Plants have hormones to sense problems and report them to the rest of the plant


ust like humans and other animals, plants have hormones.

One role of plant hormones is to perceive trouble-whether an insect attack, drought or intense heat or cold-and then signal to the rest of the plant to respond.

A multicenter team led by current and former investigators from the Salk Institute is reporting new details about how plants respond to a hormone called jasmonic acid, or jasmonate. The findings, which were published in Nature Plants on March 13, 2020, reveal a complex communication network.

This knowledge could help researchers, such as members of Salk’s Harnessing Plants Initiative, develop crops that are hardier and more able to withstand assault, especially in an era of rapid climate change.

“This research gives us a really detailed picture of how this hormone, jasmonic acid, acts at many different levels,” says Professor Joseph Ecker, co-corresponding author and Howard Hughes Medical Institute investigator.

“It enables us to understand how environmental information and developmental information is processed, and how it ensures proper growth and development.”

The plant used in the study was Arabidopsis thaliana, a small flowering plant in the mustard family.

Because its genome has been well characterized, this plant is a popular model system. Scientists can take what they learn in A. thaliana and apply it to other plants, including those grown for food. Jasmonic acid is found not only in A. thaliana but throughout the plant kingdom.

“Jasmonic acid is particularly important for a plant’s defense response against fungi and insects,” says co-first author Mark Zander, a staff researcher in Ecker’s lab.

“We wanted to precisely understand what happens after jasmonic acid is perceived by the plant. Which genes are activated and deactivated, which proteins are produced and which factors are in control of these well-orchestrated cellular processes?”

The researchers started with plant seeds grown in petri dishes. They kept the seeds in the dark for three days to mimic the first few days of a seed’s life, when it is still underground.

“We know this growth stage is super important,” says co-first author and co-corresponding author Mathew Lewsey, an associate professor at La Trobe University in Melbourne, Australia, who previously worked in Ecker’s lab.

The first few days in the soil are a challenging time for seedlings, as they face attacks from insects and fungi. “If your seeds don’t germinate and successfully emerge from the soil, then you will have no crop,” Lewsey adds.

After three days, the plants were exposed to jasmonic acid. The researchers then extracted the DNA and proteins from the plant cells and employed specific antibodies against their proteins of interest to capture the exact genomic location of these regulators.

By using various computational approaches, the team was then able to identify genes that are important for the plant’s response to jasmonic acid and, moreover, for the cellular cross-communication with other plant hormone pathways.

Two genes that rose to the top in their degree of importance across the system were MYC2 and MYC3. These genes code for proteins that are transcription factors, which means that they regulate the activity of many other genes-or thousands of other genes in this case.

“In the past, the MYC genes and other transcription factors have been studied in a very linear fashion,” Lewsey explains. “Scientists look at how one gene is connected to the next gene, and the next one, and so on.

This method is inherently slow because there are a lot of genes and lots of connections. What we’ve done here is to create a framework by which we can analyze many genes at once.”

“By deciphering all of these gene networks and subnetworks, it helps us to understand the architecture of the whole system,” Zander says.

“We now have this very comprehensive picture of which genes are turned on and off during a plant’s defense response. With the availability of CRISPR gene editing, these kinds of details can be useful for breeding crops that are able to better withstand attacks from pests.”

Another noteworthy aspect of this work is that all of the data from the research has been made available on Salk’s website. Researchers can use the site to search for more information about genes they study and find ways to target them.

Two phytohormones, jasmonic acid (JA) and salicylic acid (SA) play important roles in transducing the activation of plant defense systems against pathogen attacks. SA usually induces resistance mechanisms which are active against biotrophic and hemi-biotrophic pathogens, whereas JA induces resistance against necrotrophic phathogens.1 

In most cases, JA and SA defense signaling pathways are mutually antagonistic in dicotyledonous species.2,3 In Arabidopsis, SA downregulates the expression of JA-responsive marker genes such as PDF1.2 and VSP1 as well as genes encoding key enzymes in the JA biosynthesis pathway, such as LOX2, AOS, AOC2 and OPR3.4 

On the one hand, this antagonistic crosstalk between JA and SA-dependent defense signaling is unclear in rice, which serves as a model for molecular studies of other monocotyledonous species. A previous study reported that the expression of PR genes and overall resistance to Magnaporthe oryzae were higher in OsAOS2-overexpression rice plants, even though M. oryzae is a hemi-biotrophic pathogen.5 

In addition, our recent study demonstrated that exogenous JA application induces resistance to Xanthomonas oryzae pv oryzae (Xoo) in rice, though Xoo is a biotrophic pathogen.6 These results indicate that JA and its signaling pathway make important contributions to both hemi-biotrophic or biotrophic pathogen defense response in rice.

These results are supported by a number of previous reports.7,8 Recently, it has been demonstrated a positive contribution of JA and SA signaling in the immunity against both biotrophic and necrotrophic pathogens in Arabidopsis.9 

Here, we discuss JA and SA signaling crosstalk and propose that a common defense system is activated by both JA and SA in rice.

It has been reported that 313 BTH-upregulated genes were identified by microarray analysis in rice.10 Because BTH is a functional analog of SA, these 313 genes are very likely the genes responsible for SA defense signaling in rice.

Our resent study explored JA-responsive genes using microarray analysis and demonstrated that 1,320 genes were upregulated in response to JA in rice.6 To determine if there is crosstalk between JA and SA-transducing pathways in rice, we measured the expression of BTH-upregulated genes after JA treatment.

Although a third of BTH-upregulated genes were downregulated by JA, more than half were upregulated (Fig. 1), suggesting that much of the SA signaling pathway is independent of JA downregulation. In addition, expression of about a fifth of SA-upregulated genes doubled in response to JA, suggesting that JA and SA signaling coordinately interact during induction of a defense response.

The expression of rice PR1b gene, a commonly used marker of disease resistance, is induced by treatment of JA or SA,11 suggesting that there is a common defense system, or at least a partly shared signal transduction pathway used for both JA and SA signaling in rice. OsWRKY45 is a BTH-up-regulated gene and is a key protein in BTH-induced resistance to M. oryzae and Xoo.10,12 

Microarray analysis showed that expression of OsWRKY45 nearly doubled in response to JA treatment,6 supporting our hypothesis that JA and SA signaling, or at least a critical part of the signaling cascade, interacts coordinately in rice defense response.

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Figure 1. Categories of BTH-upregulated genes after JA treatment in rice. Percentage of BTH-upregulated genes that are also upregulated by JA are shown with the qualifying induction change. “No-hit” indicates BTH-upregulated genes that were not correlated with a corresponding gene in our microarray data.6 BTH-upregulated genes refer Shimono et al.10

Rice has high endogenous SA levels (> 1 µg g−1 fresh weight in leaves).13 To understand the relationship between JA and SA signaling on the rice immune system, it is important to understand the dynamics of endogenous JA and SA relative concentration.

However, it is not known whether endogenous SA concentrations are affected by exogenous JA application in rice. We measured the effect of exogenous application of JA on SA contents and found that SA dramatically decreased in response to exogenous JA (Fig. 2). This result suggests that SA signaling is suppressed by JA because of a decrease in tissue SA concentrations.

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Figure 2. SA content after JA treatment in rice. Free SA content after100 µM JA treatment for 24 h in the fourth leaf blades of rice. Values are means ± SE (n = 3 for Mock, 4 for JA). An asterisk represents a statistically significant difference from the mock-treated control at p < 0.05 (Student’s ttest).

No distinct antagonistic interaction between JA and SA signaling could be verified in the defense response in rice, although JA and SA synthesis may be regulated antagonistically. Rather, our results suggest that some common defense signaling system plays a crucial role in the rice defense response (Fig. 3).

Because high endogenous SA concentrations are maintained under normal conditions, SA signaling contributes mainly to the basal defense in rice. Once the JA signal is activated, endogenous SA levels would dramatically decrease and SA signaling would be suppressed.

JA would then activate the common defense system instead of SA in rice (Fig. 3). In fact, JA-Ile, a bioactive form of JA, is accumulated following inoculation with M. oryzae.14 Because the JA and SA-activated common defense system is critical to the pathogen defense response, JA signaling must be able to induce resistance against the biotrophic pathogen, Xoo, in rice.

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Figure 3. Schematic overview of the common defense system activated by JA and SA in rice. Parallel models of the activation scheme of a common defense system either when endogenous JA is low (JA signal off) or high (JA signal on). Solid lines indicate putative active signaling pathways. Dashed lines indicate putative inactive signaling pathways under the JA signaling condition of the model.

More information: Zander, M., et al. Integrated multi-omics framework of the plant response to jasmonic acid. Nat. Plants 6, 290–302 (2020).


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