Effector Proteins in Plant–Microbe Interaction

Oomycete and fungal interactions with plants can be neutral, symbiotic or pathogenic with different impact on plant health and fitness. Both fungi and oomycetes can generate so-called effector proteins in order to successfully colonize the host plant. These proteins modify stress pathways, developmental processes and the innate immune system to the microbes’ benefit, with a very different outcome for the plant. Investigating the biological and functional roles of effectors during plant–microbe interactions are accessible through bioinformatics and experimental approaches which can broaden our knowledge about structural biology, sequence motif and domain knowledge of effector proteins from filamentous microbes.

effector proteins;oomycetes;fungi;symbiotic filamentous species;pathogenic filamentous species;plant-microbe interaction

1. All Lifestyles of Filamentous Microbes Use Effector Proteins to Establish Colonization

Oomycetes and fungi are filamentous eukaryotic organisms. In contrast to fungi that contain species of symbiotic and pathogenic lifestyle, oomycete species are mostly limited to a pathogenic lifestyle. Nevertheless, some oomycetes of the Pythium class are considered beneficial to plants and are in use as bio-control organisms. Examples are Pythium olingandrum and Pythium periplocum, which are known to be mycoparasites that antagonizes fungal plant pathogens [1][2][33,34].
Until recently, effector proteins have been studied mainly in context with pathogenic fungi and oomycete species. Nevertheless, recent advances have shown that symbiotic organisms such as endophytes and mutualistic microorganisms also secrete effector proteins [3][4][35,36] (Table 1). According to Rovenich et al., 2014 effector proteins contribute to niche colonization and most likely to microbial competition [5][29]. In mutualistic connections, identical to pathogenic invasions, the microorganism is identified by the plant’s recognition system and needs solutions to evade the plant’s immune strategies to maintain a mutual beneficial connection [6][37]. Apoplastic secreted effectors, such as secreted proteins (SP’s), β-glucan, [7][38] or RiSLM that binds to chitin [8][39], are known to play a role in early establishment of mycorrhiza–plant interaction. Recently, effectors translocated into the host’s cytosol originating from symbiotic fungi become more and more the focal point of ongoing research (Table 1) and we start to understand that oomycetes and fungi of all lifestyles use effector proteins to establish an interaction with the host plant [9][10][40,41]. This includes translocated effector proteins containing RxLR motifs and crinklers (CRN’s), which will be reviewed in more detail in the next chapter. Effectors are likely to be used by plant growth promoting fungi to limit the activation of the plant’s immune system by decreasing the amount of specific MAMPs recognized by the plant’s PRRs. However, many questions remain unresolved about the molecular mechanisms governing mycorrhiza–plant interaction—with one being how they can establish interaction with such a broad host spectrum. Future research in this field will need to establish collaborative approaches, combining ecology (bigger picture), molecular interaction studies of microbe and host on the cellular level (organismal and cell level) and protein biochemistry approaches (molecular level) to resolve these important questions.
Table 1.
 List of effector proteins identified for beneficial fungi, their host species and biological function.
Effector Protein Fungal Species Host Species Characterized Biological Function References
SP7 Glomus intraradices Medicago truncatula Interacts with JA/ethylene inducible ERF19 transcription factor and down regulates PTI [8][39]
Lysm effector Tal6 Trichoderma atroviride Arabidopsis thaliana Binds to chitin of plant’s cell wall and protects the fungi hyphae from plant’s chitinase favoring Trichoderma interaction and increasing mycoparasitic effect [11][42]
][23][50,51]. More recently, it has been hypothesized that the RxLR motif is cleaved before translocation into the plant cell and only a mature effector protein containing the C-terminal effector domain is delivered into the host cell [24][52]. The RxLR motif is often followed by a downstream (D)EER motif (Glu-Glu-Arg) located within 40 AA after the signal peptide, which is also linked to the effector translocation [22][25][50,53]. The effector proteins of Phytophtora species such as P. infestans (Avr3a and PexRD2), P. capsici (Avr3a11) and downy mildews such as Hyaloperonospora arabidopsis (Hpa; Atr1) also contain a WY or WL motif, which forms an alpha-helix [26][54]. The motif, identified by analyzing the crystal structure of PexRD2, is comprised of two hydrophobic residues buried inside the protein core that contribute to interactions with host target proteins. WY-containing effectors and their structures have been recently reviewed in detail by Mukhi, et al. 2020 [26][54]. Other RxLR effectors have been shown to interact with their targets in the cellular endomembrane system, including P. infestans’s effector protein Pi03912 and Bremia Lactucae’s effector proteins BLR05 and BLR09 that interact with NAC transcription factors located in endoplasmic reticulum [27][28][55,56].
Translocated CRN effector proteins are distributed in nearly all pathogenic oomycetes and have been shown to be translocated by fungi of pathogenic and beneficial lifestyle. CRN’s share two conserved motifs in their N-terminal region, the LxLFLAK (Leu-Xaa-Leu-Phe-Leu-Ala-Lys) motif and the HVLVVVP (His-Val-Leu-Val-Val-Val-Pro) motif. The LxLFLAK motif is, comparable to the RxLR, associated with the translocation of the effector in to the host cell [29][30][57,58]. CRNs, initially identified through their ability to cause crinkling and necrosis upon expression in plant tissue are not typified by this characteristic. In fact, expression of CRNs leads to cell death only in a select few cases. So far, CRNs are less well studied than RxLRs [29][30][57,58].
Fungal species have further effector proteins with various effector motifs including but not restricted to, lysin (LysM), DELD, RSIDEDLD, RGD and the EAR (ethylene-responsive element binding factor-associated amphiphilic repression) motif.
Furthermore, most MAX effectors (Magnaporthe AVRs and ToxB- like effectors) so far have been identified to be translocated, contributing to the virulence of pathogenic fungi. These effectors contain a β-sandwich fold, showing similarities to the apoplast secreted Pyrenapohora tritici-repentis ToxB. This group of effectors have at least one disulfide bond with variable AA on their protein surface, which mediates their target interaction [31][32][59,60]. RALPHs (Rnase-like proteins expressed in haustoria) are another group of fungal translocated effectors discovered in pathogenic fungi, including the Blumeria graminis effector BEC1054. RALPHs block the function of the host’s ribosome, inactivating proteins and suppress the host cell death [33][61]. The flax rust effector AvrP is considered an HESP (haustorial expressed secreted protein) that does not contain an RxLR and the translocation mechanisms in the host cell is not clear to date. Nevertheless, it is one of the few effector proteins with a known structure. It contains Zn-finger like motifs and three Zn- binding sites. The Zn-finger motifs are necessary for maintaining the integrity of the effector protein and cell death activity [34][62]. Other structurally resolved fungal and oomycete effector proteins are presented in Table 2.
Table 2. Summary of structurally resolved effector proteins available in PDB-deposited structures [35].
 Summary of structurally resolved effector proteins available in PDB-deposited structures [63].
Effector Protein Organism Date of Release Method PDB Entry Family
Ecp11-1 Passalora fulva 4 August 2021 X-ray 6ZUS LARS
Lysm effector RiSLM Rhizophagus irregularis Medicago truncatula Binds to chitin and chitooligosaccharides of plant’s cell wall and interferes with chitin-triggered immune response protecting hyphae from plant’s chitinase and enabling symbiotic reactions [12][43]
APikL2A Magnaporthe oryzae 24 March 2021 X-ray 7NLJ MAX Laccaria bicolor
APikL2FPopulus trichocarpa Suppresses JA-mediated immune response by preventing JA-dependent degradation of PtJAZ6, a negative regulator of JA-induced genes Magnaporthe oryzae 24 March 2021 X-ray[13][44]
7NMM MAX RiCRN1 Rhizophagus irregularis Medicago truncatula Nicotiana benthamiana Establishes a functional AM symbiosis and Arbuscules phosphate transporter gene-MtP4-expression
AVR-PikD Pyricularia oryzae[ 17 Februrary 202114] X-ray[45]
7BNT MAX Strigolactone induced secreted protein 1 (SIS1) Rhizophagus irregularis Medicago truncatula Essential for AM symbiosis, gene silencing causes suppression of colonization and production of stunted arbuscules
AVR-PikF Pyricularia oryzae 3 February 2021[15][25]
X-ray 7B1I MAX RP8598 and RP23081 Rhizophagus proliferus Medicago truncatula Nicotiana benthamiana Allium schoenoprasum
AVR-PikCInteracts with JA/ethylene inducible ERF19 transcription factor and down regulates PTI Pyricularia oryzae[16] 3 February 2021[22]
X-ray 7A8X MAX Nuclear localizing effector (RiNLE1) Rhizophagus irregularis Medicago truncatula Interferes with mono-ubiquitination of 2B histone and decreases the expression of defense-related genes while enhancing AM colonization process [17][46]
SnTox3 Parastagonospora nodorum 4 November 2020 X-ray 6WES MAX Hydrophobin-like OmSSP1 Ericoid mycorrhiza
Zt-KP6-1Vaccinium myrtillu Zymoseptoria triticiMutants are unable to colonize V. myrtillu roots and OmSSP1 may strengthen the attachment of the fungi to the root protecting the hyphae from plant’s immune system [18][ 4 March 202026]
X-ray 6QPK LysM PIIN_08944 Piriformospora indica
MLP124017 Melampsora larici-populinaArabidopsis thaliana Mutants show delayed colonization and PIIN_08944 expression reveals impairment of SA-defense pathway and reduced expression of flg-22 [ 18 December 201919 Solution NMR][47]
Did1 (PIIN_05872) Piriformospora indica - Interferes with iron-mediated defense response which plays an important role in ROS generation [20][48]

2. Effector Proteins of Filamentous Microbes

Most of our knowledge on effector protein function, motifs, domains and structures derives from pathogenic species rather than beneficial and symbiotic species. Compared to oomycetes, identification of motifs and domains involved in delivering cytoplasmic effectors has been particularly challenging for fungi due to less clear sequence conservation. Nevertheless, fungi and oomycetes have been shown to translocate RxLR/RxLR-like effectors and CRNs into the host cell [10][41]. Oomycetes contain a particularly high number of RxLR effector proteins, which are likely to be secreted via the haustoria during plant–oomycete interaction [21][49]. RxLR effector proteins are composed of an N-terminal signal peptide responsible for effector secretion, followed by a highly conserved RxLR (Arg-Xaa-Leu-Arg) motif. This motif has been proposed to be in charge of the translocation of the effector protein into the host cell [22
Cys knot, NTF2-like fold
Zymoseptoria tritici
16 October 2019
X-ray 6Q40 LysM
AVR-Pia Pyricularia oryzae 10 July 2019 X-ray 6Q76 MAX
AvrPib Pyricularia oryzae 5 September 2018 X-ray 5Z1V MAX
MlpP4.1 Melampsora larici-populina 22 August 2018 Solution NMR 6H0I Cys knot, NTF2-like fold
Avr4 Passalora fulva 22 August 2018 X-ray 6BN0 Chitin-binding
PIIN_05872 Piriformospora indica 2 May 2018 X-ray 5LOS DELD
BEC1054 Blumeria hordei 20 June 2018 X-ray 6FMB RALPH
AVR-PikE Pyricularia oryzae 13 June 2018 X-ray 6G11 MAX
AVR-PikA Pyricularia oryzae 3 June 2018 X-ray 6FUD MAX
AvrP Melampsora lini 30 August 2017 X-ray 5VJJ Zn-binding
Avr2 Fusarium oxysporum 16 August 2017 X-ray 5OD4 ToxA/TRAF
PevD1 Verticillium dahliae 5 July 2017 X-ray 5XMZ C2-like
Avr4 Pseudocercospora fuligena 29 June 2017 X-ray 4Z4A Chitin-binding
AVR1-CO39 Magnaporthe oryzae 14 October 2015 Solution NMR 2MYV MAX
Prp5 Saccharomyces cerevisiae 11 December 2013 X-ray 4LK2 DEAD-box
AvrLm4-7 Leptosphaeria maculans 11 December 2013 X-ray 2OPC LARS
AvrM Melampsora lini 16 October 2013 X-ray 4BJM RXLR-like
AvrM-A Melampsora lini 16 October 2013 X-ray 4BJN RXLR-like
Ecp6 Passalora fulva 17 July 2013 X-ray 4B8V LARS
AvrPiz-t Pyricularia oryzae 12 September 2012 Solution NMR 2LW6 MAX
AvrL567-D Melampsora lini 30 October 2007 X-ray 2QVT RXLR-like
AvrL567-A Melampsora lini 6 March 2007 X-ray 2OPC RXLR-like
Avr1d Phytophthora sojae 17 March 2021 X-ray 7C96 RXLR
PsAvh240 Phytophthora sojae 6 February 2019 X-ray 6J8L RXLR/WY
SFI3 Phytophthora infestans 5 December 2018 X-ray 6GU1 RXLR/WY
PcRXLR12 Phytophthora capsici 15 August 2018 X-ray 5ZC3 RXLR/WY
PSR2 Phytophthora sojae 16 August 2017 X-ray 5GNC RXLR/WY
Avr3a Phytophthora infestans 11 January 2017 Solution NMR 2NAR RXLR/WY
PexRD54 Phytophthora infestans 3 August 2016 X-ray 5L7S RXLR/WY
ATR13 Hyaloperonospora parasitica 18 January 2012 Solution NMR 2LAI RXLR
AVR3a4 Phytophthora capsici 3 August 2011 Solution NMR 2LC2 RXLR
PexRD2 Phytophthora infestans 3 August 2011 X-ray 3ZRG RXLR/WY
Avr3a11 Phytophthora capsici 3 August 2011 X-ray 3ZR8 RXLR/WY
ATR1 Hyaloperonospora parasitica 20 July 2011 X-ray 3RMR RXLR/WY
Interestingly, even though filamentous effector proteins have been studied and defined extensively with genetic and molecular biology approaches, available protein structures are very limited (Table 2). Structural information is very valuable for elucidating the molecular mechanisms behind biological and biochemical functions. It is complimentary to genetic and molecular biology methods, giving a molecular explanation for observations seen in these studies and seeding hypothesis for further of these studies. In addition, the fundamental molecular level insights ultimately help link genome and sequence information to function and aiding improvements in effectome prediction. Considering the importance of effector molecules during infection processes of plants, but also of humans and animals, it is surprising that effector proteins have not been studied more intensively. This in part may be due to experimental challenges with structure elucidation, including the membrane-associated nature of many effector proteins and the potentially dynamic nature of their different molecular interactions along the infection/colonization cycle. Nonetheless, structures and their detailed molecular function, are a significant knowledge gap and that is true for oomycete as much as for fungal effectors.