The Role of Fungal Secondary Metabolites and sRNAs: Comparison
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Please note this is a comparison between Version 5 by Jessie Wu and Version 12 by Johannes Mapuranga.

Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant’s defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant–fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as “non-proteinaceous effectors”. Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts.

  • SMs
  • sRNAs
  • interactions

1. Introduction

Plants have developed a broad spectrum of responses to counter pathogen invasion. Likewise, plant pathogens orchestrate a highly calibrated array of pathogenicity strategies in their quest to cause diseases [1]. The recent increased availability of fungal and plant genomes in the public domain has facilitated considerable progress in molecular plant–fungal interaction studies. Using genetic techniques, pathogenicity or virulence factors have been established, and the study of these factors has increased our understanding of the interactions between pathogens and their hosts. During interaction with their hosts, fungal plant pathogens secrete many proteins known as effectors which manipulate the physiology of the host or suppress the host’s immunity to promote infection [2][3]. Most studies on effectors have focused almost exclusively on secreted proteins, without exploring the possibly equivalent functions performed by fungal secondary metabolites (SMs) (chemical effectors) and sRNAs (sRNA effectors) which are collectively referred to as non-proteinaceous effectors [2][4]. Accumulating evidence has indicated that, pathogens use sRNAs (such as siRNAs and microRNAs) and SMs to manipulate host cell functions [5][6]. Fungal SMs and sRNAs have been shown to manipulate host defense-related genes in the same was as proteinaceous effectors [7][8]. In general, SM and sRNA effectors are increasingly becoming important targets for studying the pathogenesis mechanisms of fungal pathogens [9]. It is thus important to adopt new experimental methods to elucidate the in-planta biology of SM and sRNA effectors. 

2. Fungal Secondary Metabolites Enhance Pathogenicity during Plant-Fungal Pathogen Interactions 

Fungal SMs are not required for the growth and development of the fungus, but they have the potential to improve the pathogen’s fitness under certain conditions. Fungal SMs are often divided into polyketides, terpenes, non-ribosomal peptides and alkaloids on the basis of the primary enzymes and precursors that are involved in their biosynthesis [10][11]. The existence of fungal SMs, which have no discernible effect on the viability of the producer, raises issues about their potential influence on the environment [12]. SMs production by fungal pathogens and the presence of a host protein that is specifically susceptible to the corresponding toxin determines the ability of the pathogen to infect the host plant. Because host-specific toxin targets are encoded by plant genes, such genes can be referred to as dominant susceptibility genes [13]. Accumulating evidence indicates that fungal SMs serve as avirulence factors, host defense suppressors, and fungal cell wall hardening factors [8][14]. Fungal SMs are most effective during the early stage of infection (biotrophic phase), enhancing the fungus’ ability to penetrate and colonize its host without killing its host [2]. Fungal SMs can be host specific or non-host specific and generate necrosis in plant tissue. The majority of the fungal SMs have not been defined chemically, and the plants that they are intended to affect are still a mystery. The biological actions that have been reported to be caused by fungal SMs generated in-planta suggest that they have a broad range of plant cellular targets. The production and transport of proteins are targets of a wide range of fungal SMs [15][16]. For example, the mycotoxin deoxynivalenol (DON), a member of the type B trichothecenes, produced by Fusarium spp., inhibits protein biosynthesis by binding to the ribosome, resulting in cell signaling, differentiation, reproduction and even teratogenicity disorders in eukaryotes [17]. Cochliobolus species were reported to produce host-specific toxins that enhance pathogen virulence. Victorin, a non-ribosomal peptide produced by Cochliobolus victoriae, is a virulence factor that enhances pathogenicity by inducing PCD during infection of only oat cultivars harboring susceptible genes [18]. HC-toxin, a non-ribosomal peptide produced by Cochliobolus carbonum induces histone hyperacetylation through the inhibition of histone deacetylases, during the infection of only maize varieties harboring susceptible genes [19][20]. Transcriptional activation of host plant defense genes is altered by such histone modifications, thereby enhancing pathogen virulence [20][21]. Alternaria alternata have various pathotypes that produce different host specific toxins that are active only on their corresponding susceptible hosts [22]. Some host specific toxins including destruxin which is produced by Alternaria brassicae are also essential for pathogens in susceptible host plants. A. alternata also produces AAL-toxin, an SM which enhances pathogenicity in tomato varieties harboring susceptible genes by inhibiting ceramide synthase. This will lead to free phytosphingosine and sphinganine accumulation followed by the disruption of plasma membrane [23]. 

3. Small non-coding sRNAs— - The Secret agents in Plant-Fungal Pathogen Interactions 

Plant immune responses are tightly regulated by an array of immunity-associated regulators such as sRNAs and some transcription factors [1724]. Based on their biogenesis and structural features, sRNAs can be classified into three categories: short-interfering RNAs (siRNAs), dicer-independent microRNAs (miRNAs) and dicer-independent piwi interacting RNAs (piRNAs) [1825][1926]. The fundamental sRNA pathway components and other various sRNAs function as critical gene expression regulators to fine-tune the immunity of some cereal plants such as wheat and rice against pathogen invasion [1724]. Normally, when a pathogen attacks its host, these sRNAs are either upregulated or downregulated in order to inhibit expression or to release suppression of their targets [5][2027]. Thus, plant endogenous sRNAs and sRNA pathway components play key roles in regulating and fine-tuning host immune responses to pathogens such as fungi, bacteria, and oomycetes [2128]. Accumulating evidence indicates that sRNAs produced by fungal pathogens can function as effector molecules, modulating host gene expression as a counter-defense mechanism (Table 1).
Table 1. Fungal sRNA effectors and their target genes in cross-kingdom interactions.
sRNA sRNA Origin Target Origin Target Genes Function Reference
miR408 Puccinia striiformis f. sp. tritici (Pst) T. aestivum CLP1 Negatively regulates host immune response by suppressing the expression of CLP1. [2229]
Pst-milR1 Pst T. aestivum PR2 Represses plant innate immune response by suppressing the expression of PR2. [7]
Pst-milR1 Pst T. aestivum SM638 Innate immunity. [7]
pt-mil-RNA1 Pt T. aestivum TCP14, CYB5R, and EF2 Suppresses wheat defense response to Pt by targeting wheat TCP14, CYB5R and EF2. [1825]
pt-mil-RNA2 Pt T. aestivum TCP14, CYB5R and EF2 Suppresses wheat defense response to Pt by targeting wheat TCP14, CYB5R and EF2. [1825]
miR398 Bgh Barley HvSOD1 Negatively regulates host immunity by repressing HvSOD1 accumulation. [2330]
miR9836 Bgh Barley MLA1 Dampens immune response signaling triggered by host MLA immune receptors. [2431]
Fg-sRNA1 F. graminearum Chinese spring wheat TaCEBiP Suppresses wheat defense response by targeting and silencing TaCEBiP. [2532]
Fol-milR1 Fusarium oxysporum Tomato SlyFRG4 Suppresses host immunity by silencing SylFRG4. [2633]
Osa-miR167d M. oryzae Rice ARF12, WRKY45 Negatively regulates host immunity by downregulating AR12 expression. [2734]
miR156 M. oryzae Rice SPL14 Enhances host susceptibility by suppressing the expression of SPL14 and WRKY45. [2835]
Osa-miR164a M. oryzae Rice OsNAC60 Negatively regulates host immunity by suppressing OsNAC60 expression. [2936]
miR168 M. oryzae Rice AGO1 Negatively regulates host immunity by suppressing AGO1 expression. [3037]
Osa-miR169 M. oryzae Rice NF-YAs Enhances host susceptibility by suppressing the expression of nuclear factor N-Y (NF-YA) genes. [3138]
miR319 M. oryzae Rice TCP21 Negatively regulates host immunity by suppressing TCP21 expression. [3239]
miR396 M. oryzae Rice OsGRFs Negatively regulates host immunity by suppressing the expression of OsGRFs. [3340]
Osa-miR439 M. oryzae Rice Predicted target genes LOC_Os01g23940, LOC_Os01g36270, LOC_Os01g26340 and LOC_Os06g19250 Enhances host susceptibility by suppressing the expression of predicted target genes LOC_Os01g23940, LOC_Os01g36270, LOC_Os01g26340 and LOC_Os06g19250. [3441][3542]
miR444b.2 M. oryzae Rice MADS-box family genes Negatively regulates host immunity by suppressing the expression of MADS-box family genes. [3643]
siR109944 Rhizoctonia solani Rice FBL55 Suppresses host immunity to sheath blight. [3744]
Bc-siR3.2 Botrytis cinerea (B. cinerea) A. thaliana MPK1, MPK2 Suppresses MPK1, MPK2 function in plant immunity. [3845]
Bc-siR3.1 B. cinerea A. thaliana PRXIIF Suppresses PRXIIF genes. [3845]
Bc-siR3.2 B. cinerea Solanum lycopersicum MAPKKK4 Suppresses MAPKKK4 function. [3845]
Bc-siR5 B. cinerea A. thaliana WAK Suppression the function WAK genes. [3845]
Bc-siR37 B. cinerea A. thaliana WRKY7, PMR6 and FEI2 Suppresses plant immunity by repressing the expression of WRKY7, PMR6 and FEI2. [3946]
PR2—Pathogenesis-related 2 gene, TCP14—Transcription factor, CYB5R—Cytochrome b5 reductase, EF2—Elongation factor 2, TaCEBiP—Chitin elicitor binding protein, SlyFRG4—CBL-interacting protein kinase, MPK—Mitogen-activated protein kinases, MAPKKK—Mitogen activated protein kinase kinase kinase, PRXIIF—peroxiredoxin-2F, WAK—Cell wall-associated kinase, PMR—powdery mildew resistance, FEI (named after the Chinese word corresponding to fat)—leucine-rich repeat receptor-like kinases.

4. Cross-Kingdom RNAi Interference during Plant-Fungal Pathogen Interactions

During pathogen infection, the host’s sRNA performs an endogenous role by regulating gene expression in order to maintain a healthy balance between plant development and immunity [4047][4148]. sRNAs can direct the transcriptional and post-transcriptional silencing of gene expression, and this phenomenon is known as RNA interference (RNAi). Post-transcriptional gene silencing is a mechanism through which plant miRNAs contribute to resistance by regulating the expression of defense-related genes [4249][4350]. The phenomena of cross-kingdom RNAi occurs when gene silencing is induced between unrelated species from different kingdoms, like a plant host and its interacting pathogen (Figure 1). It necessitates the translocation of a gene-silencing trigger from a donor into an interacting recipient. Several studies have reported interactions with other species in plant and animal systems through cross-kingdom RNAi [2128][4451]. sRNAs generated by pathogens and parasites, on the other hand, may also translocate into host cells and induce host gene silencing [3845][4451][4552]. This implies that sRNA transfer is bidirectional; plant-derived sRNAs serve as defense weapons to disrupt fungal pathogenicity genes, while pathogen-derived sRNAs act as offensive weapons to suppress host plant defense mechanisms.
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Figure 1. Cross-kingdom RNAi and vesicle trafficking during plant-fungal pathogen interactions. Fungal and plant sRNAs trigger cross-kingdom RNAi during plant-pathogen interactions. Fungal sRNAs translocate into plant cells and hijack the host plant Argonaute (AGO) protein of the RNAi machinery to suppress host plant immune response. The fungal sRNAs are upregulated upon infection (indicated by green arrow). Host cells also can deliver sRNAs into pathogen cell, either host induced gene silencing (HIGS) sRNAs or endogenous sRNAs, to target virulence genes and other essential pathogen genes. The generation of multivesicular bodies and release of exosomes at the site of pathogen invasion is part of the host penetration resistance pathway. Among other molecules, the putative exosomes contain sRNAs that can target vesicle trafficking components of the pathogen. Exosomes can also inhibit fungal growth and stall further ingress. The production of pathogen-derived sRNAs that may target and silence host genes can be inhibited by this form of host plant immunity. The fungal pathogens also secrete proteinaceous effectors through the haustorium into the host cells to suppress the host immunity genes, thereby causing disease. How fungal pathogens transport proteinaceous effectors and sRNAs into their host cells is still elusive. On the other hand, plants secrete extracellular vesicles to transport host sRNAs into pathogens to silence fungal genes involved in pathogenicity. Passage of host sRNAs through the haustorial cell wall, either active or passive, occurs and once inside the fungal haustorium the silencing molecules trigger RNAi of their mRNA targets, and may act as primers in the fungal silencing pathway, leading to the generation of systemic silencing signals. Cell structures are not drawn to scale.
Since the discovery of RNAi in Neurospora, sRNAs from numerous fungal species have been studied [4653]. The most well-known example of cross-kingdom RNAi from a plant to its interacting pathogen is HIGS, which occurs when a plant-produced RNAi signal triggers the silencing of a pathogen gene [4754]. RNase III-like endonucleases known as Dicers produce sRNAs from hairpin-structured or double-stranded RNA [4855]. The mature sRNAs are loaded into AGO proteins to form the RNA-induced silencing complex (RISC) [5][4956]. The RISC is responsible for silencing genes that contain sequences complementary to sRNAs. By using the component of the host RNAi machinery known as AGO1, the transfer of B. cinerea sRNA into Arabidopsis cells silenced the host’s immune genes [3845]. Fungal sRNAs can suppress host plant immunity by interfering with the RNAi pathways of the host [7][3845][3946]. During tomato and Arabidopsis infection, the most prevalent sRNAs that function as effectors factors to enhance pathogen virulence are Bc-siR3.1, Bc-siR3.2, and Bc-siR3.5 which target the host mitogen-activated protein kinases MPK1, MPK2 and MPKKK4, peroxiredoxin (PRXIIF), and cell wall-associated kinase (WAK), respectively [3845]. These pathogen-derived sRNAs target components of host plant immunity such as oxidative burst and signal transduction pathways; hence, silencing of these targets will enhance pathogen virulence and compromise resistance to the fungal pathogens [3845]. 
A group of fungal in-planta secreted sRNAs was also identified from the sequencing of sRNAs from Sclerotinia sclerotiorum during infection of Arabidopsis and Phaseolus vulgaris [5057]. The pathogen-derived sRNAs were predicted to target quantitative disease resistance-associated genes of the host and suppress host plant immunity [5057]. Mutations of two sRNA targets that encode kinase genes SERK2 and SNAK2 enhanced pathogen virulence and compromised host plant resistance, indicating that the sRNAs’ targets are involved in disease resistance [5057]. Analysis of Pst-infected leaves established that Pst is capable of suppressing the host’s defense and immunity genes as well as its endogenous genes by producing many sRNAs [6]. Fungal sRNAs can target and silence plant transcripts involved in defense, but sRNAs from plants can target and silence transcripts produced by pathogens [5158][5259]. A novel Pst miRNA (Pst-milR1) participates in cross-kingdom RNAi events in wheat by binding the pathogenesis-related 2 (PR2) gene, which may suppress the host-mediated defense mechanism in its counter defense. Silencing of the Pst-milR1 precursor using host induced gene silencing resulted in reduced Pst virulence and increased wheat resistance to the Pst isolate CRY31. Therefore, Pst-milR1 is a key pathogenicity factor in Pst, which functions as an effector to suppress host immunity [7]. Fg-sRNA1 produced by F. graminearum targets and silences wheat TaCEBiP (Chitin Elicitor Binding Protein), a pattern recognition receptor gene. F. oxysporum f. sp. lycopersici produces Fol-milR1, an sRNA effector that suppresses host immunity by targeting the tomato protein kinase SlyFRG4 via AGO4a, thus providing a novel pathogenicity strategy to achieve infection [2633]. Accumulating evidence shows that miRNAs serve crucial roles in regulating the expression of their target genes accurately and effectively during the interactions between rice and M. oryzae. Understanding the functions of rice miRNAs is crucial for managing rice blast. miR398b coordinates various pathways to increase the accumulation of H2O2 through numerous Superoxide Dismutase (SOD) family genes [60], thereby positively regulating rice defense responses to M. oryzae [50]. 

5. Applications of Cross-Kingdom RNAi Technology

Several studies have demonstrated RNAi-based fungal pathogen management with an average plant disease resistance of approximately 60% [61]. Cross-kingdom RNAi was initially studied to generate disease resistance in barley and wheat against B. graminis, the powdery mildew fungus, using HIGS, an RNAi-based approach [62]. The HIGS technique for controlling pathogens including fungi and viruses, among other plant pests, was developed with help from plant immune system’s RNA silencing machinery against viruses [62][63][64]. To silence pathogen target genes, the HIGS employs RNAi by producing sequence-specific dsRNAs in the host plant. A hairpin-structure dsRNA construct which targets a specific gene is transformed into the host plant. dsRNAs and siRNAs produced by the transgenic plant are taken up by corresponding plant pathogens during host-pathogens interactions. These siRNAs target and degrade pathogen mRNAs, hence protecting the host plant against pathogen infection [65][66]. HIGS technology has been widely adopted in plant breeding programmes as an efficient approach to enhance plant defense responses to pathogens. Obligate biotrophic fungal pathogens, Blumeria graminis f. sp. tritici (Bgt) and Bgh cause severe powdery mildew in wheat and barley, respectively. Bgh effector Avra10 and MLa10, a disease resistance gene in barley, were used to perform a proof-of-concept for HIGS [62]. Avra10 is an important Bgt pathogenicity factor. However, recognition of Avra10 by barley MLa10 triggers hypersensitive response in the host plant, resulting in suppression of biotrophic pathogen invasion [62][67]. Avra10 silencing on barley leaves exhibited attenuated pathogen development without MLa10, but not with it [62].
HIGS technique was also used in transgenic wheat plants to combat the rust pathogens Pst, and Pt [68][69][70]. Zhu and colleagues generated transgenic wheat-derived dsRNAs targeting PsFUZ7, a MAP kinase, which contributes to Pst pathogenicity by regulating the morphology and development of hyphae [68]. Strong resistance to Pst infection was exhibited by transgenic lines stably expressing dsRNA constructs by degrading PsFUZ7 transcripts, leading to the suppression of pathogen growth and development [68]. HIGS induced by barley stripe mosaic virus (BSMV)-VIGS (virus-induced gene silencing) was established to be a robust, high-throughput approach for the functional analysis and validation of rust fungi candidate genes involved in pathogenicity through quantitative estimation of infection-related traits [67]. It was discovered that wheat and barley plants that generated dsRNA or anti-sense RNA fragments, both of which were intended to alter gene expression in the fungus, silenced the fungal genes [62]. Hairpin RNAi constructs with sequence similarity to MAP kinase1 (PtMAPK1) or Cyclophilin1 (PtCYC1) silenced the respective fungal genes and conferred resistance to leaf rust pathogen Pt [69]. It was revealed that, the silencing signals in the Puccinia-wheat pathosystems are most likely host cell-derived siRNA molecules [71]. Using site specific analysis, a recent study revealed putative cross-kingdom sRNAs, tRNA and rRNA fragments, and some signs of fungal phasing in the barley-Bgh interactions [72]. This was the first research to report on phased short RNAs (phasiRNAs) in Bgh, a trait normally associated with plants that may be involved in the post-transcriptional regulation of fungal coding genes, pseudogenes, and transposable elements [72].
Fusarium head blight (FHB) caused by the fungi F. graminearum and F. culmorum is another destructive disease of wheat and barley [73][74]. Koch and colleagues generated transgenic Arabidopsis and barley plants expressing dsRNA against three CYP51 paralogous genes that are essential in the ergosterol biosynthesis pathways [75]. Inhibitors of sterol demethylation, which act on the CYP51 paralogs, are the most extensively used systemic fungicides for controlling fungal pathogens. Increased resistance to F. graminearum infection was shown after the transgenic expression of the three paralogous genes in two different plant systems [75]. The expression of three hairpin RNAi constructs in wheat transgenic lines also silenced chitin synthase (Chs) 3b, a F. graminearum pathogenicity factor, and these lines exhibited firm and consistent resistance to Fusarium seedling blight (FSB) and FHB over T3-T5 generations [76]. Fungal infection on wheat ears and seedlings was significantly reduced by the expression of dsRNAs with sequence homology to F. graminearum Chitin synthase Ch3b [76]. Transient HIGS in wheat and targeting an important housekeeping gene in Bg led to considerable decrease in virulence during early infection stages [77]. Rice blast is one of the most devastating rice diseases caused by the pathogenic fungus M. oryzae [78]. Zhu and colleagues studied the effects of silencing three virulence-related genes, ABC transporter MoABC1, membrane-bound adenylate cyclase MoMAC1, and mitogen-activated protein kinase MoPMK1, during the interactions between rice and M. oryzae [79]. The resistance of rice to blast was enhanced when three BSMV silencing vectors targeting MoPMK1, MoMAC1, and MoABC1 were inoculated into the host plant at once.  Altogether, cross-kingdom-RNAi has the potential to supplement existing pathogen management strategies, for instance, by widening the resistance spectra of host resistance genes. Furthermore, using cross-kingdom-RNAi to exploit naturally occurring RNA exchanges may open up new avenues for crop improvement through genetic engineering and classical breeding.

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