Understanding Plant Immunity: Pathogen Recognition and Defense Signaling

Plants rely on innate immune responses to fight infections. Recognition of microbial molecules leads to the production of antimicrobial compounds, improvement of physical barriers, and the recruitment of defense proteins. Understanding these mechanisms has been crucial for developing novel strategies to ensure global food security.

Image Credit: Miha Creative/Shutterstock.comImage Credit: Miha Creative/Shutterstock.com


Plant diseases significantly threaten global food security by causing substantial reductions in crop yields.1 The challenge is exacerbated by the diversity of pathogens that can affect crops, including bacteria, fungi, and viruses.1 These diseases can lead to losses ranging from 20% to 40% of agricultural productivity worldwide.1

To address this issue, it is necessary to understand how plant immunity works. In general, plants employ a variety of cell-surface and intracellular immune receptors to detect a wide range of immunogenic signals associated with pathogens, which subsequently activate their defenses.2

It was discovered that salicylic acid (SA) is their major defense hormone, potentiating immune signaling, which in turn reprograms their transcriptome for defense.2 Research in this field has led to genetic improvements that show great results in effectiveness and sustainability as a method for controlling crop diseases.1

Over the past decade, the advancements in the study of plant immunity at the molecular and genomic levels have allowed the identification of new resistance genes and the engineering of disease-resistant crop plants, which is now possible with unprecedented speed and precision promoted by the application of CRISPR-Cas9 technology.3

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Plant Immunity: Foundations and Principles

Plants lack a proper acquired immune system; however, they possess systemic acquired resistance (SAR), in addition to microbial-associated molecular-patterns-triggered immunity (MTI) and effector-triggered immunity (ETI).4

MTI involves the recognition of conserved microbial elicitors, called microbial-associated molecular patterns (MAMPs), by the pattern recognition receptors (PRRs) found in the plasma membrane.4

Their activation leads to active defense responses that assist in halting the infection before the microorganism infects the plant, triggering a variety of key signaling modules

including rapid phosphorylation of receptor-like cytoplasmic kinases (RLCKs), an influx of calcium, a burst of reactive oxygen species (ROS), and activation of calcium-dependent kinases (CPKs), mitogen-activated protein kinase (MAPK) cascades, and heterotrimeric G proteins.2

ETI involves the activation of intracellular receptors similar to animal NOD-like receptors (NLR). They are involved in Programmed Cell Death and Hypersensitive Response.5 Their activity and function are modulated by their subcellular location.5

Ultimately, SAR is the defense mechanism regulated by SA accumulation, which acts to potentiate both MTI and ETI responses.2,4

Molecular Mechanisms of Pathogen Recognition

PRRs can recognize different MAMPs, and even effector molecules commonly detected in the ETI responses.2 These MAMPs include oligogalacturonides, ergosterol, bacterial flagellin, Pep-13, xylanase, cold-shock protein, and lipopolysaccharides (LPS).2

PRRs detect both MAMPs and effector molecules. The PRR family includes receptor-like proteins (RLP) and receptor-like kinases (RLK). RLK is structurally similar to receptor-tyrosine kinases (RTKs) in animals, while RLP is structurally similar to toll-like receptors (TLR).

Like every pathogen-host relationship, plants and pathogens have co-evolved together,  provoking the development of pathogen strategies to bypass the MTI. This is made by injecting effector proteins across the cell wall into the plant cell's cytoplasm.4

Virulent bacteria deliver 15–30 types of effector molecules into the host cells, acting as transcription factors, affecting histone packing, chromatin dynamics, host transcription factors activity, and more.4

These effectors proteins are called avirulence proteins (Avr). The R proteins recognize Avr; these receptors belong to the intracellular nucleotide-binding leucine-rich repeat (NB-LRR) protein family, similar to animal NLR.2 The second major class of R proteins belongs to the extracellular LRR proteins.2

Defense Signaling Pathways in Plants

Primarily, MAMP perception triggers a rapid influx of calcium ions into the cytosol, activating downstream signaling cascades, leading to the expression of defense genes and activating enzymes for metabolite production.6

MAMP recognition also triggers a rapid production of ROS, acting as a signaling molecule and contributing directly to antimicrobial activity.6 MAPK are activated by phosphorylating several transcription factors of genes involved in defense responses, including those related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) signaling.6

ETI also involves the activation of calcium signaling cascades, the production of ROS and nitric oxide, alterations in membrane trafficking, transcriptional reprogramming, and activation of programmed cell dead to prevent the spreading of the infection.

Finally, SAR acts as a long-lasting, broad-spectrum defense mechanism activated after an initial exposure to a pathogen. It involves the transport of signaling molecules (e.g., SA) throughout the plant, leading to a primed state of defense. Upon subsequent pathogen attack, these primed tissues can mount a faster and stronger immune response for some time.6

Techniques for Studying Plant Immunity

Advancements in plant immunity have been possible due to the development and application of different techniques, such as the CRISPR-Cas9 system, which allows precise gene editing, genotyping, and mutation analysis using PCR and sequencing, assessing heritability of mutations in subsequent generations, and off-target evaluation to ensure specificity.7

Additionally, Agrobacterium-mediated transformation is used for multiplex gene editing.7 Great advancements have been made by complementing these techniques with the use of systems biology approaches (e.g., transcriptomics and proteomics) that allow the study of thousands of variables simultaneously.7  

Applications in Agriculture and Biotechnology

Currently, plant immunity applications involve the development of crops resistant to parasitic plants, pathogens, and environmental stresses using gene editing tools, such as CRISPR systems.8

CRISPR-Cas9 has engineered resistance against various plant pathogens, including viruses, bacteria, and fungi, in plant species like Arabidopsis, cucumber, rice, and tomato.8

Future Directions in Research on Plant Immunity

Plant immunity research is transforming, integrating systems biology and synthetic biology approaches to revolutionize plant resistance against diverse pathogens.9

Spatial and single-cell technologies are at the forefront of this revolution, providing unprecedented cellular resolution in studying plant-pathogen interactions. This, coupled with CRISPR/Cas9 technology, has made editing crop genomes for enhanced disease resistance a reality.9

Furthermore, merging multiomics data with artificial intelligence, particularly machine learning and deep learning, holds immense promise. This fusion of data and technology will unlock profound insights into plant defense mechanisms, potentially leading to groundbreaking crop protection strategies in the face of climate change and emerging disease threats.9


  1. Zhao Y, et al. (2022). From plant immunity to crop disease resistance. Journal of Genetics and Genomics, 49(8), 693–703. https://doi.org/10.1016/j.jgg.2022.06.003
  2. Zhou, J. M., & Zhang, Y. (2020). Plant Immunity: Danger Perception and Signaling. Cell, 181(5), 978–989. https://doi.org/10.1016/j.cell.2020.04.028
  3. Borrelli V. M. G, et al.  (2018). The Enhancement of Plant Disease Resistance Using CRISPR/Cas9 Technology. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.01245
  4. Muthamilarasan, M., & Prasad, M. (2013). Plant innate immunity: An updated insight into defense mechanism. Journal of Biosciences, 38(2), 433–449. https://doi.org/10.1007/s12038-013-9302-2
  5. Qi, D., & Innes, R. W. (2013). Recent Advances in Plant NLR Structure, Function, Localization, and Signaling. Frontiers in Immunology, 4. https://doi.org/10.3389/fimmu.2013.00348
  6. Nishad R, et al. (2020). Modulation of Plant Defense System in Response to Microbial Interactions. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.01298
  7. Zhang N, et al. (2020). Generation and Molecular Characterization of CRISPR/Cas9-Induced Mutations in 63 Immunity-Associated Genes in Tomato Reveals Specificity and a Range of Gene Modifications. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.00010
  8. Zaidi S. S. E. A, et al.  (2020). Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02204-y
  9. Murmu S, et al. (2024). A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions. Frontiers in Plant Science, 15. https://doi.org/10.3389/fpls.2024.1292054

Further Reading

Last Updated: Jun 6, 2024

Deliana Infante

Written by

Deliana Infante

I am Deliana, a biologist from the Simón Bolívar University (Venezuela). I have been working in research laboratories since 2016. In 2019, I joined The Immunopathology Laboratory of the Venezuelan Institute for Scientific Research (IVIC) as a research-associated professional, that is, a research assistant.


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