduction of molecular oxygen) at the MF level. The transcriptome of Phytophthora infestans treated with PCA had also indicated that DEGs related with oxidoreduction activity were significantly enriched ( Roquigny et al, 2018 ). For instance, the gene of eburicol 14 alpha-demethylase was significantly down-regulated by PCA ( Supplementary Tables 8 , 12 ).…”

The Differential Growth Inhibition of Phytophthora spp. Caused by the Rare Sugar Tagatose Is Associated With Species-Specific Metabolic and Transcriptional Changes

“…The decrease of amino acid content was associated also with the downregulation of amino acid transporters in tagatose-incubated P. infestans . Similarly, the downregulation of amino acid transporter genes was previously linked to P. infestans growth inhibition caused by Pseudomonas fluorescens LBUM223 ( Roquigny et al, 2018 ), indicating strong correlations between sugar metabolism, amino acid metabolism, amino acid transport and P. infestans growth.…”

Biocontrol and Action Mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in Soybean Phytophthora Blight

“…have been found to be effective against numerous plants pathogenic organisms, including bacteria, fungi, and oomycetes, such as the causal agent of the bacterial blight of rice, and the oomycetes P. infestans [45,46]. Ye et al [46] used transcriptomics to exploit the alteration in P. infestans in response to phenazine-1-carboxylic acid production by P. fluorescens , and the transcriptome analysis provided a better understanding of the molecular mechanisms, which might in turn contribute to developing and optimizing a biocontrol strategy against the late blight of potato. Transcriptomic analyses implied that the percentages of all P. infestans ’ genes significantly changed due to P. fluorescens, and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%.…”