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

Abstract

Understanding how gene expression is regulated in plant pathogens is crucial for pest control 20 and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found 25 instances of both concordant and discordant regulation of bacterial mRNAs and proteins.Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and 30 their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.Nobori, Wang et al. | In planta multi-omics of a bacterial pathogen bioRxiv | 2

Transcriptional profiling of threePseudomonas syringaepv.actinidiaebiovars reveals different responses to apoplast-like conditions related to strain virulence

“…Although the signals are poorly understood, there is compelling evidence that TTSS activation occurs upon contact with target cells (13,14) and that the hrp/hrc gene cluster is controlled by multiple physiological and environmental factors that are replicated by minimal medium (15). We therefore anticipated the significant induction of hrp/hrc genes in Pto, as reported previously (15,72,73). We also observed the same phenomenon in Psa3, whereas the hrp/hrc genes in Psa1 were induced weakly and those in Psa2 were not induced at all.…”

Dissecting the co-transcriptome landscape of plants and microbiota members

“…In this case, a gain-of-function assay is a complementary, albeit also limited, approach. For instance, we previously showed that in planta bacterial transcriptome data can predict bacterial genes that contribute to bacterial growth in planta when overexpressed (Nobori et al, 2018(Nobori et al, , 2019) . It will be necessary, in the future, to rigorously validate the biological relevance of bacterial transcriptional regulation in plants at the mechanistic level.…”

“…In this case, a gain-of-function assay is a complementary, albeit also limited, approach. For instance, in planta bacterial transcriptome data could predict bacterial genes that contribute to bacterial growth in planta when overexpressed ( 16, 40 ).…”

“…In planta bacterial omics approaches, such as transcriptomics, are powerful in understanding bacterial gene functions in the plant microbiome and how plants influence bacterial activities (15). To date, however, there are few available in planta bacterial transcriptome studies, which focus on pathogenic Proteobacteria strains (16)(17)(18)(19)(20)(21). It is, therefore, unknown whether plantassociated bacteria have any common or phylum-specific gene expression signatures and what kind of functions are important for their non-pathogenic and sometimes beneficial traits in plants.…”

Biophysical and proteomic analyses suggest functions ofPseudomonas syringaepvtomatoDC3000 extracellular vesicles in bacterial growth during plant infection

“…Plants respond rapidly to colonization by microbes, activating innate defence strategies, which can broadly be categorized into pattern-triggered immunity (PTI) activated by microbe-associated molecular patterns (MAMPs) and effector-triggered immunity (ETI) induced upon recognition of virulence factors or their actions (Couto D. & Zipfel, 2016, Dodds & Rathjen, 2010). Virulence of Pto DC3000 largely depends on the Type-III secretion system and its secreted effectors (Kvitko et al , 2009, Nobori et al , 2018, Nobori et al , 2019, Nomura et al , 2006). A number of Type-III secreted effectors from Pto DC3000 and their in planta targets have been identified, many involved in immune suppression and some with roles in gaining access to nutrients (Wei et al , 2018, Xin et al , 2018).…”