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![Structural representation of the post-leucine-rich repeat (PL) domain in TNLs (toll/interleukin-1 [TIR]-nucleotide-binding [NB]-leucine-rich repeat [LRR]) found in the genome of Arabidopsis thaliana. The illustration indicates the motif composition, the average length and standard deviation in amino acids between key conserved residues, and the predicted localization of six b-strands (blue arrows). A conserved phenylalanine residue (F) is embedded in the fifth b-strand. NLS = nuclear localization signal and TM = transmembrane.](profile/Cyril-Ghelder-2/publication/346982655/figure/fig8/AS:1050447951454208@1627457716403/Structural-representation-of-the-post-leucine-rich-repeat-PL-domain-in-TNLs.png)
Structural representation of the post-leucine-rich repeat (PL) domain in TNLs (toll/interleukin-1 [TIR]-nucleotide-binding [NB]-leucine-rich repeat [LRR]) found in the genome of Arabidopsis thaliana. The illustration indicates the motif composition, the average length and standard deviation in amino acids between key conserved residues, and the predicted localization of six b-strands (blue arrows). A conserved phenylalanine residue (F) is embedded in the fifth b-strand. NLS = nuclear localization signal and TM = transmembrane.
Source publication
Plants trigger appropriate defense responses, notably, through intracellular nucleotide-binding (NB) and leucine-rich repeat (LRR)-containing receptors (NLRs) that detect secreted pathogen effector proteins. In NLR resistance genes, the toll/interleukin-1 receptor (TIR)-NB-LRR proteins (TNLs) are an important subfamily, out of which approximately h...
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... we found 68 TNL-coding genes containing PL domain signatures. Among the 132 TNL-related sequences (TIR-only included), PL motifs were mainly found in TNLs that display the full canonical TIR-NB-LRR organization (Supplementary Table S1). A motif analysis carried out with these 68 sequences revealed four robust signatures spread out on the domain (Fig. 1). The first motif starts immediately after the LRR domain and contains conserved proline (P) and phenylalanine (F) residues embedded in a characteristic P-x-[YEW]-F signature. The second motif, predicted to form a b-strand, displays a conserved cysteine (C) followed by hydrophobic residues. As for motif 2, motifs 3 and 4 are included in ...
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... included in predicted b-strands and harbor conserved histidine (H) and cysteine-glycine (CG), respectively. The secondary structure analysis revealed a conserved structure that is exclusively made of b-strands (six in total) mainly localized inside and between motifs. The alignment also revealed a conserved phenylalanine within the fifth b-strand (Fig. 1). The core PL domain (i.e., containing motifs 1 to 4) is made of 130 aa, on average (standard deviation = 9.45 aa). However, the majority of PLcontaining sequences also harbor size-variable and polymorphic extra C-terminal peptide chains (>30 aa), which we did not consider as a part of the core PL domain, and that are predicted to code ...
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... structural annotation of TNLs showed that the majority (74%) of PL-containing TNLs (TNLPs) do not contain introns between the end of the LRR-encoding exon and the start of the PL-coding exon (Fig. 1, main structural model; Supplementary Table S2). This feature has probably helped to avoid loss of exon coding for PL domains during duplication events, which is a frequent process occurring in TNLs. Interestingly, a small subset of TNLs harbors independent PL-coding exons, among which we found all the executor TNLs or TNL-Bs, as ...
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... the Golden Gate kit from The Sainsbury Laboratory (Norwich, U.K.) ( Engler et al. 2014), we cloned an RPS4 allele missing the PL domain sequence from F960 to S1118. The wild type (wt) RPS4 allele containing all domains is referred to here as RPS4 TNLPC (T for TIR, N for NB, L for LRR, P for PL, and C for CTD) and the PL-depleted allele as RPS4 TNLC (Supplementary Fig. S1A). In the transient assay, overexpression of RPS4 TNLPC together with RRS1 and AvrRps4 triggered a strong HR ( Supplementary Fig. S1B). ...
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... wild type (wt) RPS4 allele containing all domains is referred to here as RPS4 TNLPC (T for TIR, N for NB, L for LRR, P for PL, and C for CTD) and the PL-depleted allele as RPS4 TNLC (Supplementary Fig. S1A). In the transient assay, overexpression of RPS4 TNLPC together with RRS1 and AvrRps4 triggered a strong HR ( Supplementary Fig. S1B). However, no HR was observed with RPS4 TNLC , suggesting that the PL domain is essential for RPS4 function. ...
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... regards to the different intensities of macroscopic HR cell death observed in our tobacco transient assays, we propose four levels to rate the HR, i.e., HR, HR _ , hr, and no HR (Supplementary Fig. S3). Complete cell death of the infiltrated tissue visible from the upper (Supplementary Fig. S3A) and lower ( Supplementary Fig. S3B) surface of the leaf are indicated by HR on the figures as observed with RPS4+RRS1+AvrRps4 ( Supplementary Fig. S1B). If the infiltrated area shows patches of tissue cell death visible from the upper and lower faces of the leaf, it is rated HR _ . ...
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... the deletion of the entire PL domain, we analyzed the effect of amino-acid mutations within the PL domain, to identify important residues for function. We chose to mutate, in RPS4, several of the most conserved amino acids identified in PL domain motifs of Arabidopsis (Fig. 1). We applied mutations onto RPS4 PL domain motif 1 (PSWF970-973), motif 2 (G997 and C1001), motif 3 (H1055), conserved phenylalanine F1087, and motif 4 (CG1104-1105) ( Fig. 1; Supplementary Fig. S4). We then tested the effect of each mutation on RPS4 activity, using transient HR assay. We expressed RPS4-mutated versions with the ...
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... PL domain, to identify important residues for function. We chose to mutate, in RPS4, several of the most conserved amino acids identified in PL domain motifs of Arabidopsis (Fig. 1). We applied mutations onto RPS4 PL domain motif 1 (PSWF970-973), motif 2 (G997 and C1001), motif 3 (H1055), conserved phenylalanine F1087, and motif 4 (CG1104-1105) ( Fig. 1; Supplementary Fig. S4). We then tested the effect of each mutation on RPS4 activity, using transient HR assay. We expressed RPS4-mutated versions with the b-glucuronidase gene (GUS) only to test their autoactivity and with RRS1+AvrRps4 to test their functionality. In our conditions, RPS4 wt triggered a low intensity of HR (hr) when overexpressed on its own ...
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... we found 68 TNL-coding genes containing PL domain signatures. Among the 132 TNL-related sequences (TIR-only included), PL motifs were mainly found in TNLs that display the full canonical TIR-NB-LRR organization (Supplementary Table S1). A motif analysis carried out with these 68 sequences revealed four robust signatures spread out on the domain (Fig. 1). The first motif starts immediately after the LRR domain and contains conserved proline (P) and phenylalanine (F) residues embedded in a characteristic P-x-[YEW]-F signature. The second motif, predicted to form a b-strand, displays a conserved cysteine (C) followed by hydrophobic residues. As for motif 2, motifs 3 and 4 are included in ...
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... included in predicted b-strands and harbor conserved histidine (H) and cysteine-glycine (CG), respectively. The secondary structure analysis revealed a conserved structure that is exclusively made of b-strands (six in total) mainly localized inside and between motifs. The alignment also revealed a conserved phenylalanine within the fifth b-strand (Fig. 1). The core PL domain (i.e., containing motifs 1 to 4) is made of 130 aa, on average (standard deviation = 9.45 aa). However, the majority of PLcontaining sequences also harbor size-variable and polymorphic extra C-terminal peptide chains (>30 aa), which we did not consider as a part of the core PL domain, and that are predicted to code ...
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... structural annotation of TNLs showed that the majority (74%) of PL-containing TNLs (TNLPs) do not contain introns between the end of the LRR-encoding exon and the start of the PL-coding exon (Fig. 1, main structural model; Supplementary Table S2). This feature has probably helped to avoid loss of exon coding for PL domains during duplication events, which is a frequent process occurring in TNLs. Interestingly, a small subset of TNLs harbors independent PL-coding exons, among which we found all the executor TNLs or TNL-Bs, as ...
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... the Golden Gate kit from The Sainsbury Laboratory (Norwich, U.K.) ( Engler et al. 2014), we cloned an RPS4 allele missing the PL domain sequence from F960 to S1118. The wild type (wt) RPS4 allele containing all domains is referred to here as RPS4 TNLPC (T for TIR, N for NB, L for LRR, P for PL, and C for CTD) and the PL-depleted allele as RPS4 TNLC (Supplementary Fig. S1A). In the transient assay, overexpression of RPS4 TNLPC together with RRS1 and AvrRps4 triggered a strong HR ( Supplementary Fig. S1B). ...
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... wild type (wt) RPS4 allele containing all domains is referred to here as RPS4 TNLPC (T for TIR, N for NB, L for LRR, P for PL, and C for CTD) and the PL-depleted allele as RPS4 TNLC (Supplementary Fig. S1A). In the transient assay, overexpression of RPS4 TNLPC together with RRS1 and AvrRps4 triggered a strong HR ( Supplementary Fig. S1B). However, no HR was observed with RPS4 TNLC , suggesting that the PL domain is essential for RPS4 function. ...
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... regards to the different intensities of macroscopic HR cell death observed in our tobacco transient assays, we propose four levels to rate the HR, i.e., HR, HR _ , hr, and no HR (Supplementary Fig. S3). Complete cell death of the infiltrated tissue visible from the upper (Supplementary Fig. S3A) and lower ( Supplementary Fig. S3B) surface of the leaf are indicated by HR on the figures as observed with RPS4+RRS1+AvrRps4 ( Supplementary Fig. S1B). If the infiltrated area shows patches of tissue cell death visible from the upper and lower faces of the leaf, it is rated HR _ . ...
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... the deletion of the entire PL domain, we analyzed the effect of amino-acid mutations within the PL domain, to identify important residues for function. We chose to mutate, in RPS4, several of the most conserved amino acids identified in PL domain motifs of Arabidopsis (Fig. 1). We applied mutations onto RPS4 PL domain motif 1 (PSWF970-973), motif 2 (G997 and C1001), motif 3 (H1055), conserved phenylalanine F1087, and motif 4 (CG1104-1105) ( Fig. 1; Supplementary Fig. S4). We then tested the effect of each mutation on RPS4 activity, using transient HR assay. We expressed RPS4-mutated versions with the ...
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... PL domain, to identify important residues for function. We chose to mutate, in RPS4, several of the most conserved amino acids identified in PL domain motifs of Arabidopsis (Fig. 1). We applied mutations onto RPS4 PL domain motif 1 (PSWF970-973), motif 2 (G997 and C1001), motif 3 (H1055), conserved phenylalanine F1087, and motif 4 (CG1104-1105) ( Fig. 1; Supplementary Fig. S4). We then tested the effect of each mutation on RPS4 activity, using transient HR assay. We expressed RPS4-mutated versions with the b-glucuronidase gene (GUS) only to test their autoactivity and with RRS1+AvrRps4 to test their functionality. In our conditions, RPS4 wt triggered a low intensity of HR (hr) when overexpressed on its own ...
Citations
... Such gene pairs are often divergently transcribed. Interestingly, 10 of 11 pairs of Toll interleukin-1 receptor (TIR)-NLR genes show a head-to-head configuration in Arabidopsis (Meyers et al., 2003;Saucet et al., 2021). Divergent transcription may assure balanced levels of the protein pair to meet a strict stoichiometric requirement to act together, possibly in a complex (Narusaka et al., 2009). ...
... We also revealed the requirement for two additional TIR-NB-LRR genes, RPP2C and RPP2D, adjacent to RPP2A and RPP2B and showed all four NLR proteins are required for full resistance against Hpa-Cala2. A paired head-to-head R-gene structure is often found in plant-paired NLRs (Narusaka et al., 2009;C esari et al., 2014;Saucet et al., 2021). RPP2C and RPP2D form a head-to-head orientation similar to RRS1-RPS4 (Narusaka et al., 2009;Ma et al., 2018;Guo et al., 2020). ...
... RPP2C and RPP2D form a head-to-head orientation similar to RRS1-RPS4 (Narusaka et al., 2009;Ma et al., 2018;Guo et al., 2020). The C-terminal post-LRR domain of RPS4 is homologous with C-JID suggesting that it recognizes conformational changes in RRS1 upon effector recognition (Saucet et al., 2021). The RPP2C post-LRR domain is homologous to that of RRS1 but RPP2C contains a TIR domain on its C-terminal end instead of WRKY. ...
Arabidopsis Col‐0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown.
To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa‐Cala2 and Hpa‐Noks1. We identified ATR2Cala2 as a non‐canonical RxLR‐type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection.
ATR2Cala2 is recognized in accession Col‐0 but not in Ler‐0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility.
Two additional Col‐0 TIR‐NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa‐Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2‐recognizing accessions.
... Pathogen effectors interact with the LRR and C-JID domains leading to oligomerization of the receptor and finally formation of tetrameric TIR-NB-LRR (TNL) resistosomes [33,34]. Mutations in the C-JID domain may hinder TNL-mediated resistance [35]. ...
Background
Potato virus Y (PVY) is among the economically most damaging viral pathogen in production of potato (Solanum tuberosum) worldwide. The gene Rysto derived from the wild potato relative Solanum stoloniferum confers extreme resistance to PVY.
Results
The presence and diversity of Rysto were investigated in wild relatives of potato (298 genotypes representing 29 accessions of 26 tuber-bearing Solanum species) using PacBio amplicon sequencing. A total of 55 unique Rysto-like sequences were identified in 72 genotypes representing 12 accessions of 10 Solanum species and six resistant controls (potato cultivars Alicja, Bzura, Hinga, Nimfy, White Lady and breeding line PW363). The 55 Rysto-like sequences showed 89.87 to 99.98% nucleotide identity to the Rysto reference gene, and these encoded in total 45 unique protein sequences. While Rysto-like26 identified in Alicja, Bzura, White Lady and Rysto-like16 in PW363 encode a protein identical to the Rysto reference, the remaining 44 predicted Rysto-like proteins were 65.93 to 99.92% identical to the reference. Higher levels of diversity of the Rysto-like sequences were found in the wild relatives of potato than in the resistant control cultivars. The TIR and NB-ARC domains were the most conserved within the Rysto-like proteins, while the LRR and C-JID domains were more variable. Several Solanum species, including S. antipoviczii and S. hougasii, showed resistance to PVY. This study demonstrated Hyoscyamus niger, a Solanaceae species distantly related to Solanum, as a host of PVY.
Conclusions
The new Rysto-like variants and the identified PVY resistant potato genotypes are potential resistance sources against PVY in potato breeding. Identification of H. niger as a host for PVY is important for cultivation of this plant, studies on the PVY management, its ecology, and migrations. The amplicon sequencing based on PacBio SMRT and the following data analysis pipeline described in our work may be applied to obtain the nucleotide sequences and analyze any full-length genes from any, even polyploid, organisms.
... Three resistant and two susceptible potato cultivars were used as controls. The presence of virus was tested by enzyme-linked immunosorbent assay (ELISA) at [25][26][27][28][29][30][31][32][33][34][35][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66], and/or 75-90 days post inoculation (dpi). ...
... Both LRR and C-JID (also called post-LRR; PL) domains are involved in effector recognition [32]. Mutations in the C-JID domain may hinder TNL-mediated resistance [33]. The high level of variation in the LRR and C-JID domains in the predicted Rysto-like sequences in this study might indicate potentially different pathogen or strain recognition spectra of some of the Rysto-like proteins. ...
Background
Potato virus Y (PVY) is among the economically most damaging viral pathogen in production of potato (Solanum tuberosum) worldwide. The gene Rysto derived from the wild potato relative Solanum stoloniferum confers extreme resistance to PVY.
Results
The presence of Rysto and diversity of it was investigated in wild relatives of potato (298 genotypes representing 29 accessions of 26 tuber-bearing Solanum species) using PacBio amplicon sequencing. A total of 55 unique Rysto-like sequences were identified in 72 genotypes representing 12 accessions of ten Solanum species and six resistant controls (potato cultivars Alicja, Bzura, Hinga, Nimfy, White Lady and breeding line PW363). The 55 Rysto-like sequences showed 89.87 to 99.98% nucleotide identity to the Rysto reference gene, and these encoded in total 45 unique protein sequences. While Rysto-like26 identified in Alicja, Bzura White Lady and Rysto-like16 in PW363 encode a protein identical to the Rysto reference, the remaining 44 predicted Rysto-like proteins were 65.93 to 99.92% identical to the reference. Higher levels of diversity of the Rysto-like sequences were found in the wild relatives of potato than in the resistant control cultivars. The TIR and NB-ARC domains were the most conserved within the Rysto-like proteins, while the LRR and C-JID domains were more variable. Several of the tested Solanum species, including S. antipoviczii and S. hougasii, showed resistance to PVY. This study demonstrated Hyoscyamus niger, a Solanaceae species distantly related to Solanum, as a host of PVY.
Conclusions
The new Rysto-like variants, as well as the PVY resistant potato genotypes identified in this study, could be potential resistance gene sources against PVY in potato breeding. Identification of H. niger as a host for PVY is important for cultivation of this plant, studies on the PVY management, its ecology, and migrations. The amplicon sequencing based on PacBio SMRT technology and the following data analysis pipeline described in our work may be applied to obtain the nucleotide sequences and analyze any full-length genes from any, even polyploid, organisms.
... Plants possess the remarkable ability to detect the presence of microbial organisms by utilizing components of their innate immune system. This system plays a crucial role in triggering an appropriate defense response upon pathogen invasion (Saucet et al., 2021). ...
Introduction: Chickpea is a legume crop that thrives in regions with semi-arid or temperate climates. Its seeds are an excellent source of proteins, carbohydrates, and minerals, especially high-quality proteins. Chickpea cultivation faces several challenges including Fusarium wilt (FW), a major fungal disease that significantly reduces productivity.
Methods: In this study, a Genome-wide Association Analysis (GWAS) was conducted to identify multiple genomic loci associated with FW resistance in chickpea. We conducted a comprehensive evaluation of 180 chickpea genotypes for FW resistance across three distinct locations (Ethiopia, Tunisia, and Lebanon) during the 2-year span from 2015 to 2016. Disease infection measurements were recorded, and the wilt incidence of each genotype was calculated. We employed a set of 11,979 single nucleotide polymorphisms (SNPs) markers distributed across the entire chickpea genome for SNP genotyping. Population structure analysis was conducted to determine the genetic structure of the genotypes.
Results and Discussion: The population structure unveiled that the analyzed chickpea germplasm could be categorized into four sub-populations. Notably, these sub-populations displayed diverse geographic origins. The GWAS identified 11 SNPs associated with FW resistance, dispersed across the genome. Certain SNPs were consistent across trials, while others were specific to particular environments. Chromosome CA2 harbored five SNP markers, CA5 featured two, and CA4, CA6, CA7, and CA8 each had one representative marker. Four SNPs demonstrated an association with FW resistance, consistently observed across a minimum of three distinct environments. These SNPs included SNP5826041, SNP5825086, SNP11063413, SNP5825195, which located in CaFeSOD, CaS13like, CaNTAQ1, and CaAARS genes, respectively. Further investigations were conducted to gain insights into the functions of these genes and their role in FW resistance. This progress holds promise for reducing the negative impact of the disease on chickpea production.
... ; https://doi.org/10.1101/2023. 10.27.562987 doi: bioRxiv preprint molecular patterns (PAMPs) [6]. In particular, the LRR domains of plant NLRs are highly diverse and can recognize a wide range of pathogen-derived molecules, allowing plants to mount a robust and specific immune response to a broad range of pathogens. ...
... Additionally, LRR domains can contain variable regions and insertions that can modify the binding specificity and affinity of the domain. More recently, studies such as [10] have shown that "post-LRR" domains which lie at the C-terminal end of the LRR are required for successful plant immune response. Accurate annotation of these domains and their constituent repeat units is thus essential to understanding the components which govern protein shape and binding specificity. ...
Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.
Author summary
In immune receptors across various organisms, repeating protein structures play a crucial role in recognizing and responding to pathogen threats. These structures resemble the coils of a slinky toy, allowing these receptors to adapt and change over time. One particularly vital but challenging structure to study is the Leucine Rich Repeat (LRR). Traditional methods that rely just on analyzing the sequence of these proteins can miss subtle changes due to rapid evolution. With the introduction of protein structure prediction tools like AlphaFold 2, annotation methods can study the coarser geometric properties of the structure. In this study, we visualize LRR proteins in three dimensions and use a mathematical approach to ‘flatten’ them into two dimensions, so that the coils form circles. We then used a mathematical concept called winding number to determine the number of repeats and where they are in a protein sequence. This process helps reveal their repeating patterns with enhanced clarity. When we applied this method to immune receptors from a model plant organism, we found that our approach could accurately identify coiling patterns. Furthermore, we detected errors made by previous methods and highlighted unique structural variations. Our research offers a fresh perspective on understanding immune receptors, potentially influencing studies on their evolution and function.
... Among these variants, V1040L and N1042K substitutions within the LRR domain are consistently found in the isolated new dfin mutants ( Figure S3). These two polymorphisms are located at the C-terminal end of the LRR domain, termed the C-terminal jelly roll/Ig-like domain (C-JID), which is essential for effector recognition and TNL-mediated innate immunity [41,42]. The deletion or mutation in the C-JID region of TNL genes, such as the Arabidopsis RPS4 gene and the tobacco ROQ1 and N genes, failed to trigger a hypersensitive response [42,43]. ...
... These two polymorphisms are located at the C-terminal end of the LRR domain, termed the C-terminal jelly roll/Ig-like domain (C-JID), which is essential for effector recognition and TNL-mediated innate immunity [41,42]. The deletion or mutation in the C-JID region of TNL genes, such as the Arabidopsis RPS4 gene and the tobacco ROQ1 and N genes, failed to trigger a hypersensitive response [42,43]. The C-JID core consists of approximately 130 amino acids, which form two β-sheets and fold into a β-sandwich structure [41][42][43]. ...
... The deletion or mutation in the C-JID region of TNL genes, such as the Arabidopsis RPS4 gene and the tobacco ROQ1 and N genes, failed to trigger a hypersensitive response [42,43]. The C-JID core consists of approximately 130 amino acids, which form two β-sheets and fold into a β-sandwich structure [41][42][43]. This β-sandwich core and its loop regions are responsible for pathogen effector recognition. ...
The small compound [5-(3,4-dichlorophenyl) furan-2-yl]-piperidine-1-ylmethanethione (DFPM) inhibits ABA responses by activating effector-triggered immune signal transduction in Arabidopsis. In addition to the known function of DFPM as an antagonist of ABA signaling, DFPM causes accession-specific root growth arrest in Arabidopsis Columbia-0 via the TIR-NLR protein VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response) in an EDS1/PAD4/RAR1/SGT1B-dependent manner. Although DFPM could control the specific steps of various cellular responses, the functional residues for the activity of DFPM or the existence of a stronger version of DFPM modification have not been characterized thoroughly. This study analyzed twenty-two DFPM derivatives during root growth arrest, inhibition of ABA signaling, and induction of biotic signal transduction to determine critical residues that confer the specific activity of DFPM. Furthermore, this study identified two more Arabidopsis accessions that generate significant root growth arrest in response to DFPM derivatives dependent on multiple amino acid polymorphisms in the coding region of VICTR. The isolation of novel compounds, such as DFPM-5, and specific amino acid polymorphisms critical for the compound-induced responses will help determine the detailed regulatory mechanism for how DFPM regulates abiotic and biotic stress signaling interactions.
... Though the LRR domains participate in effector recognition, C-JIDs are the key determinants. Many studies have also revealed that truncation, deletion, or mutation in the C-JIDs impairs TNL-mediated immunity (Dodds et al., 2001;Saucet et al., 2021). Some TNLs even contain more than one C-JIDs. ...
... While Arabidopsis RPS4, which forms an NLR pair with RPP1, is an exception (Birker et al., 2009;Narusaka et al., 2009). The C-JID of RPS4 is involved in the maintenance of its inactive state and cannot interact with the corresponding effectors (Saucet et al., 2021). In addition, the TNL N protein recognizes the 50 kDa helicase (p50) effector of the Tobacco mosaic virus (TMV) ...
Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies to overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) are the most common components. And recent studies have greatly expanded our understanding of how NLRs function in plants. In this review, we summarize the studies on the mechanism of NLRs in the processes of effector recognition, resistosome formation, and defense activation. Typical NLRs are divided into three groups according to the different domains at their N termini and function in interrelated ways in immunity. Atypical NLRs contain additional integrated domains (IDs), some of which directly interact with pathogen effectors. Plant NLRs evolve with pathogen effectors and exhibit specific recognition. Meanwhile, some NLRs have been successfully engineered to confer resistance to new pathogens based on accumulated studies. In summary, some pioneering processes have been obtained in NLR researches, though more questions arise as a result of the huge number of NLRs. However, with a broadened understanding of the mechanism, NLRs will be important components for engineering in plant resistance improvement.
... In addition to full-length NLR, alternative splicing generates other proteins as well, at times a truncated NLR may be produced [88][89][90]. RGA5 transcripts, for example, exhibit alternative splicing [88]. RGA5 with the integrated decoy domain confers resistance to heavy metals, unlike other alternate splicing isoforms lacking those domains. ...
Pathogens can pose challenges to plant growth and development at various stages of their life cycle. Two interconnected defense strategies prevent the growth of pathogens in plants, i.e., molecular patterns triggered immunity (PTI) and pathogenic effector-triggered immunity (ETI) that often provides resistance when PTI no longer functions as a result of pathogenic effectors. Plants may trigger an ETI defense response by directly or indirectly detecting pathogen effectors via their resistance proteins. A typical resistance protein is a nucleotide-binding receptor with leucine-rich sequences (NLRs) that undergo structural changes as they recognize their effectors and form associations with other NLRs. As a result of dimerization or oligomerization, downstream components activate “helper” NLRs, resulting in a response to ETI. It was thought that ETI is highly dependent on PTI. However, recent studies have found that ETI and PTI have symbiotic crosstalk, and both work together to create a robust system of plant defense. In this article, we have summarized the recent advances in understanding the plant's early immune response, its components, and how they cooperate in innate defense mechanisms. Moreover, we have provided the current perspective on engineering strategies for crop protection based on up-to-date knowledge.
... Its WRKY ID is essential for the detection of the bacterial effectors PopP2 and AvrRps4. The C-terminal domain (CTD) of RPS4 is composed of a post-LRR (PL) domain present at this position in most TNLs followed by sequences without similarity to other proteins [85]. The PL domain adopts a β-jelly-roll and immunoglobulin-like β-sandwich fold as revealed by the RPP1 and ROQ1 structures [78,79], where this domain acts together with the LRR in effector binding. ...
... The PL domain adopts a β-jelly-roll and immunoglobulin-like β-sandwich fold as revealed by the RPP1 and ROQ1 structures [78,79], where this domain acts together with the LRR in effector binding. The Domain 4 (D4) of RRS1, located between the LRR and the WRKY domain, also contains a PL domain that is however degenerated [85]. Domain 6 (D6) located at the C-terminus of RRS1, downstream of the ID, has no homology to other proteins. ...
The specific recognition of pathogen effectors by intracellular nucleotide-binding domain and leucine-rich repeat receptors (NLRs) is an important component of plant immunity. NLRs have a conserved modular architecture and can be subdivided according to their signaling domain that is mostly a coiled-coil (CC) or a Toll/Interleukin1 receptor (TIR) domain into CNLs and TNLs. Single NLR proteins are often sufficient for both effector recognition and immune activation. However, sometimes, they act in pairs, where two different NLRs are required for disease resistance. Functional studies have revealed that in these cases one NLR of the pair acts as a sensor (sNLR) and one as a helper (hNLR). The genes corresponding to such resistance protein pairs with one-to-one functional co-dependence are clustered, generally with a head-to-head orientation and shared promoter sequences. sNLRs in such functional NLR pairs have additional, non-canonical and highly diverse domains integrated in their conserved modular architecture, which are thought to act as decoys to trap effectors. Recent structure-function studies on the Arabidopsis thaliana TNL pair RRS1/RPS4 and on the rice CNL pairs RGA4/RGA5 and Pik-1/Pik-2 are unraveling how such protein pairs function together. Focusing on these model NLR pairs and other recent examples, this review highlights the distinctive features of NLR pairs and their various fascinating mode of action in pathogen effector perception. We also discuss how these findings on NLR pairs pave the way toward improved plant disease resistance.
... Mutagenesis assays confirmed that residues within the LRR and JID/PL domains determine the effector recognition specificity. The JID/PL domain exists in many but not all TIR-NLR proteins across multiple plant species [45,46], and could be a common effector recognition component of TNLs in addition to LRR domains. ...
Plants deploy extracellular and intracellular immune receptors to sense and restrict pathogen attacks. Rapidly evolving pathogen effectors play crucial roles in suppressing plant immunity but are also monitored by intracellular nucleotide-binding, leucine-rich repeat immune receptors (NLRs), leading to effector-triggered immunity (ETI). Here, we review how NLRs recognize effectors with a focus on direct interactions and summarize recent research findings on the signalling functions of NLRs. Coiled-coil (CC)-type NLR proteins execute immune responses by oligomerizing to form membrane-penetrating ion channels after effector recognition. Some CC-NLRs function in sensor–helper networks with the sensor NLR triggering oligomerization of the helper NLR. Toll/interleukin-1 receptor (TIR)-type NLR proteins possess catalytic activities that are activated upon effector recognition-induced oligomerization. Small molecules produced by TIR activity are detected by additional signalling partners of the EDS1 lipase-like family (enhanced disease susceptibility 1), leading to activation of helper NLRs that trigger the defense response.
