The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Abstract

The barley Mla locus contains a cluster of NLR genes and is orthologous to the Stem Rust (Sr) resistance loci Sr33 and Sr50 in wheat, which confer immunity against specific isolates of the barley powdery mildew Blumeria graminis f. sp. hordei (Bgh) and against the wheat rust pathogen Puccinia graminis f. sp. tritici (Pgt), respectively [14–16]. Prior to the molecular isolation of Bgh AVRA effectors, domain swap experiments with MLA1 and MLA6 suggested that the LRR is a determinant of isolate-specific disease resistance, an idea which is further supported by the observation that most sites under positive selection map to the predicted solvent-exposed sites of the LRR [19,20]. [...]we integrated high-confidence non-synonymous variants over each annotated Bgh gene and considered absence of a transcript as a missing genotype to obtain gene-wise genotypes. Co-expression of matching AVRa-Mla pairs in this system triggers a reduction in luciferase (LUC) reporter gene activity as a proxy for cell death [33].

Introduction

Plants have evolved sophisticated innate immune systems to protect themselves against colonization by pathogenic microbes [1,2]. At the population level, a host-adapted pathogenic species is comprised of numerous isolates/races with distinctive genetic blueprints which determine their infection phenotypes on individual accessions (genotypes) of a plant host population. In isolate-specific resistance, individual host accessions often mount a hypersensitive immune response against a subset of pathogenic isolates [3,4]. Isolate-specific resistance is mediated by genetic interactions between plant host resistance (R) genes and matching pathogen avirulence (AVR) effector genes (gene-for-gene model) [5]. Plant R genes often encode intracellular nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) [6]. These receptors have a characteristic modular domain architecture, consisting of a variable N-terminal Coiled-Coil (CC), Toll-Interleukin (TIR) domain or HeLo domain (named after the fungal HET-S and LOPB proteins), a central NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products, and CED-4) domain, and C-terminal leucine-rich repeats (LRRs) [7,8]. The LRRs often constitute a determinant for specific pathogen recognition. NLRs can detect AVRs by direct interaction [9–11], a receptor-integrated decoy [12], or indirectly detecting effector-mediated alterations of a host target [13]. Upon AVR recognition by NLRs, a localized host cell death is typically, but not invariably, associated with receptor-mediated immunity.

Here, we study the NLR gene Mildew locus a (Mla), which has the capacity to confer isolate-specific resistance against both biotrophic basidiomycete and ascomycete fungal pathogens in closely related host cereal species, including wheat and barley. The barley Mla locus contains a cluster of NLR genes and is orthologous to the Stem Rust (Sr) resistance loci Sr33 and Sr50 in wheat, which confer immunity against specific isolates of the barley powdery mildew Blumeria graminis f. sp. hordei (Bgh) and against the wheat rust pathogen Puccinia graminis f. sp. tritici (Pgt), respectively [14–16]. Bgh and Pgt are filamentous eukaryotic pathogens that belong to different phyla and diverged from each other approximately 500–650 million years ago [17]. Furthermore, Resistance to Magnaporthe oryzae (RMo1) confers immunity to the rice blast pathogen in barley, and also maps to the barley Mla locus [18].

In barley, the Mla gene has undergone tremendous diversification into over 30 different allelic resistance specificities in the host population [19,20]. This is the result of a co-evolutionary arms race in which each Mla allele recognizes a matching AVRA effector encoded by a subset of Bgh isolates [14]. Prior to the molecular isolation of Bgh AVRA effectors, domain swap experiments with MLA1 and MLA6 suggested that the LRR is a determinant of isolate-specific disease resistance, an idea which is further supported by the observation that most sites under positive selection map to the predicted solvent-exposed sites of the LRR [19,20]. A multi-allelic Powdery mildew 3 (Pm3) resistance locus also evolved in wheat populations, in which it confers isolate-specific resistance against the wheat powdery mildew Blumeria graminis f. sp. tritici (Bgt) through recognition of sequence-unrelated but possibly structurally related Bgt AVRPM3 effectors [21,22]. Although barley Mla and wheat Pm3 both encode CC-type NLRs, the receptors are sequence-unrelated and map to non-syntenic locations in the genomes of the sister host species. Most sites that are polymorphic between different Pm3 resistance alleles localize to the LRR [23–26]. For other multi-allelic NLRs, yeast two-hybrid and co-immunoprecipitation experiments with matching effectors suggested that the LRRs determine isolate-specific resistance by direct effector binding [10,27]. However, it remains unclear whether AVRPM3 effectors directly bind to PM3 receptors and whether the LRRs of allelic variants of MLA or PM3 receptors are directly responsible for specific discrimination between powdery mildew avirulence effectors, and thereby for isolate-specific recognition.

Recently, we identified the sequence-unrelated Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22 [11,28], which are recognized by barley MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively [11]. Experiments in yeast, in the absence of other plant proteins, provided evidence for direct interaction of three receptor-effector pairs, namely MLA7/AVRA7, MLA10/AVRA10, and MLA13/AVRA13 [11]. However, it is not known how MLA receptors with >90% sequence identity can recognize the sequence-unrelated fungal Bgh effectors. Structural relatedness between effectors, which is needed for recognition by allelic variants of MLA, could explain this phenomenon. For instance, based on structural predictions, ~15% of candidate-secreted effector proteins (CSEPs) were predicted as RNase-Like Proteins expressed in Haustoria (RALPHs), among them, CSEP0064 [29–31]. The X-ray structure of Bgh CSEP0064 indeed revealed a ribonuclease-like fold. Structural overlay of CSEP0064 and the active fungal F1 RNase from Fusarium moniliforme demonstrated the absence of canonical catalytic residues in the predicted substrate-binding pocket of CSEP0064 [30]. Notably, AVRA7 and AVRA13 but not the other isolated Bgh AVRA proteins were predicted by IntFOLD version 3.0 to also adopt a RNase-like fold. Here, we used a transcriptome-wide association study (TWAS) approach [11,28] to identify the effector recognized by the barley Mla6 receptor. The protein which we identified as AVRA6, CSEP0254, is very likely structurally similar to the RALPH effector CSEP0064 [30]. By applying version 5.0 of the structural prediction algorithm IntFOLD [32], we found that all identified AVRA effectors are predicted to share structural similarity with fungal RNases, but similar to all other Bgh ribonuclease-likes CSEPs, the isolated AVRA effectors also lack the residues critical for catalytic activity [30,31]. By taking advantage of previously engineered hybrid receptors of MLA1 and MLA6 we confirm that the molecular basis of isolate-specific disease resistance against Bgh isolates A6 and K1 lies in the specific recognition of AVRA6 and AVRA1 effectors by six and 12 C-terminal LRRs of MLA1 and MLA6 receptors, respectively. We find that the LRRs of allelic MLA10 and MLA22 are largely sufficient for specific perception of allelic AVRA10 and AVRA22 effector proteins. Co-expression of hybrid effectors generated from allelic AVRA10 and AVRA22 with MLA10 and MLA22 receptors revealed that multiple effector residues participate in AVRA recognition specificities. Our findings imply a model in which co-evolution of the barley Mla-Bgh AVRa pathogen interaction is driven MLA sequence diversification upon detection of a common structural effector scaffold. This co-evolutionary process may have contributed to the proliferation and sequence diversification of RALPH effectors in the powdery mildew genome.

Results

TWAS identifies BLGH_00709 (CSEP0254) as an AVRa6 candidate

For the isolation of AVRa6, we examined the gene-wise association of Bgh transcriptomes with the published infection phenotypes of 27 Bgh isolates on Mla6 barley lines [11,28]. We used the previously described in planta fungal transcripts of the 27 Bgh isolates and their published infection phenotypes on barley Mla6 near-isogenic lines (NILs) of the barley cultivars (cv.) Pallas and Manchuria [11]. In short, we integrated high-confidence non-synonymous variants over each annotated Bgh gene and considered absence of a transcript as a missing genotype to obtain gene-wise genotypes. We then tested the gene-wise genotypes for association with the observed avirulence phenotypes using Fisher’s exact test [11]. Association mapping identified a number of genes encoding CSEPs. The csep encoding genes with the lowest p-values in this analysis were BLGH_00709 (CSEP0254; gene-wise: p = 7,40E-07) and BLGH_00697 (p = 7.25E-07), suggesting them to be top-ranking candidates for AVRa6 (Fig 1A, S1 and S2 Tables). To first determine which candidate is recognized by MLA6 in barley, we transiently co-expressed the AVRa candidate gene and Mla6 receptor gene in cv. Golden Promise barley protoplasts. Co-expression of matching AVRa-Mla pairs in this system triggers a reduction in luciferase (LUC) reporter gene activity as a proxy for cell death [33]. Co-expression of BLGH_00709 and Mla6 led to a significant reduction of relative LUC activity in comparison to the empty vector (EV) control (98% reduction), while co-expression of BLGH_00697 with Mla6 did not reduce LUC activity (S1 Fig). This suggests that BLGH_00709 is recognized by Mla6 in barley, and we therefore subjected BLGH_00709 to further analysis as the top AVRa6 candidate.

[Figure omitted. See PDF.]

Fig 1. Identification of BLGH_00709 (CSEP0254) as one of the top ranking AVRa6 candidates by association of Bgh AVRa profiles on Mla6 near-isogenic lines with transcript polymorphisms.

(A) Manhattan plot summarizing the gene-wise association results for candidate AVRa6. The x axis represents the Bgh DH14 genes, sorted by Bgh gene ID; the y axis shows −lg of p-values for all genes with at least one nonsynonymous coding SNP, indels as well as presence or absence of transcripts. CSEPs with a p < 0.018 (dotted line) are depicted by arrowheads. The candidate AVRa6 gene copies BLGH_00709 (CSEP0254) and BLGH_07091 are designated in the plot with bright green arrowheads. BLGH_07092 is designated by a dark green arrowhead. The other candidates BLGH_00697 (CSEP0058) and BLGH_00700 are depicted with a dark red and a bright red arrowhead, respectively. (B) Schematic illustration of the chromosomal regions harboring the AVRa6 candidate BLGH_00709 and its paralogues and family members with corresponding gene IDs in the genomes of Bgh isolates DH14, RACE1, and K1. All CSEPs are depicted by arrows. (C) Phylogeny of CSEP family 8 containing AVRA6, which can be divided into clade 1 (BLGH_00709, BLGH_07092, BLGH_00700, BLGH_00698, BLGH_00697) and clade 2 (BLGH_05882, BLGH_05875, BLGH_05881), based on the protein sequences excluding the signal peptide and using BLGH_05397 as an outgroup. (D) Protein sequence alignment of AVRA6 and CSEP family 8 members including their respective signal peptides.

https://doi.org/10.1371/journal.ppat.1009223.g001

First, we analyzed the gene architecture of the AVRa6 candidate gene in the available genomes of the Bgh isolates DH14 and RACE1 (both avirulent on Mla6 lines). The annotated near chromosome-level reference genome of the DH14 Bgh isolate harbors two more identical copies of BLGH_00709. These copies are annotated as BLGH_00708 and BLGH_07091 (Fig 1B). Additionally, DH14 harbors another CSEP0254 paralog, called BLGH_07092. In comparison to BLGH_00709, BLGH_07092 carries a frameshift mutation that predicts an altered sequence from aa 64 onwards in the BLGH_07092 encoded protein (Fig 1D). BLGH_00708 and BLGH_00709 are located in close proximity to each other in a head-to-tail orientation next to the cyclin B1 gene on scaffold 16 of the DH14 genome, while BLGH_07091 resides with BLGH_07092 on scaffold 309 in a head-to-head orientation. In the genome of the Mla6 avirulent RACE1 isolate, three identical copies of BLGH_00709 can be found on tig00005311: BLGHR1_15960 (syntenic position to BLGH_00709) is located next to the cyclin B1 gene and on the same scaffold BLGHR1_15970 (syntenic position to BLGH_07091) and BLGHR1_15971 (syntenic position to BLGH_07092) reside in a head-to-head orientation. Further analysis of genes surrounding the AVRa6 locus in DH14 and RACE1 suggests major genomic rearrangements: a gene cluster containing a tRNA nucleotide transferase and the DNA repair protein RadR is present in inverted orientation in scaffold 16 and tig00005311, and the BLGH_00700 family member cannot be found on tig0005283 of the RACE1 genome (Fig 1B). For simplicity, from here on we will refer to the three sequence-identical paralogues BLGH_00709, BLGH_00708, and BLGH_07091 as AVRa6. AVRA6 is part of the CSEP family 8, which contains six additional members and can be subdivided into two clades: AVRA6, BLGH_07092, BLGH_00698 (CSEP0333), BLGH_00700, and BLGH_00697 (CSEP0058) belong to clade 1, whereas BLGH_05881 (CSEP0151), BLGH_05875 (CSEP0147), and BLGH_05882 (CSEP0148) belong to clade 2 (Fig 1C). The clade 1 CSEP family 8 members share a 48.3–60.4% sequence identity with AVRA6, while the clade 2 family members share a 32.9–39.7% sequence identity with the avirulence effector candidate. As BLGH_07092 is most likely a non-functional copy of AVRa6, and its expression is lower when compared to AVRa6 in every Bgh isolate (S2 Fig), we did not subject it to further analysis.

Analysis of transcriptomic data revealed that all isolates avirulent on the cv. Manchuria and cv. Pallas Mla6 NILs express AVRa6, which encodes a 115-aa-long protein with a predicted 24-aa-long signal peptide (SP) (S3 and S4 Figs). AVRa6 possesses one intron, which is spliced out in all transcripts of avirulent isolates. However, we identified transcripts of AVRa6 carrying this intron in all Bgh isolates virulent on Mla6 NILs. The transcription of the AVRa6 intron may be facilitated by two different mechanisms (S4 Fig): The AVRa6 transcript variant expressed in the virulent isolates CC66 and CC148 exhibits a T270C mutation in the intron branch point consensus sequence, suggesting that intron retention may be caused by inefficient or nonexistent U2 spliceosome recognition (S4B Fig). If this is the case, the intron retention leads to a premature stop codon and a truncated protein, which is only 79 aa-long including the signal peptide. This deduced truncated protein variant, which we named AVRA6-V1, would also harbor A48S, A75T, and R79S amino acid substitutions. The isolates K1, K2, K3, B103, S15, S16, S22, and S25 are virulent on Mla6 lines and contain a splice donor site mutation (S3 and S4B Figs) in the transcripts that maps to the AVRa6 gene of the reference genome. Genome analysis of isolate K1 [11] confirmed this splice-site mutation (Fig 1B). The predicted intron retention in the transcript of the AVRa6 variant expressed by the K1, K2, K3, B103, S15, S16, S22, and S25 isolates leads to a premature stop codon as well as to a predicted 79-aa-long truncated protein (S4B Fig). In addition, the encoded protein exhibits two amino acid substitutions when compared to AVRA6: A75T and R79I and we named this variant AVRA6-V2. Furthermore, the number of transcripts from virulent Bgh isolates that map to AVRa6 is approximately four-fold lower than the AVRa6 transcripts in the avirulent DH14 isolate (S2 Fig), which could be a consequence of nonsense-mediated mRNA decay. In conclusion, virulence of Bgh isolates on barley NILs harboring Mla6 is likely conferred by SNPs in splice sites that may lead to intron retention in the respective genes. This is associated with reduced levels of the transcripts that map to the AVRa6 gene in Bgh isolates virulent on Mla6 lines.

Transient co-expression assays provide evidence for specific recognition of AVRa6 by Mla6

To determine if the candidate AVRA6 is specifically recognized by MLA6, we first co-expressed AVRa6 and Mla6 in a transient barley protoplast system containing leaf mesophyll cells [33]. Co-expression of matching AVRa6 or AVRa1 with Mla6 or Mla1, respectively, triggered significant reductions in LUC activity, when compared to reference samples where the effector gene has been exchanged to an EV (98% and 85% reductions, respectively, Fig 2A). Co-expression of Mla6 with a DNA sequence that encodes a truncated version of AVRa6 (likely encoded by AVRa6-V2) or co-expression of AVRa6 with Mla1 did not lead to significantly reduced LUC activity compared to samples co-expressing AVRa6 with Mla6, confirming the specificity of the recognition (Fig 2A).

[Figure omitted. See PDF.]

Fig 2. Mla6 and AVRa6 co-expression in barley protoplasts and N. benthamiana causes a specific cell death response.

(A) Barley cv. Golden Promise protoplasts were transfected with pIPKb002 vectors containing cDNAs of Mla6 or Mla1 and either an empty vector (EV), AVRa6, AVRa6-V2, AVRa1, AVRa1-V1, or AVRa1-V2 variants lacking their respective signal peptides together with a pUBI:Luciferase construct. The LUC activity relative to the EV sample was measured as a proxy for cell death 16 h post transfection. Box plot diagrams show median of the relative LUC activity of six independent transfections, which are represented by dots, while the box shows the interquartile range. Significant differences between samples were analyzed using non-parametric Kruskal-Wallis (KW) analysis followed by a Dunn’s test. Calculated KW p-values are as follows: Mla6: p = 0.007146; Mla1: p = 0.0007392. Samples labeled with identical letters did not differ significantly (p < 0.05) in the Dunn’s test for the corresponding Mla variant. (B) cDNAs of clade 1 AVRa6 family members BLGH_00698, BLGH_00697, BLGH_00700, AVRa6, and AVRa1 variants were expressed without their respective signal peptides and stop codons and with a C-terminal mYFP fusion under the control of a 35S promotor in N. benthamiana. The effectors were co-expressed with Mla1 and Mla6 cDNAs fused C-terminally with a 4xmyc tag under the control of a 35S promotor. Cell death was scored five days post infiltration and Figures show a representative of at least 15 co-transformations. (C) Protein levels of AVRA1-mYFP, AVRA6-mYFP, AVRA6-V2-mYFP, BLGH_00698-mYFP, BLGH_00697-mYFP and BLGH_00700-mYFP. Samples for total protein extraction were harvested two days post infiltration. mYFP fusion proteins were enriched by an GFP-Trap. Proteins were separated using 10% or 12% polyacrylamide gels and proteins were detected using α-GFP and α-myc western blotting (WB). IP = immunoprecipitation. CBB = Coomassie Brilliant Blue.

https://doi.org/10.1371/journal.ppat.1009223.g002

To examine whether AVRA6 is recognized by MLA6 in a heterologous expression system without the presence of other barley proteins, we co-expressed the C-terminally mYFP-tagged effector fusion protein with the C-terminally 4xmyc-tagged receptor in N. benthamiana. Unlike the essentially complete cell death observed in the barley protoplast system (as evidenced by the very low levels of LUC activity), co-expression of AVRa6-mYFP and Mla6-4xmyc triggered a cell death of varying confluence in Agrobacterium tumefaciens infiltrated tissue in independent N. benthamiana leaves compared to the cell death observed when co-expressing AVRa1 and Mla1 (Figs 2B and S14). Co-expression of AVRa6-mYFP with Mla1-4xmyc did not elicit cell death, confirming the specific recognition of candidate AVRA6 by MLA6 but not MLA1. No cell death was observed when Mla6-4xmyc was co-expressed with a DNA sequence that encodes a truncated version of AVRa6-mYFP (here named AVRA6-V2-mYFP), even though both AVRA and MLA proteins are detectable in N. benthamiana leaf extracts (Figs 2B, 2C and 5C). Furthermore, co-expression of the clade 1 CSEP family 8 member BLGH_00698-mYFP, which shares the highest sequence similarity with AVRa6, with Mla6 did not lead to cell death, even though BLGH_00698-mYFP is detectable in N. benthamiana leaf extracts (Fig 2B and 2C). Detection of BLGH_00700 and BLGH_00697 proteins was possible only after enrichment with a GFP-Trap, suggesting that their protein stability is lower than those of AVRA6 and BLGH_00698 in this system. A faster-migrating protein band for BLGH_00697-mYFP and a double band visible after blotting for BLGH_00700-mYFP suggest that these proteins may either be cleaved post-translationally by proteases in heterologous N. benthamiana or that they are not stable in the plant extraction buffer (Fig 2C). Taken together, co-expression of AVRA6 with MLA6 in both homologous and heterologous plant expression systems triggers a significant and specific cell death response, indicating specific effector recognition by the matching MLA immune receptor.

AVRA effectors have low sequence similarity, but show predicted structural homology to RNases

We subjected AVRA6 to a phylogenetic analysis including all annotated CSEPs in B. graminis formae speciales poae, lolium, avenae, tritici (isolate 96224), hordei DH14, secalis (isolate S1459), triticale (isolate T1-20), and dactylidis, but were unable to detect significant polypeptide sequence relatedness to other known Bgh AVRA effector proteins or to the so far isolated wheat powdery mildew avirulence effectors, AVRPM2, AVRPM3A2/F2, AVRPM3B2/C2, and AVRPM3D3 (Fig 3A). However, we noted that all the avirulence proteins isolated from barley and wheat powdery mildews belong to CSEPs with a length of approximately 80 to 130 amino acids when neglecting their respective signal peptides. The same is true for CSEP0064, which was shown to form a RNase-like protein structure. To determine potential structural similarity between AVRA6 and known Bgh effectors, we subjected AVRA6 to structural prediction using IntFOLD version 5.0 [32]. AVRA6 exhibited high predicted structural similarity to the RNase-like fold observed for the X-ray structure, suggesting that AVRA6 possesses a ribonuclease-like fold similar to AVRA13 and AVRA7 (S5 Fig). This prompted us to also reanalyze all isolated AVRA effectors using the with IntFOLD version 5.0. We found that AVRA1, AVRA9, and AVRA10/AVRA22 are also predicted to harbor a central α-helix directly facing three to four β-sheets with a topology characteristic of ribonucleases (Fig 3B). This is reminiscent of structural predictions for Bgt effectors AVRPM2 and AVRPM3D3, which also suggested structural similarities to ribonucleases (Fig 3, [22,34–36]). Although the relationship to ribonucleases is less clear for Bgt AVRPM3A2/F2 and AVRPM3B2/C2, these two effectors were predicted to exhibit a central α-helix and two to four ß-sheets like AVRPM3D3 ([22], Fig 3B). We examined AVRa and AvrPm gene models for the presence of an intron, which is thought to be characteristic for RALPH effector-encoding genes [29,31] and identified one intron at position +163 to +201 bp after the end of the signal peptide (S6A and S7A Figs). The relative intron position in the structural predictions is in an unstructured loop between the first and the second ß-sheet, except in AVRA13, AVRPM3A2/F2, and AVRPM3B2/C2 (Fig 3B). For the latter three effectors, the intron is positioned in a predicted unstructured loop C-terminal to the second ß-sheet (Figs 3B and S6). No common sequence motifs are detectable in the highly diverse intron sequences (S7B Fig). Thus, it remains unclear whether all known Blumeria avirulence effectors are descendants of one common “ur-RALPH” ancestor [29]. Irrespective of this, our analysis suggests that isolated Bgh and Bgt avirulence effectors are structurally related to fungal ribonucleases.

[Figure omitted. See PDF.]

Fig 3. Bgh AVRA and Bgt AVRPM effectors are sequence-unrelated but exhibit predicted structural similarity to RNases.

(A) Maximum likelihood phylogeny including all predicted CSEPs from B. graminis formae speciales poae, lolium, avenae, tritici 96224, hordei DH14, secalis S1459, triticale T1-20, and dactylidis. Depicted in red are the BLGH-IDs of all so far isolated Bgh AVRA and Bgt AVRPM effectors. Depicted in blue are the clade-1 family members of AVRA6, while the clade-2 family members are colored in green. CSEP clades that were collapsed (grey circles) to improve legibility of the tree do not include AVR members and are indicated by grey circles. (B) Structural prediction of isolated AVRAs and AVRPM by IntFOLD version 5.0 in red (p-values: AVRA1 = 4.888e-4 most similar to PDB IDs 5gy6, 3who and 1rds, AVRA6 = 3.293e-5 to 6fmb, AVRA7 = 2.114e-4 to PDB ID 5gy6, AVRA9 = 1.18e-5 most similar to PDB IDs 6fmb, 3who, and 1ch0, AVRA10 = 9.759e-5 most similar to PDB ID 1fusa and to 3whoa, AVRA13-1 = 7,359e-7 most similar to 6fmb, AVRPM2 = 8.741e-9 most similar to 6fmb, 1chOA, and 1rmsA, AVRPM3D3 = 8.82e-5 most similar to PDB 6fmb and 5gy6A, AVRPM3A2/F2 = 1.145e-5 to 3ub1A2, AVRPM3B2/C2 = 7.079e-2, no structural similarities predicted). Yellow arrow depicts relative position of the characteristic RALPH intron in effector structures.

https://doi.org/10.1371/journal.ppat.1009223.g003

RNase-like AVRA effectors do not show ribonuclease activity

Using an RNase activity assay, we tested whether AVRA proteins are truly catalytically inactive as suggested for RNase-like Bgh effectors previously [29,30]. First, we expressed N-terminally GST-tagged AVRA6, AVRA10, and AVRA13 in Escherichia coli and purified them by GST affinity chromatography. We then cleaved the GST tag and applied size-exclusion chromatography (S8A Fig). Successful protein expression and purification of the AVRA effector proteins was tested by SDS-PAGE (S8B Fig). We then incubated AVRA6, AVRA10, and AVRA13 effectors with denatured HvRNA or native rRNA to test for ribonuclease activity [37]. Using RNA gel electrophoresis, we observed a degradation of RNA when co-incubated with a commercially available T1 RNase, which has the same function as the Fusarium F1 RNase. We did not observe RNA degradation when incubating HvRNA or rRNA with the AVRA effectors (Fig 4A and 4B). These results were independently validated with AVRA6, AVRA10, and AVRA13 effector proteins that were produced in eukaryotic insect cells, followed by affinity chromatographic purification (S9A and S9B Fig). Taken together, the data indicate that AVRA effectors have no RNase activity, which is consistent with the previous prediction that ascribed pseudoenzymatic function to the RALPHs [29,30].

[Figure omitted. See PDF.]

Fig 4. Recombinant AVRA6, AVRA10, and AVRA13 effector proteins do not exhibit ribonuclease activity.

To test for ribonuclease activity, heterologous AVRA6, AVRA10, and AVRA13 proteins, purified upon expression of the respective genes in E. coli, or T1 RNase were co-incubated with (A) denatured HvRNA and (B) native rabbit rRNA always. All samples were separated on non-denaturing 2% agarose gels (top panels) and analysed on a Bioanalyzer (lower panels) to check for RNA degradation.

https://doi.org/10.1371/journal.ppat.1009223.g004

The C-terminal leucine-rich repeats of MLA1 and MLA6 receptors account for specific discrimination of structurally homologous AVRA1 and AVRA6 effectors in planta

A previous study showed that most of the residues under positive selection in allelic MLA resistance specificities in barley populations are located in the LRR region [19]. Using single-cell expression of MLA chimeras in barley leaf epidermal cells, C-terminal LRR regions of Mla1 and Mla6 were shown to encode determinants for isolate-specific immunity in barley to Bgh isolates K1 (carrying AVRa1) and A6 (carrying AVRa6) [38]. Here, we tested if the LRRs determine isolate-specific immunity by specifically recognizing AVRA effectors in barley. Therefore, we made use of the previously constructed intron-containing DNAs of the chimeric receptors M16666, M11166, M61111, and M66111 ([38] (protein sequence shown in S10 Fig) and co-expressed them with matching AVRa6, AVRa6-V2, AVRa1, and AVRa1-V1 cDNAs lacking the signal peptide (SP) in the pIPKb002 vector under the control of a strong maize ubiquitin promoter in barley protoplasts. Upon co-expression of AVRa6 with M16666 or M11166 we detected a significant 79% or 92% reduction in relative LUC activity when compared to the EV samples, respectively (Fig 5A). This reduction was not observed when M16666 or M11166 were co-expressed with AVRa6-V2, AVRa1, or AVRa1-V1, respectively, suggesting that both chimeric receptors specifically recognize their matching effector (Fig 5A). These findings suggest that the last six C-terminal leucine-rich repeats of a total of 15 deduced LRRs in MLA6 account for the recognition specificity of AVRA6 in barley. Furthermore, we discovered that co-expression of AVRa1 with M61111 or M66111 triggered a significant and specific 92% reduction of relative LUC activity in barley protoplasts indicative of a cell death response compared to the EV sample (Fig 5A). This suggests that, out of 15 predicted LRRs in the MLA1 receptor, the 12 C-terminal ones contribute to the specific recognition of AVRA1. Together, these findings corroborate previous experiments that show a significant growth reduction of Bgh isolate A6 when barley cells express M16666 and M11166, or growth reduction of Bgh isolate K1, when barley cells express M61111 or M66111 [38]. While our data does not exclude that other MLA domains contribute to the association with the Bgh AVRA effector proteins, we conclude that the MLA LRR regions confer Bgh recognition specificities to of the different Mla alleles in barley.

[Figure omitted. See PDF.]

Fig 5. Specific recognition of AVRA6 and AVRA1 by MLA1/MLA6 chimeric constructs in planta.

(A) Barley cv. Golden Promise protoplasts were transfected with a LUC reporter construct and pIPKb002 vectors containing cDNAs of AVRa6, AVRa6-V2, AVRa1, AVRa1-V1 or an empty vector (EV) together with vectors harboring intron-containing DNA of receptor chimeras M16666, M11166, M61111, or M66111 under the control of a pZmUBI promotor. Transfections were performed at least seven times independently. Significant differences between samples were analyzed using non-parametric Kruskal-Wallis (KW) analysis followed by a Dunn’s test. Calculated KW p-values are as follows: M16666: p = 0.001883; M11166: p = 0.000559, M61111: p = 0.0001582, M66111: p = 1.658e-05. Samples labeled with identical letters did not differ significantly (p < 0.05) in the Dunn’s test for the corresponding Mla variant. (B) Transient transformation of N. benthamiana leaves with empty vector (EV) or cDNAs of AVRa6 or AVRa1 variants fused C-terminally with a mYFP tag together with Mla1 or Mla6 cDNAs or M16666, M11166, M61111, or M66111 intron-containing DNAs with a C-terminal 4xmyc fusion. All constructs were expressed from a 35S promotor. Figures show a representative of at least three independent co-transformations. (C) MLA-4xmyc proteins were extracted two days post infiltration and separated using a 10% polyacrylamide gels and detected using α-myc western blotting, CBB = Coomassie Brilliant Blue.

https://doi.org/10.1371/journal.ppat.1009223.g005

To determine if these results can be independently validated in a heterologous system, we co-expressed C-terminally 4xmyc-tagged M16666, M11166, M61111, and M66111 and C-terminally mYFP-tagged AVRa6 and AVRa1 variants in N. benthamiana. We observed a strong cell death response upon co-expression of M11166-4xmyc with AVRa6-mYFP, suggesting that the last six C-terminal LRR repeats of MLA6 are sufficient for recognition of AVRa6 even in the absence of further barley-specific host proteins (Fig 5B). We detected weak recognition of AVRA1 by M61111 under UV light at 302 nm in N. benthamiana (indicative of accumulation of autofluorescent compounds in dying plant cells; S11 and S14 Figs), whereas the specific recognition of AVRA6 by M16666 and AVRA1 by M66111 seen in barley protoplasts was completely lost, suggesting that other barley-specific protein(s) might be necessary for the functionality of these chimeric receptors in the heterologous expression system.

The LRRs of the MLA10 and MLA22 receptors specifically recognize allelic AVRA10 and AVRA22

To test if the LRRs of MLA NLRs are necessary to specifically recognize not only sequence unrelated, but also sequence related allelic AVRA effectors, we designed two chimeric receptor genes encoding the MLA10 CC-NB fused with the MLA22 LRRs (MLA10LRR22) and the MLA22 CC-NB domain fused with the MLA10 LRRs (MLA22LRR10) (S12 Fig). Subsequently, Mla10-4xmyc, Mla22-4xmyc, Mla10Lrr22-4xmyc or Mla22Lrr10-4xmyc were co-expressed with AVRa10-mYFP, AVRa10-V/AVRa22-V-mYFP, or AVRa22-mYFP in heterologous N. benthamiana. Co-expression of Mla10-4xmyc or Mla22Lrr10-4xmyc with AVRa10-mYFP led to cell death in N. benthamiana leaves, but no cell death was observed when these Mla NLRs were co-expressed with an empty vector (EV), AVRa10-V / AVRa22-V-mYFP, or AVRa22-mYFP (Fig 6A). Additionally, expression of Mla22-4xmyc and Mla10Lrr22-4xmyc led to cell death when co-expressed with AVRa22-mYFP, but not when these proteins were co-expressed with AVRa10-mYFP, AVRa10-V/AVRa22-V-mYFP, or an EV control (Fig 6A). The MLA10LRR22 and MLA22LRR10 receptor chimeras were detectable in N. benthamiana leaf extracts at levels comparable with the MLA10 and MLA22 receptors (Fig 6B). To determine whether these results were reproducible in the homologous barley protoplast system, we expressed Mla10Lrr22 or Mla22Lrr10 together with AVRa10 and AVRa22 in leaf protoplasts and measured reduction of LUC activity as a proxy for cell death. In comparison to the EV reference sample, co-expression of AVRa22 with Mla10Lrr22 and AVRa10 with Mla22Lrr10 lead to an average 80% and 40% reduction of relative LUC activity, respectively, and this was not the case when AVRa10 was co-expressed with Mla10Lrr22 or when AVRa22 was co-expressed with Mla22Lrr10 (Fig 6C). Taken together, the results suggest that the 58 amino acid differences between the LRRs of Mla10 and Mla22 are major determinants of respective recognition specificities for the allelic AVRA10 and AVRA22 effectors.

[Figure omitted. See PDF.]

Fig 6. The LRR domains of MLA10 and MLA22 distinguish between AVRA10 and AVRA22.

(A) Transient transformation of Nicotiana benthamiana leaves with EV or cDNAs of AVRa10, AVRa10-V/AVRa22-V, and AVRa22 fused C-terminally with mYFP together with Mla10 or Mla22 cDNAs fused C-terminally with a 4xmyc tag. All constructs were expressed from a 35S promotor. Cell death was scored five days post infiltration (dpi) and Figures show a representative of at least 15 co-transformations. (B) Protein levels of MLA-4xmyc after total protein extraction from N. benthamiana leaves at two dpi. Proteins were separated on a 10% polyacrylamide gel and a detected using α-myc western blotting (WB) (C) Barley cv. Golden Promise protoplasts were transfected with a LUC reporter construct and pIPKb002 vectors containing cDNAs of AVRa10 or AVRa22 together with Mla10Lrr22 and Mla22Lrr10 chimeras. Transfections were performed at least eight times independently. Significant differences between samples were analyzed using non-parametric Kruskal-Wallis (KW) one-way analysis of variance. Calculated KW p-values are as follows: Mla10Lrr22: p = 0.0007775; Mla22Lrr10: p = 0.01654. Samples labeled with different letters differed significantly (p < 0.05).

https://doi.org/10.1371/journal.ppat.1009223.g006

An association between MLA10 and AVRA10 was previously shown to be detectable in plant extracts and in yeast [11]. Using a previously established split-LUC complementation assay, we therefore tested, whether the MLA22LRR10 hybrid receptor also specifically interacts with the AVRA10 effector when co-expressed in planta. We generated constructs expressing AVRa variants fused C-terminally to the N-terminal part of the LUC reporter (AVRa-nLUC); and Mla variants fused C-terminally to the C-terminal part of the LUC reporter (Mla-cLUC) [11]. We then performed A. tumefaciens-mediated transformation of N. benthamiana leaves to express AVRa10-nLUC or AVRa10-V/AVRa22-V-nLUC (not recognized AVRa10 variant) together with either Mla10-cLUC, Mla22Lrr10-cLUC or Mla10Lrr22-cLUC. Forty hours post infiltration, we determined LUC activity as a proxy for AVRA/MLA association, as described previously [11]. LUC activity was significantly higher in samples that co-expressed AVRa10-nLUC with Mla10-cLUC or Mla22Lrr10-cLUC, when compared to samples where AVRa10-nLUC was exchanged with its virulent variant AVRa10-V/AVRa22-V. This was not the case when the AVRa10-nLUC variants were co-expressed with Mla10Lrr22-cLUC (Fig 7A and 7B). Our data suggests a reduced association of AVRA10 with the MLA22LRR10 hybrid receptor compared to wild-type MLA10, which is in agreement with differences in cell death scores of N. benthamiana leaves co-expressing AVRa10-mYFP with Mla10-4xmyc and Mla22Lrr10-4xmyc (S14D Fig).

[Figure omitted. See PDF.]

Fig 7. The LRR domain of MLA10 accounts for the specific interaction with AVRA10 in planta and in yeast.

(A) Nicotiana benthamiana leaves were transformed transiently with vectors containing cDNAs of Mla10-cLUC, Mla10Lrr22-cLUC or Mla22Lrr10-cLUC together with vectors containing cDNAs of AVRa10-nLUC or AVRa10-V/ AVRa22-V nLUC lacking signal peptides (SPs), under the control of a 35S promoter. LUC activity was determined forty hours after transfection. The experiment was performed on at least three independent days with two to four replicates (independent set of plants) each day. Significant differences between AVRa10-nLUC or AVRa10-V/ AVRa22-V nLUC were analyzed using one-way Kruskal-Wallis (KW) analysis. Calculated KW p-values are as follows: Mla10: p = 0.0001491; Mla22Lrr10: p = 0.009035; Mla10Lrr22: p = 0.8079. Samples labeled with different letters differed significantly (p < 0.05). (B) Protein levels of MLA10-cLUC, MLA22LRR10-cLUC and MLA10LRR22-cLUC in N. benthamiana leaf extracts. Proteins were separated on a 8% SDS-PAGE gel and a detected using anti-LUC western blot (WB). (C) Yeast was co-transformed with cDNAs of N-terminal LexABD-fused MLA and N-terminal B42AD-fused AVRA variants. Growth on media lacking Leucine indicates association of respective proteins fused to AD (activation domain) and BD (Binding domain). (D) Protein levels of LexABD-MLA and B42AD-AVRA variants. Proteins were precipitated using an ammonium-acetate buffer and dissolved in a urea-SDS sample buffer before separation on a 10% or 12% polyacrylamide gel and detection by either α-LexA or α-HA WB.

https://doi.org/10.1371/journal.ppat.1009223.g007

We also tested whether AVRA10 can interact with MLA22LRR10 in the absence of other plant proteins in yeast. We co-expressed LexABD-Mla10Lrr22 or LexABD-Mla22Lrr10 under the control of a constitutive ADH1 promoter with B42AD-AVRa10, B42AD-AVRa10-V/AVRa22-V, or B42AD-AVRa22 under the control of a galactose (GAL1)-inducible promoter. Co-expressing B42AD-AVRa10 with LexABD-Mla22Lrr10 or with LexABD-Mla10 in a yeast two-hybrid assay (Y2H) led to yeast growth on leucine-deprived media (Fig 7C). Little growth was detectable when LexABD-Mla22Lrr10 or LexABD-Mla10 was co-expressed with B42AD-AVRa10-V/AVRa22-V, while no growth was detected when co-expressing B42AD-AVRa22 (Fig 7C), even though all effector and receptor fusion proteins were detectable in yeast extracts (Fig 7D). Taken together, our findings suggest that the MLA10 LRR domain is responsible for specific recognition of AVRA10 and that this is dependent on effector-receptor association. However, we were unable to detect an interaction of LexABD-Mla22 or LexABD-Mla10Lrr22 with B42AD-AVRa22 in this Y2H assays (Fig 7C).

Multiple residues in AVRA10 and AVRA22 are responsible for differential recognition specificities of MLA10 and MLA22

It has been proposed that direct fungal effector-plant NLR receptor interactions are mediated by cumulative binding of multiple effector aa residues to the surface of its corresponding NLR receptor [27,39]. We aimed to resolve which of the 11 amino acid residues that are polymorphic between AVRA10 and AVRA22 alleles (excluding the SP) are responsible for the specific recognition by the cognate MLA10 and MLA22 receptors. On the basis of AVRA10 secondary structural predictions, we divided AVRA10/AVRA22 proteins into three equally long parts: an N-terminal (residues 22–54 aa, comprising ß1-ß2 sheets and the α1-helix, which included the two amino acid substitutions D45G, D53E), a central (55–86aa; comprising the ß3-ß4 sheet and cluster of most amino acid differences Q55H, D58N, G59D, Q61P, H64Y, and the residue F77Y), and a C-terminal part (87–118 aa; including the ß5-ß6 sheets and three amino acid differences V93L, W96L, I111N) (Fig 8A). These individual regions were exchanged between AVRA10/AVRA22 effector peptides and we then tested the interactions of the six resulting chimeric AVRA10/AVRA22 effector constructs (called chimera11, chimera12, chimera13, chimera14, chimera15 and chimera16) with MLA10 and MLA22, in N. benthamiana as described above. All chimeric proteins were detectable after GFP-Trap enrichment except for chimera16-mYFP, which was not consistently detectable (Fig 8C). Co-expression of chimera14-mYFP with Mla22-4xmyc led to cell death (Figs 8B, S13 and S14). These findings suggest that the C-terminal polymorphic residues V93, W96, and I111 are not responsible for the specific recognition by MLA22.

[Figure omitted. See PDF.]

Fig 8.

Co-expression of AVRA10 and AVRA22 chimeras with MLA10 and MLA22 in N. benthamiana. (A) Protein sequence alignment of the AVRA10/AVRA22 chimeric construct. Grey boxes below sequences show the length of the N-terminal, the central and the C-terminal effector part. Dashes represent missing/deletion of effector parts and points designate identical amino acid residues (B) Co-expression of N. benthamiana with cDNAs of AVRa10, AVRa22, or chimeric AVRa10/AVRa22 constructs fused C-terminally with mYFP and Mla10 or Mla22 cDNAs fused C-terminally with a 4xmyc tag from the 35S promotor in N. benthamiana leaves. Cell death was scored five days post infiltration and Figures show a representative of at least seven co-transformations. (C-E) Protein levels of AVRA-mYFP and chimeric AVRA10/AVRA22mYFP variants after total protein extraction from N. benthamiana leaves at two dpi. Proteins were separated on a 12% polyacrylamide gel and detected by α-mYFP western blotting.

https://doi.org/10.1371/journal.ppat.1009223.g008

While in chimera14-mYFP, the three C-terminal residues of AVRA22 are exchanged for the respective amino acids found at these positions in AVRA10, in chimera12-mYFP the three C-terminal residues of AVRA10 are exchanged for AVRA22-specific amino acid residues (Fig 8A). Even though both effector chimeras were stable in planta, chimera12-mYFP was not recognized by MLA10-4xmyc (Figs 8B, 8C and S13 and S14). This suggests that single, double, or triple amino acid mutations at aa positions 93, 96, or 111 within the C-terminus of AVRA10 can lead to a loss of MLA10-specific recognition. We sought to determine which amino acid residues at the C-terminus, if exchanged to the respective AVRA22 residues, would result in abrogation of MLA10-specific recognition. To this end, we introduced L93V, L96W, or N111I single amino acid substitutions in chimera12-mYFP. The resulting chimera28-mYFP (L93V), chimera29-mYFP (L96W), and chimera30-mYFP (N111I) constructs were co-expressed with Mla10-4xmyc and with Mla22-4xmyc. Co-expression of chimera29-mYFP with Mla10-4xmyc led to cell death, while co-expression of chimera28-mYFP or chimera30-mYFP with Mla10-4xmyc did not (Figs 8B–8D and S13 and S14), suggesting that the tryptophan at position 96 in AVRA10 is important for MLA10-specific recognition. However, we cannot exclude that differences in protein stability between mYFP fused chimera 29 and 28, or 30, accounts for the lack of cell death in samples co-expressing chimera28-mYFP and chimera30-mYFP together with Mla10-4xmyc.

Even though chimera14-mYFP and chimera15-mYFP differ by only two N-terminal amino acids at positions 45 and 53 and both proteins are detectable, co-expression of chimera15-mYFP with Mla22-4xmyc did not trigger cell death (Figs 8B, 8C and S13 and S14). This suggests that residues at one or both of these N-terminal positions are necessary for the specific recognition by MLA22. To test this hypothesis, we introduced single D45G or D53E substitutions into chimera15-mYFP (Fig 8A). The resulting chimera21-mYFP (D53E) and chimera22-mYFP (D45G) constructs were co-expressed with Mla10-4xmyc or Mla22-4xmyc. Co-expression of chimera22-mYFP but not chimera21-mYFP with Mla22-4xmyc led to cell death, while no cell death was observed upon co-expression of chimera21-mYFP with Mla22-4xmyc, suggesting that the glycine at position 45 but not the glutamic acid at position 53 is essential for MLA22-specific recognition (Fig 8A, 8B and 8E).

To test if the N-terminal and central parts of the AVRa22 effector are sufficient to trigger cell death when co-expressed with Mla22, we constructed a deletion construct (Δ93–118) of chimera22, which we termed chimera23 (Fig 8A). Co-expression of chimera23-mYFP with Mla10-4xmyc or Mla22-4xmyc did not trigger cell death, although the chimera23-mYFP protein was seemingly more stable than AVRA10 and all other chimeric proteins (Figs 8B–8E and S13 and S14). Even though the C-terminal residues L93, L96, and N111 are not specifically recognized by MLA22, our findings suggest that the C-terminal region of the AVRA22 effector potentially stabilizes the conformation of the N-terminal and central regions, which are necessary for MLA22-specified recognition. In summary, the N-terminal glycine at position 45 and the C-terminal tryptophan at position 96 are important for MLA22- and MLA10-specific recognition, respectively.

In addition, we assessed the role of amino acids in the central positions 55, 58, 59, 61, 64, and 77 for MLA10- and MLA22-specific recognition. We introduced double mutations in chimera22-mYFP to generate chimera24-mYFP (H55Q and N58D), chimera25-mYFP (D59G and P61Q) and chimera26-mYFP (Y64H and Y77F), which were co-expressed with Mla10-4xmyc or Mla22-4xmyc (Fig 8A). While co-expression of chimera24-mYFP with Mla22-4xmyc, but not with Mla10-4xmyc led to a specific cell death response, co-expression of chimera25-mYFP with Mla22-4xmyc or with Mla10-4xmyc did not lead to cell death in N. benthamiana leaves (Figs 8B–8E and S13 and S14). Surprisingly, chimera26-mYFP triggered a strong cell death response when co-expressed with Mla10-4xmyc and a subtle but consistent cell death phenotype when co-expressed with Mla22-4xmyc, suggesting that it is recognized by both receptors (Fig 8B–8E).

To independently verify the data, we also co-expressed a selection of AVRa10/AVRa22 chimeras (chimera12, chimera14, chimera21, chimera22, chimera24, chimera26 and chimera29) together with Mla10 or Mla22 in protoplasts of barley cv. Golden Promise and determined cell viability by LUC activity, as described above. LUC activity was approximately 50% lower in samples co-expressing Mla10 with AVRa10 when compared to samples that co-express Mla10 with AVRa22, and this is in agreement with previously published data [11] (Fig 9A). We detected intermediate LUC activity when co-expressing Mla10 together with chimera26 or chimera29, but this reduced LUC activity did not differ significantly from the sample co-expressing Mla10 and AVRa10 (Fig 9A). This was not the case for samples co-expressing Mla10 together with chimera12, chimera14, chimera21, chimera22, or chimera24 (Fig 9A).

[Figure omitted. See PDF.]

Fig 9. Co-expression of a selection of AVRA10/AVRA22 chimeras with MLA10 and MLA22 in barley protoplasts.

Barley protoplasts of cv. Golden Promise were co-transfected with a LUC reporter assay and pIPKb002 vectors containing cDNAs of AVRa10, AVRa22, chimera12, chimera14, chimera21, chimera22, chimera24, chimera26 or chimera29 without signal peptide or with an empty vector (EV) together with either (A) Mla10 or (B) Mla22 in pipkb002. Transfections were performed at least six times independently. Significant differences between samples were analyzed using non-parametric Kruskal-Wallis (KW) analysis followed by the Dunn’s test. Calculated KW p-value are as follows: Mla10: p = 1.439e-07, Mla22: p = 5.374e-11. Samples labeled with different letters differed significantly (p < 0.05) in the Dunn’s test.

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LUC activity was on average 80% lower in samples co-expressing Mla22 with AVRa22 when compared to samples that co-express Mla22 with AVRa10, and this is again in agreement with published data [11]. LUC activity of samples co-expressing Mla22 together with chimera14, chimera22, chimera24 and chimera26 was not statistically different from the activity observed when co-expressing Mla22 and AVRa22 (Fig 9B). This was not the case for samples co-expressing Mla22 together with chimera12, chimera21 or chimera29. Notably, we detected an intermediate relative LUC activity when co-expressing Mla22 together with chimera26 (Fig 9B). Similarly, cell death scores of N. benthamiana leaves co-expressing Mla22-4xmyc together with chimera26-mYFP were also lower than when co-expressing Mla22-4xmyc together with AVRa22-mYFP (Figs 8 and S14). We thus conclude that the barley protoplast cell death data (Fig 9) overall recapitulate the MLA10 and MLA22 specificities towards AVRA chimeric constructs observed in the heterologous N. benthamiana system (Fig 8).

In summary, our findings suggest that for triggering MLA10-specific cell death, the four residues D53, H64, F77, and W96 of AVRA10 cannot be exchanged to the residues found in AVRA22. In turn, to trigger MLA22-specific cell death, the five amino acid residues G45, H55, N58, D59, and P61 of AVRA22 cannot be exchanged to the residues found in AVRA22. Furthermore, deletion of the C-terminal third of the AVRA10 and AVRA22 effectors leads to loss of avirulence function (Fig 8).

To determine if MLA-mediated cell death initiated by recognition of the AVRA effector also correlates with receptor-effector association in plant extracts, we again applied the split-LUC complementation assay. We transiently expressed Mla10-cLUC together with AVRa10-nLUC, chimera26-nLUC, chimera29-nLUC and as a control, chimera22-nLUC in N. benthamiana leaves, followed by LUC measurements at 40 hours post infiltration of leaves with the A. tumefaciens carrying constructs of interest. LUC activity of samples co-expressing Mla10-cLUC with AVRa10-nLUC, chimera26-nLUC and chimera29-nLUC was significantly higher than the LUC activity observed in the samples expressing Mla10-cLUC together with chimera22-nLUC (Fig 10A and 10B). Chimera26 and chimera29 but not chimera22, can trigger MLA10-mediated cell death in co-expression assays (Figs 8 and 9), and as such, we conclude that the recognition specificities mediated by MLA10 towards the AVRA chimeric variants 26, 29 and 22 correlate with receptor-effector association. We again only observed intermediate levels of LUC activity in samples co-expressing Mla10-cLUC together with chimera26-nLUC or chimera29-nLUC (Fig 10A). This is in agreement with the quantitative cell death assay in barley protoplasts (Fig 9A), and suggests that when compared to AVRa10, these constructs are impaired in their ability to activate and associate with MLA10 in planta and this may be associated with levels of protein expression (Fig 10B).

[Figure omitted. See PDF.]

Fig 10. AVRA10 amino acid residues that are responsible for specific recognition correlate with residues that interact with the MLA10 receptor.

(A) N. benthamiana plants were transformed transiently with vectors containing cDNAs of Mla10-cLUC together with cDNAs of AVRa10-nLUC without signal peptide, chimera22-nLUC, chimera26-nLUC or chimera29-nLUC under the control of a 35S promoter. LUC activity was determined 40 h after A. tumefaciens-mediated transformation. The experiment was performed on at least four independent days with two to four replicates (independent set of plants) each day. Significant differences between samples were analyzed using non-parametric Kruskal-Wallis (KW) analysis followed by the Dunn’s test. Calculated KW p-value = 5.03e-05. Samples labeled with different letters differed significantly (p < 0.05) in the Dunn’s test. (B) Protein levels of AVRA10-nLUC, chimera22-nLUC, chimera26-nLUC and chimera29-nLUC. Proteins were separated on a 8% SDS_PAGE gel and a detected using anti-LUC western blotting (WB).

https://doi.org/10.1371/journal.ppat.1009223.g010

Two amino acids of AVRA10 that cannot be exchanged to respective AVRA22 residues are located in a predicted positively charged area that corresponds to the catalytic cleft of the fungal F1 RNase

Microscale thermophoresis assays suggested that CSEP0064 has some affinity to total RNA but its X-ray structure suggests that it lacks residues required for RNA hydrolysis [30]. Our data also suggests that the putative RNase-like fold of AVRA effectors is not associated with RNase activity (Fig 4). Here, we examined the location of the AVRA10 and AVRA22 residues that are required for specific recognition by MLA10 and MLA22, and if the corresponding residues in the F1 RNase are required for RNA binding and hydrolysis. To do this, we superimposed AVRA10 and AVRA22 predicted structures on the structure of Fusarium moniliformis F1 RNase. Residues Y38, Y42, and Y45 of the F1 RNase are involved in binding the ribose and phosphate of 2’ GMP and the respective amino acids found in AVRA10 (F51, F54, and H57) are identical to those of AVRA22, and as such, do not account for specific MLA recognition (Fig 11A–11C). The R77 residue in the F1 RNase, also forms a contact with the phosphate in 2’ GMP. The corresponding residue can also be found in AVRA10 and AVRA22 (residue R81, Fig 11A–11C) but not in the CSEP0064 structure or the predicted structures of any other AVRA effector isolated so far. The residues W96 and H64 of AVRA10 are L96 and Y64 in AVRA22 and have dissimilar properties to the corresponding residues (H92 and E58, respectively) in the F1 RNase. Electrostatic potential prediction using Adaptive Poisson-Boltzmann Solver (APBS) of surfaces suggests that H64, R77, and W96 in AVRA10 and L64, R77, and L96 in AVRA22 belong to a positively charged cleft (Fig 11B–11D). In AVRA10, these residues are predicted to be part of the positively charged surface patch. For recognition by MLA10, H64 and W96 can indeed not be exchanged to the respective residues found in AVRA22 (Fig 11B). In contrast, the AVRA22 residues that cannot be exchanged to the respective AVRA10 residues without losing MLA22 avirulence activity, can be found in a negatively charged surface patch away from the positively charged area, presumably required for MLA10 recognition (Fig 11D). These results suggest that the AVRA residues, which confer specific recognition by MLA10 and MLA22 receptors, are located in distinct predicted surface patches of the avirulence proteins encoded by allelic AVRa10 and AVRa22.

[Figure omitted. See PDF.]

Fig 11. The location of amino acid residues in AVRA10 and AVRA22 that determine MLA10 and MLA22 recognition specificities.

(A and C) show structural superimposition of the crystal structure of Fusarium moniliformis RNase F1 (yellow) and IntFOLD version 5.0 structural predictions of AVRA10 or AVRA22 (grey). Depicted in green is the F1 RNase ligand 2’-guanosine monophosphate (2’ GMP); residues of the F1 RNase catalytic triad and corresponding AVRA residues are depicted in red; residues of the F1 RNase RNA binding pocket and corresponding AVRA residues are shown in blue. The residues of AVRA10 and AVRA22 required for specific MLA10 and MLA22 recognition as determined in Figs 8–10 are framed with a purple rectangle. (B and D) Predicted electrostatic surface potential of the AVRA10 and AVRA22 effector surface calculated using Adaptive Poisson Boltzmann Solver (APBS) [67]. The residues of AVRA10 and AVRA22 required for specific MLA10 and MLA22 recognition as determined in Figs 8–10 are indicated. Below is a scale bar of the electrostatic potential (red = negative charge, white = neutral charge, blue = positive charge).

https://doi.org/10.1371/journal.ppat.1009223.g011

Discussion

Identification of AVRA6

Long-read DNA sequencing and high-quality genome assembly of the DH14 Bgh isolate recently recovered 30 Mb of previously unassembled repetitive regions of the Blumeria genome, which linked together multiple non-contiguous series of genomic sequences, including scaffold 16 [40]. This may explain why we failed to identify BLGH_00708, BLGH_00709 and BLGH_07091 as AVRA6 in our previous studies [11,28] and emphasizes the importance of high-quality Blumeria genome assemblies for identification of novel AVRA effectors. We found three AVRa6 paralogues in the RACE1 genome, and in line with this observation, three non-identical paralogues of AVRa7 have been described in RACE1 [11], indicating that these AVRa effectors were duplicated [11]. Similarly, BLGH_07092 is likely an AVRa6 copy with a frameshift mutation. This AVRa duplication could facilitate the gain of new virulence functions.

Unlike other virulent variants of Bgh AVRa effectors that carry SNPs in the coding region or transposon insertions, or are transcriptionally silent [11,28], here we report that virulence of Bgh isolates on Mla6 NILs is possibly caused by splice site mutations in the intron of transcripts from isolates virulent on Mla6 lines that map to the AVRa6 gene. The intron retention observed in most of these transcripts is potentially caused by either a splice branch point mutation or a splice donor site mutation and leads to premature stop codons (S3 and S4 Figs).

Even though the encoded truncated proteins are detectable in heterologous N. benthamiana (Fig 2C), RNA-Seq analysis of virulent Bgh isolates on barley leaves suggests that these mutations result in significantly reduced transcript levels. The latter is possibly a consequence of nonsense-mediated mRNA decay (NMD) [41]. This observation, together with a high virulence frequency on Mla6 NILs in European Bgh populations [42], suggests that the loss of the AVRa6 effector gene does not have a detrimental impact on Bgh virulence. Future studies might clarify whether AVRa6 virulence function can be compensated by AVRa6 family members or more distantly related effectors.

A predicted common ribonuclease-like fold among Blumeria AVRA, AVRPM3 and AVRPM2 effectors

AVRA6 was predicted to be structurally similar to CSEP0064 (Fig 3). Upon re-analysis of all previously reported Bgh AVRA effectors using the version 5.0 of the IntFOLD structural prediction server, we report here evidence supporting a common structural fold amongst the so far isolated AVRA effectors despite the lack of relatedness between their DNA and protein sequences (Fig 3). Moreover, AVRA effectors appear to share this structural fold at least with Bgt AVRPM2 and AVRPM3D3 effectors that are recognized by wheat NLRs PM2 and PM3, respectively (Fig 3; [22,35,36]). In addition, protein alignments and in silico tertiary structure modelling suggest that Bgt AVRPM3A2/F2 and AVRPM3B2/C2 also have a central α-helix that faces three to four β-sheets [22]. Even though AVRA effectors seem to have a common predicted fold similar to RNases, the residues critical for catalytic activity are lacking in the predicted AVRA structures and we did not detect ribonuclease activity when AVRA effectors were co-incubated with RNA (Fig 4A).

Given that multi-allelic barley MLA, multi-allelic wheat PM3, and wheat PM2 NLRs are sequence-unrelated and are encoded on non-syntenic chromosomal locations, it is possible that these immune receptors arose by convergent evolution to detect distinct members of the structurally related superfamily of powdery mildew RALPH effectors.

We speculate on two evolutionary scenarios that might explain the diversity of extant RNase-like effectors in Bgh and Bgt. In a common descent scenario, all RALPH effectors have diversified from an “ur-RALPH”, which was present in the last common ancestor prior to host specialization of grass powdery mildews [29]. For instance, striking sequence conservation of AvrPm2 among Blumeria ff spp secalis, tritici and hordei [36] and the presence of orthologous candidate effector gene families among specialized forms of grass powdery mildews support a common descent model [43]. The relatively small number of RALPH effectors in dicot-infecting powdery mildew species such as Erysiphe pisi [44] and in the early-diverged Parauncinula polyspora [45] suggests that RALPHs could have evolved 80–90 million years ago [46]. However, the variable intron location in Blumeria AVR genes (S6 and S7 Figs) questions this hypothesis. In an alternative scenario, the predicted structural relatedness of known AVRPM and AVRA effectors could be the product of convergent evolution from different fungal RNases in the order Erysiphales after the differentiation of formae speciales. In summary, our data is reminiscent of findings indicating the existence of sequence unrelated but structurally related MAX effectors (Magnaporthe Avrs and ToxB-like) that account for 10% of the M. oryzae effector repertoire in this Ascomycete pathogen [47]. Another example for sequence-diversified but structurally-related effectors are oomycete RXLR effectors, such as ATR1 and ATR13 in Hyaloperonospora arabidopsidis [48,49], and PexRD2 and AVR3a11 in Phytophthora infestans [50].

The LRRs of allelic MLA receptors determine recognition of matching AVRA effectors

Earlier work with hybrids built from MLA1 and MLA6 receptors demonstrated that the MLA LRR is a determinant of Bgh isolate-specific recognition [38]. In this previous study it could not be clarified whether the respective AVRA effectors are the only fungal components that determine isolate-specific recognition by the MLA LRR domains. We show here that the LRR of four MLA receptors (MLA1, MLA6, MLA10, and MLA22) is responsible for specific recognition of matching AVRA effectors. We found that for the recognition of AVRA6, the C-terminal six LRR repeats of MLA6 cannot be exchanged to the ones found in MLA1, while the 12 C-terminal LRR repeats of MLA1 cannot be exchanged to those of MLA6 for recognition of AVRA1. Similarly, four C-terminal LRR repeats of the flax allelic L5 and L6 receptors are necessary for recognition of matching AvrL567 effectors [27]. Most sites of positive selection among MLA resistance specificities cluster on the predicted concave site of the C-terminal LRRs [19,20]. Thus, it is possible that these LRR residues are contact sites for specific recognition and association with structurally related AVRA effectors. We confirmed this assumption for the LRRs of MLA10 by observing an association of MLA22LRR10 with AVRA10 when the proteins were co-expressed in plants or in yeast (Fig 6C).

Unexpectedly, whereas M11166, M16666, M61111, and M66111 chimeras clearly recognize the corresponding AVRA effectors in barley protoplasts (Fig 5A), the latter three hybrid receptors are non-functional in heterologous N. benthamiana. The resistance function of several barley Mla recognition specificities, including Mla6, is genetically dependent on HvRar1, HvSgt1, and HvHsp90 [38,51,52], which form a chaperone/co-chaperone complex in which HvHSP90 directly interacts with the LRR of MLA [52,53]. Thus, the hybrid MLA1/MLA6 receptors might be dependent on an additional barley protein for full resistance function. Interestingly, the function of M11166 is known to be fully independent of HvSGT1 and HvRAR1 in barley and we have shown here that this is the sole MLA6/MLA1 chimeric receptor functional in N. benthamiana [38,51].

Multiple polymorphic AVRA10/AVRA22 residues influence recognition by MLA10 and MLA22

AVRa10 and AVRa22 effector alleles are maintained as a balanced polymorphism in a worldwide collection of Bgh isolates [11], which implies an important virulence function for the AVRa10/AVRa22 gene, supported by its membership in the Blumeria core effectorome [40]. As the effector alleles with only 11 polymorphic amino acids likely adopt an identical protein structure, we aimed here to pinpoint polymorphic residues in AVRA10/AVRA22 recognized by MLA10 and MLA22, respectively. Some effector chimeras, including chimera11 or chimera13 containing only two polymorphic residues compared to the respective WT avirulence effectors, escaped recognition by MLA10 and MLA22, even though these are stable proteins in N. benthamiana. This is consistent with the observation that other naturally occurring virulent AVRA effector variants can escape recognition by only one or two amino acid substitutions in the respective AVRA polypeptides [11,28]. Similarly, one amino acid exchange in Bgt AVRPM3A2/F2 leads to a loss of pathogen recognition [54]. We identified four residues in AVRA10 that cannot be exchanged to the ones found in AVRA22 without losing recognition by MLA10. Four different residues in AVRA22 cannot be exchanged to the ones found in AVRA10 without losing recognition by MLA22. Of note, chimera26 can be recognized by MLA10 and MLA22 (Figs 8 and 9), further suggesting that differential regions in AVRA10 and AVRA22 are recognized by MLA10 and MLA22, respectively. Our findings are consistent with the identification of multiple residues, spread along the Bgt AVRPM3B2/C2 effector polypeptide, that cannot be exchanged for specific detection by wheat PM3b or PM3c NLRs [22]. Multiple, additive contact points of the AvrL567-A and -D flax rust fungus alleles are recognized by the flax receptors L5 and L6, respectively [27]. In summary, our findings suggest that multiple residues on the AVRA effector surface determine the specific recognition by MLA receptors, and this may influence the functional diversification process of these receptors.

Previous studies suggested that RALPH effectors are pseudoenzymes that cannot cleave RNA due to the absence of a catalytic amino acid triad present in the fungal F1 RNase that are needed for enzymatic RNA catalysis [30]. These catalytic residues are E58, R77, and H92 [55]. We found that only one residue involved in RNA catalysis (R81) is conserved in the deduced AVRA10/AVRA22 RNase-like effectors. Notably, four amino acids in AVRA10 cannot be exchanged to the ones found in AVRA22 (D53, F77, H64, and W96), and these are located close to a predicted positively charged area on the effector’s surface. In the F1 RNase, the corresponding area forms the catalytic cleft. Residues required for MLA22 recognition are found in a negatively charged surface patch away from the negatively charged area presumably recognized by MLA10 (Fig 11A and 11B). This data is underlined by the recognition of chimera26 through MLA10 and MLA22, as chimera26 carries both of the described recognition patches. Recently, a few RALPH effectors were found in E. pisi, which infects a dicotyledonous host, and structural predictions showed that residues for RNA catalysis are partially conserved and are located within a positively charged binding cleft [44]. This is in agreement with our findings for Bgh AVRA10 and AVRA22 but contrasts with the absence of any catalytic triad residue as well as a positively charged binding cleft in the structure of Bgh CSEP0064 [30]. If these residues, which are located in the predicted positively charged cleft, and are recognized by MLA10, are also involved in potential RNA binding of AVRA10 and AVRA22 remains to be determined.

Methods

Phylogenetic analysis of Blumeria graminis formae speciales candidate-secreted effector proteins

Secretomes for the B. graminis formae speciales poae, lolium, avenae, tritici 96224, hordei DH14, secalis S1459, triticale T1-20, and dactylidis were obtained as described in Frantzeskakis et al. 2019 [40]. Subsequently, protein sequences without the signal peptide were aligned using MAFFT v7.310 (command used: mafft—amino —6merpair—maxiterate 1000—thread 12; [56]). The resulting alignment was then passed to IQ-TREE v1.6.beta4 (command used: iqtree-1.6.beta4-Linux/bin/iqtree -m VT+R8 -s all_seqs.fa.aln -nt 12 -bb 1000; [57]), and the phylogenetic tree generated was visualized using ITOL (https://itol.embl.de/tree/13461102183294661576347461; [58]). If not already publicly available [40,43,59], proteomes used for secretome prediction were generated using the MAKER pipeline [60] as described previously [40].

Plant material

The barley cultivar Golden Promise was grown at 19°C, 70% humidity and under a 16 h photoperiod. N. benthamiana plants were grown and maintained under standard greenhouse conditions.

Association analysis

RNA-seq read alignment, variant calling, and association analysis were performed as described in Saur et al., 2019 [11].

Generation of expression vectors

Entry clones and destination constructs for the expression of AVRa1, AVRa1-V1, AVRa10, AVRa22, AVRa10-V/AVRa22-V, Mla10, Mla22, Mla1, and Mla6 were previously published by Saur et al., 2019 [11]. CSEP0058 (BLGH_00697) was cloned from the cDNA of Bgh isolate DH14 using the primers listed in S3 Table. M16666, M61111, M11166, and M66111 DNA sequences with introns in the pUBI-NOS vector were previously published by Shen et al., 2003 [38], and for expression in N. benthamiana were amplified from the pUBI-NOS vector [38] and cloned into pENTR/D-TOPO without a stop codon (S3 Table). cDNAs of AVRa6, AVRA6-V2, CSEP0333 (BLGH00698), and BLGH_00700, chimeras 11, 12, 13, 14, 15, 16, and 23, chimeric Mla10Lrr22 and Mla22Lrr10 were synthesized with or without a stop codon as pDONR221 (KmR) entry clones by GeneArt (Thermo Fisher). Chimeras 21, 22, 24, 25, 26, 28, 29, and 30 were generated by site-directed mutagenesis PCR using primers listed in S3 Table. The integrity of all entry clones was confirmed by Sanger sequencing.

For transient expression assays in barley protoplasts, N. benthamiana, and yeast, the genes were recombined using LR-Clonase II (Thermo Fisher) into the pIPKb002 (SpecR) [61], pGWB517 (SpecR) [62], pXCGS-GW-mYFP (CarbR) [63], the pLexA-GW (CarbR) [64], or the pB42AD-GW (CarbR) [64] gateway-compatible destination vectors. Additional constructs used in this study were described in Saur et al., 2019 [11].

Transient gene expression assays in barley protoplasts

The isolation and transfection of barley protoplasts was performed as described in Saur et al., 2019 [33]. In short, cDNAs of the AVRas were co-expressed with cDNAs of Mla10, Mla22, Mla10Lrr22, and Mla22Lrr10 using the pIPKb002 vector with a strong ubiquitin promoter or with intron-containing DNA of chimeras M16666, M11166, M61111, or M66111 in a pUBI-NOS-vector (described in Shen et al., 2003 [38]) in barley cv. Golden Promise protoplasts. Protoplast solution (300 μl of 3.5 x 105 cells/ml) was transfected with 4.5 μg of LUC reporter construct, 10 μg of Mla plasmid, and 6.5 μg of the respective AVRa effector or an empty vector (EV). The protoplasts were incubated for 16 h at 21°C in a plant growth chamber and then harvested by centrifugation at 1,000 x g. Subsequently, the supernatant was removed, and protoplasts were lysed by addition of 180 μl of cell culture lysis reagent (Promega, E1531). The LUC activity of samples was measured in a luminometer (Centro, LB960) using a 96-well plate in which 50 μl of protoplast lysate were mixed with 50 μl of the LUC substrate (Promega, E1501). The relative LUC units (RLU) were calculated by setting the absolute value of the EV sample to 1.

Transient gene expression assays in Nicotiana benthamiana

Expression constructs for AVRA and MLA and respective chimeras were always freshly transformed into Agrobacterium tumefaciens strains GV3101::pm90 and GV3101::pm90RK and selected on LB media containing the respective antibiotic resistance. Single colonies were inoculated into liquid LB medium and grown overnight at 28°C with agitation at 220 rpm to a maximal OD600 = 1.5. Agrobacteria were centrifuged at 2500 x g for 15 min and the pellet was resuspended in infiltration buffer (10 mM MES, pH 5.6, 10 mM MgCl2, and 200 μM acetosyringone) to an OD600 of 1 to 1.2. The suspensions of Agrobacteria were incubated at 28°C with shaking 150 rpm for at least 2 h. Leaves of four-week-old N. benthamiana plants were infiltrated with a 1:1 mix of bacteria carrying AVRa constructs or Mla constructs. The cell death score was assessed at four days post infiltration. Leaf tissue was harvested two days post infiltration for western blot analysis and 40 hours for split-LUC assays.

Split-luciferase complementation assay

The assay was performed as described in Saur et al., 2019 [11].

Plant protein extraction and immunoprecipitation for detection of fusion proteins

N. benthamiana leaf material was frozen in liquid nitrogen and ground to a fine powder using a Retsch bead beater.

For the detection of AVRA-nLUC and MLA-cLUC proteins, 50 mg of leaf tissue was resuspended in 150 μl of urea-SDS sample buffer (50 mM Tris-HCl pH 6.8, 2% SDS, 8 M urea, 2% β-mercaptoethanol, 5% glycerol, and 0.004% bromophenol blue) and vortexed at room temperature for 10 min before centrifugation at 16,000 × g for 10 min.

For the detection of AVRA-mYFP and MLA-4xmyc proteins, 300 mg of ground leaf tissue were dissolved in 2 mL of ice cold extraction buffer (150 mM Tris-HCl, pH 7.5, 150 mM NaCl, 10 mM EDTA, 10% (v/v) glycerol, 10 mM DTT, 2% (v/v) plant protease inhibitor cocktail (Sigma), 1 mM NaF, 1 mM Na3VO4, 1 mM PMSF, and 0.5% (v/v) IGEPAL). Extracts were centrifuged twice for 16 min at 16,000 x g at 4°C. For the detection of MLA-4xmyc proteins, the extracts were diluted 4:1 with 4 x SDS loading buffer for SDS-PAGE. Samples were heated for 5 min at 95°C. For the detection of AVRA-mYFP, the proteins were concentrated using GFP-trap-MA (Chromotek) beads. Beforehand, the beads were incubated in equilibration buffer (150 mM Tris-HCl, pH 7.5, 150 mM NaCl, 10 mM EDTA, pH 7.5, 10% Glycerol, 1.5% (w/v) BSA) for 1 hour at 4°C with slow rotation. The protein extracts were incubated with the equilibrated beads for 4 h at 4°C with slow rotation. Subsequently, the beads were washed five times with cold wash buffer at 4°C. The conjugated proteins were stripped off the beads by boiling the samples in 30 μl 4 x Laemmli sample buffer at 95°C for 10 min.

Samples were separated on 8% or 10% SDS-PAGE gels, blotted onto PVDF membranes and detected using anti-LUC (SIGMA L0159), anti-GFP (abcam ab6556) or anti-myc (abcam ab9106) antibodies followed by anti-rabbit IgG-HRP (Santa Cruz Biotechnology sc-2313). Proteins were detected with the SuperSignal West Femto chemiluminescent substrate (Thermo Fisher, catalog number 34095) using Gel Doc XR and a gel documentation system (Bio-Rad).

Protein expression and purification from Escherichia coli

AVRA6 (25–115) AVRA10 (21–119), and AVRA13 (21–122) were expressed in E. coli as fusion proteins with N-terminal GST tags. The expression plasmids pGEX6p-1 (GE Healthcare) were transformed into the E. coli strain BL21 (DE3) (Novagen) by heat shock and grown at 37°C in Luria-Bertani broth to an OD600 of 0.6. Isopropyl-β-D-thiogalactoside (IPTG, Sigma) was added to induce protein expression at 18°C for a further 12 h. The cells were harvested by centrifugation at 6,000 x g for 10 min at 4°C and resuspended in resuspension buffer (25 mM TRIS pH 8, 150 mM NaCl). Cell suspensions were lysed by sonification. Cell debris was removed by centrifugation at 30,000g for 2 h. The soluble fractions were collected and allowed to flow through GST resin (GE Healthcare). After washing with two column volumes of the same buffer used for resuspension, another 2 ml of buffer and 10 μl of PreScission protease (GE Healthcare) were added to the column followed by overnight incubation to cleave off the AVRA proteins from the GST resin. The cleaved AVRA proteins were then eluted and further purified by size-exclusion chromatography using a Superdex 200 10/30 gel filtration column (GE Healthcare).

Protein expression and purification from insect cells

AVRA6 (25–115) AVRA10 (21–119), and AVRA13 (21–122) were expressed in insect cells as fusion proteins with N-terminal GST tags. The expression plasmids pFASTBAC1 (Invitrogen) were transformed into the E. coli strain DH10Bac (Invitrogen) by heat shock. Successful transformation was validated by blue-white selection and bacmids of positive colonies were subsequently isolated with a DNA Mini Kit (QIAGEN). Sf21 insect cells (Invitrogen) were transfected with sequence verified bacmids by CellfectinII (Thermo Fisher). After five days incubation at 28°C, recombinant baculovirus P0 were harvested and used to amplify P1 virus for another three days. Insect cells were infected at concentration of 2.0 x 106–2.5 x 106 cells/ml with P1 virus for 60 h. Insect cells were harvested and re-suspended in resuspension buffer (25 mM TRIS pH 8, 150 mM NaCl,15mM imidazole) followed by sonification lysis. Cell debris were removed by centrifugation at 30,000g for 2 h. The soluble fractions were collected and allowed to flow through a GST affinity trap. After washing with two column volumes of the same buffer used for resuspension, another 2 ml of buffer and 10 μl of PreScission protease (GE Healthcare) were added to the column, followed by overnight incubation to cleave off the AVRA proteins from the GST resin. The cleaved AVRA proteins were then eluted and further purified by size-exclusion chromatography using a Superdex 200 10/30 gel filtration column (GE Healthcare). The proteins were tested for RNase activity with the same method applied for E. coli purified proteins.

RNase activity assays

Leaf material from three-week-old barley cv. Golden Promise plants was harvested to extract total RNA using the RNeasy Plant Mini Kit (QIAGEN). The remaining genomic DNA was removed by treating RNA with TURBO DNase enzyme (Ambion). Purified AVRA effectors from E. coli were incubated with denatured total barley RNA. Then, 30 μl reaction mixtures (1 μg RNA, 1 μM protein in 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 50 mM KCl, and 2.5 mM EDTA) were incubated at 25°C for 90 min. RNase F1 (Sigma) was included as a positive control. For analysis by the Bioanalyzer 2100 (Agilent Technologies, USA) 10 μl of sample were used.

To test the consumption of native rabbit rRNA, purified AVRA effectors were incubated with 20 μl of rRNA from rabbit reticulocyte lysate (Promega) following the method of Kao et al. 2001 [37]. 30 μl reaction mixtures (20 μl rabbit reticulocyte lysate, 1μM purified AVRA effectors in 15 mM Tris-HCl pH 8.0, 15 mM NaCl, 50 mM KCl, 2.5 mM EDTA) were incubated at 25°C. After 60 or 30 min, the reaction was terminated by adding 20 μl phenol/chloroform and was vortexed for 30 seconds. Samples were sedimented at 14,000 rpm for 15 min and 30 μl of the aqueous layer was removed and mixed with 6 μl electrophoresis loading buffer. For analysis by the Bioanalyzer 2100 (Agilent Technologies, USA) 10 μl of sample were used.

Yeast two-hybrid assays

Mla variants were cloned into the pLexA-GW vector [64] for expression with an N-terminal LexA activation domain under the control of a constitutive ADH1 promoter (BD-MLA). The AVRa variants were cloned into pB42AD-GW [64] for expression with an N-terminal B42 activation domain followed by the HA tag under the control of an inducible GAL1 promoter (AD-AVRa). Using the lithium acetate method [65], Mla bait constructs and AVRa prey constructs were co-transformed into the yeast strain EGY4.8 p8op-lacZ and successful transformants were selected by colony growth on SD-UHW/Glu (4% (w/v) Glucose, 0.139% (w/v) yeast synthetic drop-out medium pH 5.8 without uracil, histidine, tryptophan, 0.67% (w/v) BD Difco yeast nitrogen base, and 2% (w/v) Bacto Agar). Yeast transformants were grown to OD600 1 in liquid SD-UHW/Glu before harvesting cells for serial dilution on SD-UHW/Gal/Raf media (SD-UHW without glucose but with 2% (w/v) Galactose 1% (w/v) Raffinose, with (-UHW) or without Leucine (-UHWL)) and incubated for 14 days at 30°C.

Yeast protein extraction

For protein extraction, 10 ml of co-transformed yeast strains were grown to an OD600 of 1 in SD-UHW/Gal/Raf liquid medium at 30°C with shaking at 200 rpm. The proteins were precipitated using the ammonium acetate method (modified from Karginov and Agaphonov et al., 2016 [66]). In short, cells were harvested by centrifugation at 700 xg for 5 min. The pellets were resuspended in 200 μl NH4-acetate buffer (1 M NH4(CH3COO), 150 mM NaCl, 30 mM Tris-HCl, pH 7.5, 10 mM PMSF, 5 mM EDTA, and one tablet of Protease Inhibitor Cocktail (Roche). The yeast suspension was transferred into BeadBug-prefilled tubes with 0.5-mm silica glass beads (Sigma) and ground in a Precellys homogenizer (two times at 6,200 rpm for 30 sec, break: 15 sec). Afterwards, the DNA was sheared using a Diogenode Bioruptur ultrasonic water bath (twice for 30 sec at high power, break: 90 sec). The suspension without the beads was transferred into a Protein LoBind tube (Eppendorf). The glass beads were washed three times with 250 μl NH4-acetate buffer. The washes were combined with the suspension and incubated for 1.5 h on ice. Precipitated proteins were harvested by centrifugation (16,000 x g for 10 min). Precipitates were washed with 1 ml 1 M NaCl and the pellet was resuspended with 200 μl Urea-SDS sample buffer (50 mM Tris-HCl, pH 6.8, 2% SDS, 8 M Urea, 1% ß-mercaptoethanol, 2 mM EDTA, 5% glycerol, and 0.004% bromophenol blue) at room temperature. Resuspension in urea-SDS buffer and omission of the boiling step is essential for detection of LexA-MLA fusion proteins. For western blotting, 10–15 μl of the sample were loaded on 8% or 12% SDS page gels, blotted onto PVDF membranes and probed with either anti-HA (Merck, clone 3F10, RRID:AB_390914) or anti-LexA (Santa Cruz, Biotechnology, sc7544, RRID:AB_627883) primary antibodies, followed by incubation with secondary anti-rat (Santa Cruz Biotechnology, sc2065, RRID:AB_631756) or anti-mouse IgG-HRP antibodies (Santa Cruz Biotechnology, sc2005, RRID:AB_631736) for the detection of AVRA or MLA proteins, respectively. HA and LexA fusion proteins were detected by HRP activity on SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher 34095) using a Gel Doc XR and gel documentation system (Bio-Rad).

Supporting information

S1 Fig. Transient co-expression of AVRa6 candidates with Mla6 in cultivar (cv.) Golden Promise barley protoplasts.

Transient co-expression of EV or cDNAs of BLGH_00709 or BLGH_00697 lacking their respective signal peptides together with Mla6 and pUBI:Luciferase in cv. Golden Promise protoplasts. The LUC activity relative to the EV sample was measured as a proxy for cell death 16 hours post transfection. Bar diagrams represent mean relative LUC activity of eight transfections, which are represented by dots, while the standard deviation is indicated by error bars. Significant differences between samples were analyzed using a one-way ANOVA and siginificant difference is indicated by different letters. Calculated p-value: p = 0.000331

https://doi.org/10.1371/journal.ppat.1009223.s001

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S2 Fig. Association of AVRa6 transcriptomic data with phenotypes of Bgh isolates on Mla6 NILs.

The table depicts infection phenotypes of 27 Bgh isolates on barley Mla6 near-isogenic lines (NILs) [11,28] of the cultivar (cv.) Manchuria and cv. Pallas, a heatmap of the fragments per kilobase million (fpkm) expression data of AVRa6, BLGH_07092 and AVRa6 family members BLGH_00698, BLGH_00697 and BLGH_00700 and a list of the deduced AVRA6 proteins expressed by each isolate.

https://doi.org/10.1371/journal.ppat.1009223.s002

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S3 Fig. Schematic illustration of splice site mutations in AVRa6, which presumably lead to virulence of Bgh isolates on Mla6 NILs.

(A) Schematic illustration depicting the three observed splice site mutations: Splice donor site, splice branch point, and splice acceptor site mutations. (B) Schematic illustration of the genomic, transcriptomic, and deduced protein sequences of the three AVRa6 effector variants: AVRa6, AVRa6-V1, and AVRa6-V2. Depicted is the mutation in the consensus sequence of the branch point in AVRa6-V1 transcripts of Bgh isolates CC66 and CC148 and the splice donor site mutation in AVRa6-V2, which can be found in transcripts and the genome of Bgh isolate K1. This splice site mutation likely lead to an intron retention, which is supported by RNA-seq reads. Intron retention introduces an early stop codon leading to anticipated truncation of the AVRA6-V1 and AVRA6-V2 proteins.

https://doi.org/10.1371/journal.ppat.1009223.s003

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S4 Fig. Alignment of DNA, RNA, and protein sequences of AVRA6, AVRA6-V1 and AVRA6-V2 variants including the signal peptide.

(A) DNA sequence alignment of AVRa6, AVRa6-V1, and AVRa6-V2. The sequence of AVRa6-V1 was deduced from RNA-seq reads. (B) RNA sequence alignment of AVRa6, deduced AVRa6-V1, and AVRa6-V2. (C) Protein sequence of AVRA6, deduced AVRA6-V1, and AVRA6-V2.

https://doi.org/10.1371/journal.ppat.1009223.s004

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S5 Fig. Overlay of predicted AVRA6 structure (red) with the X-ray crystallography structure of CSEP0064 (yellow) (PDB ID: 6fmb).

https://doi.org/10.1371/journal.ppat.1009223.s005

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S6 Fig. Examination of the intron characteristic for RALPHs in Bgt and Bgh avirulence effectors.

(A) Position of the intron, which was found to be characteristic for RALPH-like effectors in the gene models of Bgt and Bgh AVR effectors. Black boxes are the 5′ UTR and 3′ UTR, white boxes are the gene coding regions, dark grey boxes denote the signal peptides, and light grey boxes depict introns. The characteristic intron, which was found in RALPH effectors, is shown in yellow. (B) Protein sequence alignment of Bgt and Bgh avirulence effectors showing the amino acid similarity and identity using grey and black backgrounds, respectively. Red arrows depict the relative position of the intron. Two black bars at positions 37 and 133 of the alignment show two characteristic cysteines present in all effectors except for AVRA13, which are predicted to form a disulfide bond.

https://doi.org/10.1371/journal.ppat.1009223.s006

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S7 Fig. DNA sequence alignments of Bgh and Bgt AVR effectors.

(A) DNA sequence alignment of Bgt and Bgh avirulence effectors including the signal peptide. Yellow background depicts the characteristic intron in RALPH effectors. B) Alignment of the intron sequence, which can be found in Bgt and Bgh RALPH avirulence effectors. Intron gDNA sequence alignment depicting identical nucleotides with a black background.

https://doi.org/10.1371/journal.ppat.1009223.s007

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S8 Fig. Size exclusion chromatography and SDS-PAGE of purified AVRA6, AVRA10, and AVRA13 effector proteins.

(A) Size exclusion chromatogram (SEC) of AVRA6, AVRA10, and AVRA13 showing absorbance at 280 nm (y-axis) against the retention volume (ml) (x-axis) and the respective fraction above (A34 and A36 for AVRA6, A31 and A33 for AVRA10; A32 and A34 for AVRA13), which was used for further RNase activity assays. (B) Stain-free SDS-PAGE (Bio-rad) showing the fractions of purified AVRA6, AVRA10, and AVRA13 proteins used for further RNase activity assays with a white arrow. AVRA protein fractions were separated on a 12% polyacrylamide gel and visualized by the ChemiDoc MP Imaging System (170–8280).

https://doi.org/10.1371/journal.ppat.1009223.s008

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S9 Fig. Protein quality control of AVRA6, AVRA10, and AVRA13.

(A) Size exclusion chromatogram of AVRA6, AVRA10, and AVRA13 purified from insect cells. Fractions eluted at 18.5, 17, 17.5ml of AVRA6, AVRA10, and AVRA13 proteins were verified by SDS-PAGE (indicated by red, green and blue arrows) and used for further RNase activity assays. (B) After size exclusion, insect cell-purified AVRA6, AVRA10, and AVRA13 proteins or T1 RNase were incubated with denatured HvRNA. All samples were separated on non-denaturing 2% agarose gels and analyzed on a Bioanalyzer to determine for RNA degradation.

https://doi.org/10.1371/journal.ppat.1009223.s009

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S10 Fig. Amino acid sequence alignment of M61111, M66111, M16666, and M11166.

Colored boxes depict different domains of the receptors: blue = CC-domain, green = NB-ARC domain, red = LRR as defined previously in [19]. Grey boxes depict individual LRRs.

https://doi.org/10.1371/journal.ppat.1009223.s010

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S11 Fig. N. benthamiana corresponding to results of Fig 5.

Pictures were taken under UV light (302 nm) at 5 days post transformation.

https://doi.org/10.1371/journal.ppat.1009223.s011

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S12 Fig. Amino acid sequence alignment of MLA10, MLA22, MLA10LRR22, and MLA22LRR10 receptors.

Colored boxes depict different domains of the receptors: blue = CC-domain, green = NB-ARC domain, red = LRR as defined previously in [19]. Grey boxes depict individual LRRs.

https://doi.org/10.1371/journal.ppat.1009223.s012

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S13 Fig. N. benthamiana leaves corresponding to results shown in Fig 8.

Pictures were taken at 5 days post transformation.

https://doi.org/10.1371/journal.ppat.1009223.s013

(TIF)

S14 Fig. HR indices of N. benthamiana leaf infiltrations.

(A) HR index used for scoring cell death in N. benthamiana. 0 = no cell death, 1 = weak chlorosis of infiltrated spot, 2 = chlorosis, 3 = strong chlorosis with rare spots of collapsed, dead leaf material, 4 = strong cell death with collapsed leaf material. The color of the frames around cell death pictures indicates HR indices in stacked bar plots B-E. (B–E) Stacked bar plots showing the count of individual HR indices from independent leaf infiltrations. Significance of cell death scores was calculated by Fisher’s exact test and an asterisk depicts p < 0.05: (B) MLA6, AVRA6-1: 8.68xe-13; MLA1, AVRA1: 2.6xe-11 (C) M11166, AVRA6-1: 3.98xe-12; (D) MLA10, AVRA10: 1.25xe-10; MLA22LRR10, AVRA10: 3.07xe-07; MLA22, AVRA22: 7.74xe-08; MLA10LRR22, AVRA22: 5.8xe-07 (E) MLA10, AVRA10: 3.07xe-29; MLA10, chimera26: 1.54xe-13; MLA10, chimera29: 3.73xe-12; MLA22, AVRA22: 2.77xe-49; MLA22, chimera14: 6.68xe-28; MLA22, chimera22: 6.39xe-14; MLA22, chimera24: 1.5xe-11, MLA22; chimera26: 9.59xe-09.

https://doi.org/10.1371/journal.ppat.1009223.s014

(TIF)

S1 Table. Top-ranking AVRa6 candidates in the transcriptome-wide association study (TWAS) determined by gene-wise calling.

* *The table columns show the new and former BLGH_ID, the description, the scaffold localization and the p-value of the top-ranking candidates for the gene-wise association of Bgh transcriptomes with infection phenotypes on Mla6 near-isogenic lines (NILs). Color codes depict top-ranking AVRa6 candidates and are consistent with the color code used in Fig 1A: bright green: CSEP0254 paralogues, dark green: BLGH_07092, dark red: BLGH_00697, bright red: BLGH_00700.

https://doi.org/10.1371/journal.ppat.1009223.s015

(TIF)

S2 Table. Top-ranking AVRa6 candidates in the transcriptome-wide association study (TWAS) determined by variant-wise calling.

* *The table columns depict the scaffold localization, the effect that the mutation has on the reference gene (non-synonymous mutation, gained stop codon), the codon change and the respective aa exchange, a gene description, the CSEP_ID and the p-value of the top-ranking candidates for the variant-wise association of Bgh transcriptomes with infection phenotypes on Mla6 near-isogenic lines (NILs). Color codes designate top-ranking AVRa6 candidates and are consistent with the color code used in Fig 1A: bright green: CSEP0254 paralogues, dark green: BLGH_07092 and bright red: BLGH_00700.

https://doi.org/10.1371/journal.ppat.1009223.s016

(TIF)

S3 Table. Primers used in this study.

https://doi.org/10.1371/journal.ppat.1009223.s017

(TIF)

Acknowledgments

We thank Sabine Haigis and Petra Köchner for excellent technical assistance and Yu Cao for the preparation of barley leaf RNA.

Citation: Bauer S, Yu D, Lawson AW, Saur IML, Frantzeskakis L, Kracher B, et al. (2021) The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold. PLoS Pathog 17(2): e1009223. https://doi.org/10.1371/journal.ppat.1009223

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