Department of Biology, Université de Moncton, Moncton, Canada.
Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Canada.
BMC Genomics. 2018 Jun 19;19(1):474. doi: 10.1186/s12864-018-4852-1.
Phytophthora 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.
Both 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.
Our 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.
致病疫霉是引起晚疫病的主要病原体之一，晚疫病是一种最重要的马铃薯病害。本实验室分离的产吩嗪-1-羧酸（PCA）荧光假单胞菌菌株 LBUM223 对各种植物病原体具有生物防治潜力。为了研究 LBUM223 对致病疫霉转录组的影响，我们进行了一项体外时间进程研究。使用单独接种致病疫霉（对照）或接种 LBUM223、其 phzC 缺失突变体（不产 PCA）或外源添加 PCA 进行对峙试验。在 6、9 和 12 天进行破坏性采样，并使用 RNA-Seq 分析致病疫霉的转录组。通过 RT-qPCR 验证了一组差异表达基因的表达。
LBUM223 和外源添加的 PCA 均显著抑制了致病疫霉的生长。与对照处理相比，转录组分析表明，LBUM223 和外源添加的 PCA 处理显著改变的致病疫霉基因比例随着时间的推移而增加，分别从 50%增加到 61%和从 32%增加到 46%。当对所有三个收获时间的 3 倍变化或更多的绝对截止值进行应用时，发现 207 个基因由于 PCA 的作用而显著差异表达，这些 PCA 可以由 LBUM223 或外源添加产生。GO 分析表明，这两种处理都改变了与磷酸化机制、跨膜运输和氧化还原活性等主要功能相关的关键功能基因的表达。有趣的是，即使在体外系统中不存在植物宿主组织，PCA 也导致了编码效应子的几个基因的过表达。突变体仅略微抑制了致病疫霉的生长，几乎没有改变其转录组。
我们的研究表明，PCA 参与了致病疫霉的生长抑制，并通过随时间的推移上调和下调致病疫霉的基因表达，导致了重要的转录组变化。改变了不同的代谢功能，并发现许多效应子被上调，这表明它们在生物防治中的作用。
