In nature, plants are constantly surrounded by a wide range of microbes (mutualists, commensals and pathogens), and at the same time exposed to environmental fluctuations such as abiotic stresses. Phytohormones are small molecules produced and perceived in plants that govern plant responses to the environments as well as plant growth. Thus, understanding phytohormone signaling networks at the molecular level is crucial for understanding how plants adapt to their environments. Using systems approaches and molecular genetics, we dissect phytohormone signaling networks in A. thaliana as well as other Brassicaceae plants during plant-microbe interactions. Our aim is to reveal underlying molecular mechanisms and ultimately to understand plant-bacteria interactions in a holistic way.
[Berens et al PNAS 2019; Wang et al Plant Cell 2018; Mine et al Plant Cell 2018; Nobori et al FEBS Lett 2018; Tsuda Plant Cell Physiol 2018; Mine et al EMBO Rep 2017; Anver and Tsuda Springer 2015; Seyfferth and Tsuda Front Plant Sci 2014; Kim et al Cell Host Microbe 2014; Tintor et al PNAS 2013; Wang et al Plant J 2011; Sato et al PLoS Pathogens 2010; Qi et al MPMI 2010; Tsuda et al PLoS Genet 2009; Wang et al PLoS Pathogens 2009; Tsuda et al Plant J 2008].

PAMP/pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) are well-defined modes of plant immunity against pathogens that are triggered when plants sense microbial molecules. Recognition of pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) shared by certain types of microbes, such as flg22, a part of bacterial flagellin, triggers PTI. MAMPs are recognized by pattern-recognition receptors (PRRs), which are typically receptor-like kinases (RLKs). Plant-derived damage-associated molecular patterns (DAMPs) that are released upon infection or herbivore feeding are recognized similarly to MAMPs and also trigger immune responses [Yamada et al EMBO J 2016; Ross et al EMBO J 2014]. Adapted pathogens deliver virulence effectors into the plant cell that manipulate plant immune systems, for instance PTI signaling [Tsuda et al Plant J 2012]. ETI is triggered by specific recognition of effectors by resistance (R) proteins, typically nucleotide-binding leucine-rich repeat (NLR) proteins [Cui et al Annu Rev Plant Biol 2015]. Common immune responses such as the production of reactive oxygen species, activation of MAP kinases (MAPK), and transcriptional reprogramming occur in both PTI and ETI, but with temporal and quantitative differences [Tsuda and Katagiri Curr Opin Plant Biol 2010].

We comprehend plant adaptations to environments only when we understand why, when, and how defense signaling pathways and their crosstalk evolved. We focus on genome-sequenced species of the Brassicaceae family to which A. thaliana belongs and compare immune responses such as transcriptional reprogramming and defense metabolites.
[Berens et al Annu Rev Phytopathol 2017]

Time-series transcriptome analysis is a powerful tool for disentangling complex biological processes. We have generated large scale data for transcriptome response of various genotypes of A. thaliana infected with the bacterial pathogen Pseudomonas syringae or treated with the MAMP flg22 at multiple time points by RNA-seq. These data provided tremendous insights into mechanisms for transcriptional reprogramming and its significance for resistance and generated many testable hypotheses.
[Mine et al Plant Cell 2018; Jacob et al New Phytol 2018; Hillmer et al PLoS Genet 2017; Tsuda and Somssich New Phytol 2015]

A trade-off between abiotic and biotic stress responses is thought to contribute to maximizing responses to one stress over the other thereby increasing plant fitness in one stress condition. However, this does not explain if and how this trade-off is beneficial in combined stress environments, expected in nature. Our work on this problem has led to the discovery that plants actively balance trade-offs between biological and physical stress responses based on leaf age and that this active balancing mechanism is important for plant fitness under combined stresses [Berens et al PNAS 2019].

Molecular mechanisms underlying the suppression of bacterial growth by plant immunity (Yiming Wang). The mechanism(s) by which bacterial growth is suppressed by plant immunity is not understood at a molecular level. We have uncovered evolutionarily conserved plant-secreted proteases that serve as molecular scissors to directly suppress the growth of P. syringae in A. thaliana. Overexpression of these proteases, whose function was previously unknown, increases resistance but triggers neither immune activation nor plant growth retardation. Our findings suggest that we have uncovered an interaction with broad relevance for understanding how plants protect themselves against bacterial invaders. Boosting this process might be one way of producing disease-resistant crops without reducing yield.


MAP kinases in plant defense (Maria Salazar Rondon). MPK3 and MPK6 are MAP kinases that are essential for the resistance of Arabidopsis thaliana against the pathogen Pst, but how exactly they carry out this function is not yet known. In this project, we are interrogating the role of the different domains of these proteins in transcriptional activation and aim to discover novel targets of MPK3 and MPK6 important for their functions during plant immunity.


In planta bacterial transcriptomics (Tatsuya Nobori). There is an enormous gap in our understanding of how plant immunity affects bacterial defense behavior. In this project, we have established a method for in planta bacterial transcriptomics of P. syringae in A. thaliana leaves. Bacterial cells were physically isolated from infected plant leaves in a condition that fixes and stabilizes bacterial RNA, followed by RNA-seq for bacterial mRNA. This method allows us to monitor bacterial gene expression in a large number of samples at a reasonable cost. The work revealed hundreds of bacterial genes under control of immunity and generated many testable hypotheses [Nobori et al PNAS 2018; Nobori et al FEBS Lett 2018]. On the basis of this date, we constructed co-expression networks of bacterial genes and could predict and also verify gene regulatory logics which involved bacterial transcription factors and their targets.


Co-transcriptome analysis of the interplay between plants and bacteria (Yu Cao). Despite extensive studies into the interplay between plants and mutualistic or pathogenic bacteria, the interactions between plants and commensal bacteria are poorly understood at the mechanistic level. I aim to better understand the interactions between plant immunity and individual commensal bacterial strains by performing co-transcriptome analyses of plants and a variety of plant-associated commensal bacteria in A. thaliana leaves.


Stomata aperture regulation (Kaori Fukumoto). Regulation of stomata aperture is important for water vapor and gas exchange as well as immunity. Plants close stomata upon recognition of microbes to restrict their entry into plant tissues. Some pathovars of the bacterial pathogen Pseudomonas syringae produce the jasmonate mimic coronatine to open stomata allowing them to invade plant leaves. Also, many pathogens are known to activate JA signaling. In this project, we aim to dissect the molecular mechanisms by which microbes manipulate stomata aperture in A. thaliana, allowing them to get a foothold inside plant tissues.


Role of plant immunity in shaping plant-associated microbial communities (Frederickson D. Entila). The overall goal in this project is to assess plant-microbe-microbe functional interactions in binary or mixed associations in a community context. To this end, we will apply -omics approaches (transcriptomics, proteomics, metabolomics) to microbes isolated from natural environments and plants with mutations that compromise immunity. We aim to dissect how plants discriminate pathogens from mutualists/commensals at the community level, but also wish to understand how microbes alter plant host defenses to allow successful establishment of the microbiome and how plant-microbe-microbe interactions confer fitness under unfavorable conditions.