One of two major response pathways is initiated when plants are attacked by microbial pathogens. One major difference difference between these two pathways is the specificity with which the plant identifies the pathogen. In one pathway, the plant recognizes general signals common to a broad array of pathogens. These signals are known as pathogen-associated molecular patterns (PAMPs), thus this pathway is called PAMP-triggered immunity (PTI). In the second kind of signaling pathway, the plant responds to highly specific molecules secreted by the pathogen. These molecules are called effectors, hence this pathway is known as effector-triggered immunity (ETI).

PAMP-triggered immunity (PTI)

The hallmark of PTI is the ability of the plant to detect the molecular signature of pathogens. These signatures may take many different forms, including peptides derived from bacterial flagellum proteins, chitin (which makes up the cell wall of fungi), double-stranded RNA, and certain sequences of DNA common to microbes. Each of these presents a specific molecular pattern recognizable by the plant as indicating the presence of a potentially pathogenic organism.

These molecular signatures are detected by the cell through a class of proteins known as pattern recognition receptors (PRRs) that are specific for certain molecules. For example, the flagellum peptide known as flg22 is perceived by a PRR called FLS2. It is important to note that the flg22 peptide is a common motif found in all bacterial flagella as they are hydrolyzed. Upon perceiving flg22, FLS2 interacts with and phosphorylates the first member in a kinase cascade called MEKK1. MEKK1 phosphorylates one or more of several kinases (MEK4/5), which target several other kinases (MPK3/6). This series of events is known as a mitogen-activated protein kinase cascade, a signal transduction pathway common across all organisms. This kind of signaling system is modular and achieves the amplification of a single signal. The end result of all of this kinase activity is the activation of several transcription factors (WRKY22/29) that control defense-regulated genes. One example of these genes is those involved in synthesis of salicylic acid and jasmonic acid. There is also evidence that the kinase cascade can modify chromatin structure through acetylation and methylation, both of which can have a strong effect on genome-wide gene expression. All of this signaling has the overall result of “priming” the plant defense response.

Effector-triggered immunity (ETI)

The fundamental difference between PTI and ETI is the degree of specificity, with ETI representing a highly-specific, gene-for-gene defense response. The high specificity makes this pathway less durable than PTI and more targeted against an individual pathogen.

The ETI response is initiated by the secretion of effector molecules by the secretory system of bacterial cells. These effector molecules, called Avr (avirulence) proteins, are detected by the plant through recognitional resistance genes, or R-genes. The R genes encode Ser/Thr protein kinases, which interact with partners called nucleotide binding leucine-rich repeat proteins (NB-LRRs). This signaling complex also touches of a kinase cascade, but the overall result is the activation of the hypersensitive response and rapid cell death around the site of infection.

The avirulence (Avr) proteins represent an interesting evolutionary riddle: how is it adaptive for the bacteria to secrete a molecule that signals its presence to the plant? In at least one case, the answer seems to be related to the function of the Avr protein. AvrAC, secreted by a strain of Xanthomonas, acts as a uridyl transferase that modifies a component of the signal cascade such that its phosphorylation site is masked. Unable to be phosphorylated, the kinase cascade is interrupted and the plant fails to activate the hypersensitive response.

Plants are under constant attack in the environment, with the attackers trying to breach the perimeter by chewing, ripping, dissolving, penetrating, or tearing open the organs, tissues, and cells making up the plant body. These attackers include everything from acellular viruses and single-celled bacteria to multicellular mammals. Plants have evolved defense systems to address this wide variety of potential attackers. Those systems include physical barriers and anatomical structures to prevent the penetration of an attacker, general chemical defenses that act as a deterrent against attack, and highly specific immune-type responses that recognize and protect against familiar pathogens.

Kinds of Pathogens

In addition to the multicellular attackers such as nematodes and insect larvae, single-celled microbes are a constant threat to a plant’s health. This class of attacker falls into one of three possible categories depending on the mode of action employed by the pathogen. On one end of the spectrum, some microbes seek to destroy the plant tissue and absorb as much of the remaining organic matter as quickly as possible. This category of pathogen is known as the necrotropic pathogens due to the fact that these microbes feed on dead tissue. On the other end of the spectrum, some microbes attempt to penetrate the host plant’s defenses and soak up as many organic resources as possible without the host mounting a defense response. These are biotrophic pathogens, attempting to evade host detection and keep the host tissue alive because it benefits them the most to do so. These are the microbes that often induce tumor formation in host organs by transferring genes into the host cell that encode hormone biosynthesis enzymes, resulting in increased cell division. These pathogens are the equivalent of a squatter taking up residence in a home and building and addition onto the kitchen so they can get more to eat. In between these extremes are the hemibiotropic pathogens, which keep the host tissue alive for a time after invasion, but eventually kill it and take its resources.

Structural Defenses

The first line of defense plants present to an invading pathogen is the thick cuticle found on the surface of the epidermis throughout the aerial tissues of the plant. The cuticle is made up mostly of waxes and fatty acid esters known as cutins that are secreted by the epidermal cells. In addition to making the surface more water-tight, these waxes and cross-linked esters deter some smaller animal herbivores and many microbes.

While the cuticle forms an effective barrier on leaves and stems during primary growth, stems undergoing secondary growth secrete a different kind of coating for protection. These organs produce a layer of cells that contribute to an increase in girth of the stem by dividing in a ring around the stem parallel to the surface, forming cork. These cork cells, which make up part of the bark of stems, synthesize a waterproof substance called suberin, which is secreted into the apoplast and permeates the cell wall of cork cells. Once suberin is manufactured and secreted, these cells can no longer take up water and die. Suberin is a polyphenolic substance and is not only hydrophobic but also has some antimicrobial properties as well as providing a physical barrier.

Trichomes, or hair cells, provide a physical impediment on the surface of many stems and leaves that deters the feeding of many insects. Not only do trichomes offer a physical challenge, they are often filled with secondary compounds that are irritants or toxins to feeding insects or other animals. Cooking herbs are an abundant example, often having leaves covered in terpene-bearing glandular trichomes that burst when contacted. Another example is poison ivy (Toxicodendron radicans), which secretes an irritating oil from trichomes called urushiol.

If an attacker manages to make it through cuticle covering the surface of the plant, perhaps through a wound opening, it will still find one last line of defense: the tough, rigid, lignified cell wall. Made up of cellulose and other structural polysaccharides impregnated with the polyphenol lignin, the cell wall presents a formidable barrier for microbial attackers like bacteria and fungi. Some species of fungi form elaborate multicellular structures with their hyphae (called an appresorium) that can puncture the highly-pressurized cell wall, while other fungi and bacteria secrete cellulose-degrading enzymes that help to digest the wall away.

Defense Responses

Once the structural defenses have been compromised, the plant begins to mount one or several simultaneous defense responses leading to only a few outcomes. In many cases, the results of an attack include the increased biosynthesis of secondary compounds through the induced expression of genes encoding enzymes in terpene or phenolic compound synthesis. These molecules are always being synthesized by the cell at a baseline rate, but that rate increases when an attack is detected.

Another outcome of infection can be the initiation of programmed cell death at or near the site of infection. When the plant dectects certain features of a pathogen or herbivore, these can trigger those cells to cut themselves off from the rest of the plant to try to contain the infection. If you inspect a leaf, it is not uncommon to find brown spots scattered throughout the leaf. These spots are a common indicator of such cell death activity.

Pathogen and herbivore attack can also induce the plant to produce signal molecules that communicate an infection throughout the rest of the plant body. Salicylic acid and jasmonic acid are two such hormones that serve to prime the immune response of distant organs in advance that a pathogen or herbivore has attacked.

Plants synthesize a wide range of metabolites that are not known to be essential for their survival. Because they are not a part of primary metabolism, they are often lumped together in a category of metabolites called secondary compounds. This is an entirely artificial categorization given that there is no unifying characteristic of the entire group. Many of these compounds are involved in defense responses, but others produce pigments involved in pollinator attraction, and still others make up important photoprotective pigments in leaves that guard against damage due to high light conditions. Most of the secondary compounds are strongly oxidizing, and thus are sequestered in the vacuole after production to protect the proteins of the cytoplasm from damage.

While the structures and functions of these molecules are diverse, they can be grouped into 3 major classes based on common structure and biosynthetic pathways. The classes include the phenolic compounds, terpenes, and nitrogen-containing compounds. No single plant species makes a full complement of all secondary compounds, but each makes a select subset of them.

Phenolic compounds

Phenolic compounds are united by having a phenol group — a phenyl ring with a hydroxyl group. Such structures are assembled through the shikimic acid pathway, which branches off of primary metabolism through phosphoenolpyruvate in the respiration pathway and leads to the synthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Phenylalanine serves as the entry substrate to form the phenolic secondary compounds, with the first committed step being the deamination of phenylalanine by the enzyme phenylalanine ammonia lyase (PAL). The simplest resulting molecules are the simple phenolics, phenylpropanoids, and the precursors to lignin. When these simpler phenolics condense with a second phenyl ring, they form flavonoids, isoflavonoids, and flavonols.

One example of a common flavonoid is the family of pigment known as anthocyanins, which contribute the reds, purples, and blues to flower pigments. The different colors of anthocyanin pigments are the result of varying degrees of hydroxylation on one of the 2 rings of the flavonoid. Many other examples of flavonoids are encountered every day in the foods humans eat, specifically from the herbs and spices added to food for flavoring and spice. Flavonoids are the primary flavor constituents in such spices as cinnamon, ginger, cloves, nutmeg, coffee, and vanilla. These flavonoids probably serve as a deterrent to herbivorous insects and larger animals, and many also show antimicrobial properties.

Terpenes

Terpenes are long chain hydrocarbon molecules having 10-40 carbons. Most are toxic in some way to animals and so are deterrents to herbivory. In addition to these defense compounds, the plant hormones GA and ABA are examples of terpenes, as are the carotenoids, yellow-orange pigments involved in photosynthesis. Like the phenolic compounds, the terpenes are synthesized by a pathway that branches from respiration through either acetyl CoA or glyceraldehyde 3-phosphate and pyruvate. The results of either pathway are 5-carbon units that can be joined together in a variety of ways to produce the long chain structures associated with this class. As a consequence of this biosynthetic process, the terpenes always occur in multiples of 5 carbons (10, 15, 20, etc).

The monoterpenes are the smallest of the terpenes, composed of 10 carbons, and are often volatile essential oils found on the surface of leaves and stems. The familiar scent of pine, for example, is produced by α-pinene and β-pinene. Another familiar monoterpene is limonene, responsible for the lemon scent. In the case of both pine and citrus, these essential oils are found in a sub-epidermal duct or ‘oil gland’ where they are maintained until the tissue is disrupted. Most of the flavor compounds associated with the mint (Lamiaceae) family, including basil, oregano, mint, and thyme, are produced by monoterpene essential oils. In these examples, the oils are found in modified trichomes atop the surface of the leaf, where they are easily ruptured and released as a potential herbivore merely contacts the tissue.

Another class of terpene is the diterpenes (20 carbons) that are represented by pine resins, found in ducts throughout the stems of most pine species. Another important diterpene is the anti-cancer drug taxol, found in the bark of the Pacific Yew tree. This complex diterpene binds to microtubules and stabilizes them, resulting in an arrest of mitosis. The triterpenes (30 carbons) are large, complex structures that undergo ring condensation to form steroidal compounds and cardiac glycosides, so named because of their effects on vertebrate heart function. Several of these compounds are used to treat heart conditions, including digoxin, from the foxglove plant (Digitalis sp.) and oleandrin, from the oleander plant (Nerium oleander). Finally, the tetraterpenes (40 carbons) include latex and chicle.

N-containing compounds

Whereas representative molecules of both phenolics and terpenes are found in all plants, the nitrogenous compounds are only found in about 20% of plant species. Many nitrogenous compounds defend the plant through profound effects on the nervous system of animals, often interfering with nerve cell signaling in the central nervous system by binding to neurotransmitter receptors. Molecules such as nicotine, cocaine, heroin, and morphine are all alkaloids and act in this way. Other alkaloids such as those produced in the Nightshade family (Solanaceae) effect nerve cell signaling in the peripheral nervous system and can disrupt digestive processes of potential herbivores. In addition to the alkaloids, this class includes the cyanogenic glycosides. These potent deterrents release cyanide gas when the tissues containing the cyanogenic glycosides are ruptured.