Transcriptome landscape of a bacterial pathogen under plant immunity

Abstract

Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes and determined high-resolution transcriptome patterns of the foliar bacterial pathogen in with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities We identified specific "immune-responsive" bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

“…implying that dynamic transcriptional reprogramming at an early stage of infection is crucial for Pto to adapt to the plant apoplastic environment and become virulent. This notion is supported by our previous observation that bacterial transcriptome patterns at this early stage 90 of infection can predict bacterial growth in plants at a later stage (8).…”

“…Despite the distinct regulation of certain specific mRNAs and proteins, the overall moderate 245 correlation between transcriptome and proteome patterns of Pto suggests that mRNA expression can be a good indicator of bacterial functional expression in planta. Also, transcriptome-based analysis would be aided by additional transcriptome data available from a previous study (8) and by the fact that a greater number of Pto mRNAs were detected compared to proteins (Fig. 1C).…”

“…Gene correlation networks were created in Cytoscape with the yFiles Layout Algorithm. 525 Gene co-expression analysis RNA-seq data obtained in a previous study (8) and the present study were combined (see Data S12 for the full dataset). Data were TMM-normalized and voom-(log 2 ) transformed.…”

Evolutionary and ecological functional genomics, from lab to the wild

“…The attention to different environments goes hand‐in‐hand with increased interest in modeling evolutionary responses in relation to climate change and environmental stress (Nagano et al ., ; Plessis et al ., ; Fournier‐Level et al ., ; Watson‐Lazowski et al ., ). Because transcriptional reprogramming was the standard in examining plant defense responses, in the EEFG framework, the transcriptional implications of responses to biotic interactors are more rigorously being considered at the systems level in natural environments (Turner et al ., ; Liao et al ., ; Nobori et al ., ; Young et al ., ).…”

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

“…Thus, by measuring the transcriptome in both the pathogen and the host, it should be possible to map how genetic variation in the pathogen is conveyed through the pathogen's transcriptome and concurrently how the host's transcriptome responds. Recent work has shown that it is possible to measure the pathogen's transcriptome in planta in A. thaliana -Pseudomonas syringae leading to new hypothesis about virulence (Nobori, Velásquez et al 2018). To date in plants, co-transcriptome work where both the host's and pathogen's transcripts have been measured has been shown to work in the A. thaliana -B. cinerea system through single sample RNA-Seq (Zhang, Corwin et al 2017, Zhang, Corwin et al 2018.…”