Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland.
BMC Genomics. 2017 Nov 13;18(1):868. doi: 10.1186/s12864-017-4251-z.
Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. amylovora 650 strain during infection of shoots of susceptible (Idared) and resistant (Free Redstar) apple cultivars.
The highest number of differentially expressed E. amylovora genes between the two apple genotypes was observed at 24 h after inoculation. Six days after inoculation, only a few bacterial genes were differentially expressed in the susceptible and resistant apple cultivars. The analysis of differentially expressed gene functions showed that generally, higher expression of genes related to stress response and defence against toxic compounds was observed in Free Redstar. Also in this cultivar, higher expression of flagellar genes (FlaI), which are recognized as PAMP (pathogen-associated molecular pattern) by the innate immune systems of plants, was noted. Additionally, several genes that have not yet been proven to play a role in the pathogenic abilities of E. amylovora were found to be differentially expressed in the two apple cultivars.
This RNA-seq analysis generated a novel dataset describing the transcriptional response of the lowly virulent strain of E. amylovora in susceptible and resistant apple cultivar. Most genes were regulated in the same way in both apple cultivars, but there were also some cultivar-specific responses suggesting that the environment in Free Redstar is more stressful for bacteria what can be the reason of their inability to infect of this cultivar. Among genes with the highest fold change in expression between experimental combinations or with the highest transcript abundance, there are many genes without ascribed functions, which have never been tested for their role in pathogenicity. Overall, this study provides the first transcriptional profile by RNA-seq of E. amylovora during infection of a host plant and insights into the transcriptional response of this pathogen in the environments of susceptible and resistant apple plants.
在表型和遗传特征方面，Erwinia amylovora 通常被认为是一个同质物种。然而，菌株在其毒力方面表现出变异，特别是在对火疫病易感性不同的宿主上。我们应用 RNA-seq 技术来阐明低毒力的 E. amylovora 650 菌株在侵染易感（Idared）和抗性（Free Redstar）苹果品种的枝条时转录组水平的变化。
在接种后 24 小时，两个苹果基因型之间差异表达的 E. amylovora 基因数量最多。接种后 6 天，在易感和抗性苹果品种中仅有少数细菌基因差异表达。差异表达基因功能分析表明，一般来说，Free Redstar 中与应激反应和防御有毒化合物相关的基因表达较高。在这个品种中，也观察到了鞭毛基因（FlaI）的高表达，这些基因被植物的先天免疫系统识别为 PAMP（病原体相关分子模式）。此外，还发现了一些尚未被证明在 E. amylovora 致病能力中发挥作用的基因在两个苹果品种中差异表达。
这项 RNA-seq 分析生成了一个新的数据集，描述了低毒力 E. amylovora 菌株在易感和抗性苹果品种中的转录响应。大多数基因在两个苹果品种中的调控方式相同，但也存在一些品种特异性反应，表明 Free Redstar 中的细菌环境对其更为紧迫，这可能是其无法感染该品种的原因。在实验组合之间表达倍数变化最大或转录丰度最高的基因中，有许多具有未赋予功能的基因，从未对其在致病性中的作用进行过测试。总的来说，这项研究提供了 E. amylovora 在感染宿主植物过程中首次通过 RNA-seq 的转录谱，并深入了解了该病原体在易感和抗性苹果植株环境中的转录响应。
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