Humboldt Review
Recognition and defence of plant-infecting fungal pathogens

https://doi.org/10.1016/j.jplph.2020.153324Get rights and content

Abstract

Attempted infections of plants with fungi result in diverse outcomes ranging from symptom-less resistance to severe disease and even death of infected plants. The deleterious effect on crop yield have led to intense focus on the cellular and molecular mechanisms that explain the difference between resistance and susceptibility. This research has uncovered plant resistance or susceptibility genes that explain either dominant or recessive inheritance of plant resistance with many of them coding for receptors that recognize pathogen invasion. Approaches based on cell biology and phytochemistry have contributed to identifying factors that halt an invading fungal pathogen from further invasion into or between plant cells. Plant chemical defence compounds, antifungal proteins and structural reinforcement of cell walls appear to slow down fungal growth or even prevent fungal penetration in resistant plants. Additionally, the hypersensitive response, in which a few cells undergo a strong local immune reaction, including programmed cell death at the site of infection, stops in particular biotrophic fungi from spreading into surrounding tissue. In this review, we give a general overview of plant recognition and defence of fungal parasites tracing back to the early 20th century with a special focus on Triticeae and on the progress that was made in the last 30 years.

Introduction

For adapted fungal pathogens, plants represent a source of nutrients and provide a favourable environment for parasitic growth. In the past, plant breeders could only distinguish between crops displaying disease symptoms and those lacking symptoms upon pathogen attack. Today we know that when pathogens attempt host infection, they face the plant immune system. But even before the advent of modern genetics and molecular biology, phytopathologists had described the existence of variable races of fungal phytopathogens with differential infection phenotypes on individual host lines and had observed that radiation can affect disease outcomes by eliciting inheritable changes in host and pathogen genes (Anderson and Hart, 1956; Bridgmon and Wilcoxson, 1959; Caldecott et al., 1959; Flor, 1942, 1960). Because of their economic importance, studies of crops and crop pathogens were of particular interest in the middle of the 20th century. These studies led to the conceptualization and development of the first near-isogenic lines with specific resistance traits and ultimately the onset of cereal crop genetics (Briggle, 1969; Day, 1966; Dyck and Samborski, 1968; Flor, 1956; Moseman and Schaller, 1960).

The ability to genetically manipulate plants and the development of model plants later laid the groundwork for a clearer elucidation of what occurs at the molecular level when a plant becomes infected with fungi. The basic principles of molecular plant-microbe interactions were largely elucidated based on the results of studies from model plant-pathogen systems but are thought to be generally applicable to interactions between Triticeae and fungal pathogens.

It has been known for decades that fungal-derived components must be recognised by plant hosts as specific host responses elicited during infection were associated with reduced fungal proliferation (Esquerretugaye et al., 1979; Hadwiger and Beckman, 1980; Kogel, G. et al., 1988; De Wit and Roseboom, 1980). Some of these components, termed fungal elicitors, were biochemically purified and their actions on host cells further defined (De Wit and Kodde, 1981; Kogel, G. et al., 1991), and many of these molecules were shown to induce a host cell death response (Beardmore et al., 1983; De Wit et al., 1984; Mayama et al., 1986). Currently, microbial elicitors are generally divided into two classes. The first are so-called microbe- or pathogen-associated molecular patterns (M/PAMPs), which are molecules commonly released by a whole class of microbes including non-pathogens. The second class are referred to as effectors, which are specific to certain pathogen species or races and manipulate host components to promote the pathogen’s virulence (Jones and Dangl, 2006).

M/PAMPs are diverse molecules that include peptides and polysaccharide. M/PAMPs are usually recognised in the host apoplast through extracellular-facing transmembrane proteins such as receptor kinases (RLKs) and receptor-like proteins (RLPs) called pattern recognition receptors (PRRs) (Fig. 1) (Couto and Zipfel, 2016; Smakowska-Luzan et al., 2018). The fungal cell wall component chitin is a prominent example for a fungal M/PAMP (Felix et al., 1993; Kombrink et al., 2011; Kuchitsu et al., 1993). The first PRRs that sense chitin were isolated from Arabidopsis thaliana and rice (Kaku et al., 2006; Miya et al., 2007), and later, functional homologs were also identified in Triticeae (see section ‘Triticeae cell surface receptors that mediate Triticeae basal immunity to fungal parasites’ below). Detection of M/PAMPs by PRRs activates signal transduction across the plasma membrane and ultimately induces immune responses collectively called pattern-triggered immunity. One well-described immune response that is effective against fungal invaders involves the production and secretion of plant chitinases to limit fungal proliferation (Schlumbaum et al., 1986). Penetration of host cellular structures by fungal invaders may also be arrested by immune responses such as host cell wall strengthening including lignification and callose deposition (Bishop et al., 2002; Ellinger et al., 2013). Fungal attempts to penetrate host cells can also lead to the release of so-called damage-associated molecular patterns (DAMPs). DAMPs are host components released or produced and secreted upon cell or cell wall damage and are perceived by PRR-like proteins in the extracellular space leading to signalling outputs similar to PTI (Choi and Klessig, 2016). The perception of D/M/PAMPs may greatly contribute to resistance to infection by non-adapted pathogens (Niks and Marcel, 2009; Nürnberger and Lipka, 2005).

The fungal virulence factors now designated effectors are pathogen components that promote fungal proliferation on certain hosts (see section Effectors hijack Triticeae immunity and steer host physiology toward fungal accommodation’ below). Most effectors are proteinaceous or metabolites, and fungal effectors are sometimes described as toxins. The molecular functions of numerous fungal effectors in the host apoplast have been described in detail (He et al., 2020; Lo Presti et al., 2015), and the molecular principles underlying plant-microbe interactions suggest that at least some effectors target the microbial recognition machinery of the host downstream of D/M/PAMP recognition, i.e. they interfere with PTI (Dodds and Rathjen, 2010; Jones and Dangl, 2006). Effectors that activate cell death pathways to promote virulence have also been described, but these are specific to necrotrophic fungi, which benefit from dead host tissue (Tan et al., 2010; Wang et al., 2014a).

The localised host cell death also known as the hypersensitive response (HR) elicited during host infection with obligate biotrophic pathogens or by the infiltration of biotroph elicitors into host tissue is usually the result of effector recognition by host immune receptors encoded by host Resistance (R) genes (Cui et al., 2015; Dodds and Rathjen, 2010; Greenberg and Yao, 2004). The HR is likely heavily implicated in arresting the invasion of biotrophs because these pathogens strictly require living host cells for proliferation, as already speculated by Ward and Marshall in 1902 and Stakman in 1915 (Stakman, 1915; Ward, 1902). The termination of fungal infection by R protein function is known as race-specific resistance and also referred to as effector-triggered immunity (ETI) (Fig. 1). The genetic concept underlying ETI was first described by Harold Flor, who investigated the genetic basis of flax (Linum usitatissimum) resistance to the flax rust fungus Melampsora lini (Flor, 1942). Flor’s investigations led to development of the gene-for-gene theory, which stipulates that resistance to a specific pathogen isolate is determined by an R gene in the plant, and a corresponding Avirulence (Avr) gene in the pathogen (Flor, 1956). It has become clear that Avr genes usually encode effector proteins and that these effectors are secreted (Fig.1) by pathogens to promote pathogen proliferation on susceptible hosts e.g. to overcome basal host immune responses (i.e. PTI).

It is thought that the evolution of secreted effector proteins resembles an evolutionary response to plant basal immunity and further led to the evolution of plant R genes that often encode proteins for effector recognition (receptors). As such, the recognition specificities of R genes towards pathogen effectors and the resulting ETI are often considered an evolutionary countermeasure to adapted plant pathogens.

Because many R genes were found to encode nucleotide-binding leucine-rich repeat receptors (NB-LRRs or NLRs) the terms ‘R protein’ and ‘ETI’ are often used to specifically describe NLRs with recognition specificities towards intracellular effectors encoded at pathogen Avr genes. However, studies on the interaction of fungal pathogens of cereals and other crops have shown that R gene products are variable. For example, they can also encode receptors for the detection of apoplastic effectors (Fig.1) or have enzymatic activity that disables the virulence function of fungal effectors (e.g. detoxification of fungal toxins; see sections ‘Triticeae Resistance (R) gene products as sensors of fungal invasion’ and ‘Non-conventional Resistance genes, Susceptibility genes and major QTL’ below).

Here, we provide an overview of mechanisms underlying fungal defence in Triticeae. We highlight molecular principles of pathogen recognition and discuss advances in understanding fungal effector-mediated infection strategies. Finally, we summarize findings that give insight into how a Triticeae host terminates fungal infection. We apologize to those colleagues, who contributed to the field but whose publications have not been discussed here, because we aimed to condense available data to a digestible volume.

Section snippets

Triticeae cell surface receptors that mediate basal immunity to fungal parasites

Plants sense fungal pathogens at the cell surface/plasma membrane via PRRs (Fig. 1). Indeed, an immunogenic elicitor from Puccinia graminis f. sp. tritici was isolated already in the late 1980ies and found to specifically bind to the plasma membrane of wheat and barley cells (Kogel et al., 1988, 1991). In spite of this early demonstration, we still know relatively little about Triticeae cell surface PRRs. Some candidate PRRs have been identified in Triticeae. For instance, a candidate barley

Triticeae Resistance (R) gene products as sensors of fungal invasion

Specific lines of a certain host plant that completely lack or display only low susceptibility to an adapted pathogen are known as resistant. Already decades ago, breeding for resistant traits and the generation of near-isogenic cereal lines, also known as inbred or backcross lines, demonstrated that resistance traits can be dominantly or recessively inherited (Jorgensen, 1994; Keller et al., 2018). Mapping and cloning of dominantly inherited R genes and the molecular characterisation of their

Non-conventional resistance genes, susceptibility genes and major QTL

Although the modes of action of the majority of molecularly characterised R genes involve receptor-mediated recognition of a pathogen’s effector, genetic dissection of resistance traits has shown that a number of non-receptor-like coding R genes exist in nature (Table 3). Some of these confer gene-for-gene resistance, while others mediated broad-spectrum disease resistance. In addition, it has become clear that recessively inherited resistance traits are often associated with the disruption of

Effectors hijack Triticeae immunity and steer host physiology toward fungal accommodation

Fungal pathogens utilize so-called effector molecules to manipulate host functions for their own benefit (Fig. 1). The largest class of characterised effectors are probably effector proteins, but small RNAs and metabolites are also secreted during host infection and these molecules have been shown to act as virulence factors too.

Susceptibility factors, Achilles heels of triticeae crops

Our understanding of disease susceptibility has advanced greatly in the last 20 years and with that susceptibility became a target of breeding and targeted mutagenesis approaches (Büschges et al., 1997; Dangl et al., 2013; Engelhardt et al., 2018; Faris et al., 2010; Hückelhoven, 2005; Lapin and Van den Ackerveken, 2013; van Schie and Takken, 2014). Initially, this field of research was driven by forward genetic approaches that identified the genes underlying recessively inherited resistance

Cell autonomous and non-cell autonomous defence in Triticeae

Strikingly, we still only poorly understand what actually stops a fungus from growing on resistant plants. However, we know that tissue-wide resistance is achieved by a number of preformed metabolic antimicrobial compounds collectively called phytoanticipins (VanEtten et al., 1994). E.g. Benzoxazinoids (BXs) are phytoanticipins mostly found in grasses and their biosynthesis from indole has been thoroughly studied (Elnaghy and Shaw, 1966; Elnaghy and Linko, 1962; Niculaes et al., 2018). Biocidal

Future research

Our understanding of Triticeae pathology has advanced greatly in the last 30 years, progress, which has been largely facilitated by better genomic resources and the development of tools for functional genetics in small grain cereals (Alqudah et al., 2020; Feuillet et al., 2012; Hensel, 2020; Lin et al., 2020; Monat et al., 2019). Despite this, our mechanistic understanding of the factors that promote or hinder pathogen proliferation on a particular host genotype is still fragmented. We now have

Concluding remarks

More than hundred years of research on the interaction of fungal pathogens with Triticeae hosts revealed a treasure of fascinating mechanisms of host resistance to diseases caused by those fungi. We learned about host resistance genes, mechanisms of pathogen recognition, cellular and chemical defence. We have seen a major investment of society in supporting this research because the food supply threatened by pathogens and the biological principles underlying diseases are of socioeconomic and

CRediT authorship contribution statement

Isabel M.L. Saur: Conceptualization, Writing - original draft, Writing - review & editing. Ralph Hückelhoven: Conceptualization, Visualization, Writing - original draft, Writing - review & editing.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

I.M.L.S. is supported by the Daimler and Benz Foundation. Projects in the R.H. lab have been recently supported by the German Research Foundation (SFB924, HU886/8, HU886/11), by the Bavarian State Ministry of the Environment and Consumer Protection (TGC01GCUFuE69781), by the BASF Plant Science GmbH and by German Ministry of Economics and Energy (AIF 17221 N).

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