Kenichi Tsuda
Group leader

Original publication

Tatsuya Nobori, André C. Velásquez, Jingni Wu, Brian H. Kvitko, James M. Kremer, Yiming Wang, Sheng Yang He, Kenichi Tsuda
Transcriptome landscape of a bacterial pathogen under plant immunity

Revealing the intricacy of plant-bacteria interactions

Revealing the intricacy of plant-bacteria interactions

A team of researchers from Germany and the US led by Kenichi Tsuda at the Max Planck Institute for Plant Breeding Research (MPIPZ) in Cologne have now developed a method that can be used to probe the complexity of plant-bacteria interactions.

March 13, 2018

All plant species are home to a huge array of different bacteria that can be either beneficial or harmful to their hosts. These interactions could be exploited in agriculture or for crop breeding, but we lack a detailed understanding of how bacteria mediate their effects. A team of researchers from Germany and the US led by Kenichi Tsuda at the Max Planck Institute for Plant Breeding Research (MPIPZ) in Cologne have now developed a method that can be used to probe the complexity of plant-bacteria interactions. In a first application of their method, the authors show how a bacterial pathogen responds to plant defence mechanisms during infection. They also identify a hitherto unknown strategy used by plants to inhibit bacterial growth. Their findings are published in the journal PNAS.

In response to attack from bacterial invaders, plants call on two potent defence systems: in the first, called pattern-triggered immunity, receptors on plant cells initiate responses after recognising characteristic structural features of microbes; but due to the fact that bacteria have evolved molecules that subvert pattern-triggered immunity, plants have in turn evolved a second defence system, called effector-triggered immunity, which targets exactly these molecules. While both systems are highly effective at blocking bacterial growth, the responses that these systems elicit in colonising or infecting bacteria remain unclear.

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To gain more insight into this question, the researchers used two common model organisms, the bacterial pathogen P. syringae pv. tomato DC3000 (Pto) and the thale cress Arabidopsis thaliana. The authors infected A. thaliana with Pto and then analysed the bacterial transcriptome, the whole set of mRNA transcripts the bacteria produced, to determine changes in gene expression. Specifically detecting the bacterial transcriptome in the sea of plant nucleic acid is tricky, and the authors began by developing a new method whereby bacterial cells could be efficiently extracted from plant material. This allowed them to enrich for the bacterial transcriptome, even when present at very low levels.

The authors focused on the period shortly after infection when bacterial numbers were still relatively low in order to exclude any effects of increased population density on gene expression. The team made several novel observations regarding the interplay between plant defence mechanisms and bacterial pathogens during infection. They found that pattern-triggered immunity responses not only targeted processes involved in plant infection but also housekeeping genes that carry out the most basic cellular functions. They also discovered that changes in the bacteria’s gene expression differed significantly depending on whether pattern-triggered immunity or effector-triggered immunity was induced. Finally, they also found that a substantial proportion of the genes whose expression changed during infection have not yet been characterised, indicating that much remains to be learned about how bacteria respond to plant immunity.

When the scientists further analysed the data they also found a strong correlation between expression patterns at 6 hours and growth over 40 hours later, suggesting that the pattern of gene expression early during infection can be used to predict subsequent growth. This observation validated their experimental approach.

A closer inspection of the bacterial genes whose expression was changed in response to plant immunity revealed the suppression of a large number of genes involved in iron acquisition. This suggested a concerted strategy to block bacterial growth, and, in fact, when the authors artificially elevated the level of one of these genes, pvdS, bacteria could escape the inhibitory effects of plant immunity on proliferation.

“Also healthy plants are colonised by huge numbers of microorganisms which interact with their hosts in ways that are still poorly understood,” underlines lead author Kenichi Tsuda.

First author Tatsuya Nobori stresses that the development of the new method to extract bacterial from plant material will allow analysis of the proteome of the bacteria that live inside leaves, an endeavour which has not been feasible until now. “Our approaches will help us to better understand the interplay between plant immunity and colonising microorganisms,” says Nobori. Such insights could be exploited to improve crop yields.

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