Global Gene Expression Analysis of Cross-Protected Phenotype of <i>Pectobacterium atrosepticum</i>

The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.对不良环境的适应能力，使得众多细菌物种几乎无处不在，并能在多样的生态位中存活。该能力对于诸多植物病原细菌而言尤为关键——这类细菌除寄主植物外，还需在土壤、水体、昆虫媒介等多种环境中存活。在部分此类环境中，细菌会面临营养匮乏并持续存活，同时获得针对多种胁迫因子的抗性相关新特性，即交叉保护（cross-protection）。尽管已有诸多研究对交叉保护现象进行了描述，且部分诱导抗性细胞形成的调控组分已被阐明，但目前尚未有研究对交叉保护表型细胞与增殖细胞的生理学特征开展全面比较。在本研究中，我们借助RNA测序（RNA-Seq）技术，以一种在全球范围内造成作物损失的有害植物病原细菌——胡萝卜软腐果胶杆菌黑腐亚种（Pectobacterium atrosepticum, Pba）为研究对象，深入解析其交叉保护细胞的生理学特征。该细菌能够成功定殖植物，与其致病潜力以及在各类胁迫条件（包括营养匮乏）下有效存活并后续仍保留侵染植物的能力密切相关。在既往研究中，我们证实Pba可通过多种适应性策略，使细胞表现出对多种胁迫因子的抗性。本研究中，我们首先明确了饥饿条件下Pba交叉保护表型形成所需的时长，并在交叉保护效应达到峰值时，对比未适应的增殖细胞与适应细胞的转录组图谱。所得数据通过实时定量反转录聚合酶链反应（qRT-PCR）进行了验证。我们采用多种方法，将两种细胞类型中的差异表达基因（DEGs）划分为不同功能类群与类别。最终，我们阐明了区分交叉保护表型细胞与增殖细胞的生理学特征。