Autoactive alleles of the flax L6 rust resistance gene induce non-race-specific rust resistance associated with the hypersensitive response

L6 is a nucleotide binding site-leucine rich repeat (NBS-LRR) gene that confers race-specific resistance in flax (Linum usitatissimum) to strains of flax rust (Melampsora lini) that carry avirulence alleles of the AvrL567 gene but not to rust strains that carry only the virulence allele. Several mutant and recombinant forms of L6 were made that altered either the methionine-histidine-aspartate (MHD) motif conserved in the NBS domain of resistance proteins or exchanged the short domain C-terminal to the LRR region that is highly variable among L allele products. In transgenic flax some of these alleles are autoactive; they cause a gene dosage-dependent dwarf phenotype and constitutive expression of genes that are markers for the plant defense response. Their effects and penetrance ranged from extreme to mild in their degree of plant stunting, survival, and reproduction. Dwarf plants were also resistant to flax rust strains virulent to wild-type L6 plants, and this nonspecific resistance was associated with a hypersensitive response (HR) at the site of rust infection. The strongest autoactive allele, expressed in Arabidopsis from an ethanol-inducible promoter, gave rise to plant death dependent on the enhanced disease susceptibility 1 (EDS1) gene, which indicates that the mutant flax (Linaceae) L6 gene can signal cell death through a defined disease-resistance pathway in a different plant family (Brassicaceae).     

Tobacco transgenic for the flax rust resistance gene L expresses allele-specific activation of defense responses

Tobacco was transformed with three different alleles (L2, L6, and L10) of the flax rust resistance gene L, a member of the toll interleukin-1 receptor, nucleotide-binding site, leucine-rich repeat (TIR-NBS-LRR) class of plant disease resistance genes. L6 transgenics had a stunted phenotype, expressed several defense response genes constitutively, and had increased resistance to the fungus Cercospora nicotianae and the oomycete Phytophthora parasitica pv. nicotianae. L2 and L10 transgenics, with one exception for L10, did not express these phenotypes, indicating that the activation of tobacco defense responses is L6 allele-specific. The phenotype of the exceptional L10 transgenic plant was associated with the presence of a truncated L10 gene resulting from an aberrant T-DNA integration. The truncated gene consisted of the promoter, the complete TIR region, and 39 codons of the NBS domain fused inframe to a tobacco retrotransposon-like sequence. A similar truncated L10 gene, constructed in vitro, was transiently expressed in tobacco leaves and gave rise to a strong localized necrotic reaction. Together, these results suggest that defense signaling properties of resistance genes can be expressed in an allele-specific and pathogen-independent manner when transferred between plant genera.     

Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity

Thirteen alleles (L, L1 to L11, and LH) from the flax L locus, which encode Toll/interleukin-1 receptor homology-nucleotide binding site-leucine-rich repeat (TIR-NBS-LRR) rust resistance proteins, were sequenced and compared to provide insight into their evolution and into the determinants of gene-for-gene resistance specificity. The predicted L6 and L11 proteins differ solely in the LRR region, whereas L6 and L7 differ solely in the TIR region. Thus, specificity differences between alleles can be determined by both the LRR and TIR regions. Functional analysis in transgenic plants of recombinant alleles constructed in vitro provided further information: L10-L2 and L6-L2 recombinants, encoding the LRR of L2, conferred L2 resistance specificity, and an L2-L10 recombinant, encoding the LRR of L10, conferred a novel specificity. The sequence comparisons also indicate that the evolution of L alleles has probably involved reassortment of variation, resulting from accumulated point mutations, by intragenic recombination. In addition, large deletion events have occurred in the LRR-encoding regions of L1 and L8, and duplication events have occurred in the LRR-encoding region of L2.     

Recombination among genes at the L group in flax conferring resistance to rust

Summary Fourteen of the known genes conferring resistance to rust in flax occur in the L group, and recombinational analysis has been used to study their fine structure. Three important features were observed. (a) Similar to the findings of Shepherd and Mayo, only susceptible recombinants were detected among the testcross progeny of 11 of the 15 heterozygotes involving pairs of L genes. Some of these recombinants showed variation in the degree of their susceptibility and appeared to be unstable in nature. (b) A new class of recombinants exhibiting a modified type of resistance was recovered. They occurred rarely but consistently, with frequencies similar to that of susceptible recombinants. (c) Rare resistant plants occurred among the progeny of susceptible recombinants. In each case, the specificity of the resistant plant corresponded to only one of the parental types. The relative roles of seed contamination, mutation, recombination and the transposition of genetic elements are discussed to account for these features.     

Relationships between rust resistance genes at the M locus in flax

Genes at the M locus in flax ( Linum usitatissimum ) that confer resistance to flax rust ( Melampsora lini ) occur in complex haplotypes containing up to 15 related genes or gene fragments. We have cloned two additional functional resistance genes at this locus, M1 and M3 , by transposon tagging and candidate gene approaches, and investigated the genetic relationships between four genes ( M , M1 , M3 and M4 ) by recombination analysis. M1 and M3 , like M , are members of the nucleotide binding site, leucine-rich repeat (NBS-LRR) family. Comparisons of the predicted M1 and M3 amino acid sequences with M and L6 reveal that: (i) M1 contains four additional LRRs, probably as a result of an unequal crossover event between duplicated regions; (ii) M1 shares large segments of exact identity with M and M3, indicative of intragenic recombination events; and (iii) a large number of amino acid differences are scattered throughout the M, M1 and M3 proteins. Recombination analysis (here and in previous studies) has revealed that M readily recombines with M1 , M3 and M4 , whereas these three genes fail to recombine despite large family sizes (>5800) in two test-cross families, suggesting that they may occupy allelic positions in the gene cluster. Several restriction fragment length polymorphism markers within or near the M locus were mapped with respect to seven crossover events between M and M1 . The results of this and previous studies provide evidence of structural differences between: (i) homoeologous loci in the different genomes of flax; (ii) different haplotypes at the M locus; (iii) different resistance genes in the M group; and (iv) the flanking regions downstream of M locus resistance genes.     

Dynamic reorganization of microtubules and microfilaments in flax cells during the resistance response to flax rust infection

The cytoskeleton in plant cells is a dynamic structure that can rapidly respond to extracellular stimuli. Alteration of the organization of microtubules and actin microfilaments was examined in mesophyll cells of flax, Linum usitatissimum L., during attempted infection by the flax rust fungus, Melampsora lini (Ehrenb.) Lev. Flax leaves that had been inoculated with either a compatible (yielding a susceptible reaction) or an incompatible (yielding a resistant reaction) strain of M. lini were embedded in butyl-methylmethacrylate resin; sections of this material were immunofluorescently labelled with anti-tubulin or anti-actin and examined using confocal laser scanning microscopy. In uninfected leaves, microtubules in the mesophyll cells formed a transverse array in the cell cortex. Microfilaments radiated through the cytoplasm from the nucleus. In an incompatible interaction, microtubules and microfilaments were extensively reorganized in mesophyll cells that were in contact with fungal infection hyphae or haustorial mother cells before penetration of the cell by the infection peg. After the initiation of haustorium development, microtubules disappeared from the infected cells, and growth of the haustoria ceased. In an incompatible interaction, hypersensitive cell death occurred in more than 70% of infected cells but occurred in less than 20% of cells in compatible interactions. After the infected cell had undergone hypersensitive cell death, the cytoskeleton in neighbouring cells became focused on the walls shared with the necrotic cell. In compatible interactions, reorganization of the cytoskeleton was either not observed at all or was observed much less frequently up to 48 h after inoculation.Abbreviations FITC fluorescein isothiocyanate - WGA wheatgerm agglutinin We thank Dr. G.J. Lawrence for providing valuable discussions and materials.     

Instability of the L6 gene for rust resistance in flax is correlated with the presence of a linked Ac element

In a programme aimed at tagging rust-resistance genes in flax with the maize transposable element Ac , a primary transformant of a line called 'Forge' that is homozygous for four rust-resistance genes, L ⁶, M, N and P ², was identified that possessed 10 copies of the Ac element, one of which was linked (29 map units) to L ⁶. Descendants of this plant, which had from 8 to 15 copies of Ac , were crossed to a rust-susceptible line and the progeny screened for rust-susceptible mutants. When the Ac linked to L ⁶ was present in the parent, a high frequency of L ⁶ mutants was observed (29 mutants in 30 575). By contrast, when this Ac was absent, no such mutants were observed in 9258 progeny. The background frequency of L ⁶ mutants was low (five in 124 088). A detailed analysis was made of the first 11 L ⁶ mutants recovered from parents carrying the L ⁶-linked Ac element. While none of the mutants possessed a tagged resistance gene, all lacked an RFLP marker closely linked to L ⁶, suggesting that deletions were responsible for loss of the L ⁶ specificity. In many of the mutants, one or more RFLP markers in the vicinity of the linked Ac were also absent. These findings suggest that the linked Ac may be inducing chromosome breakage.     

A novel gene for rust resistance

The Rpg1 gene, which has provided North American cultivars of barley with resistance to the stem rust fungus Puccinia graminis f.sp. tritici for more than 60 years, has been cloned. A single copy of the gene can confer resistance to a susceptible barley variety. Although unexplained, the progeny are consistently more resistant than the variety from which the gene was obtained. The gene might represent a new class of plant resistance genes.     

Contrasting modes of evolution acting on the complex N locus for rust resistance in flax

Three rust resistance specificities, N, N1 and N2, map to the complex N locus of flax. We used a degenerate PCR approach, with primers directed to the nucleotide binding site (NBS) domain characteristic of many plant resistance genes, to isolate resistance gene analogs (RGAs) from flax. One RGA clone detected RFLPs co-segregating with alleles of the N locus. With this probe we isolated four related genes that occur within a 30kbp region and encode proteins with NBS and leucine-rich repeat (LRR) domains and N-terminal Toll/Interleukin-1 Receptor homology (TIR) domains. One of these four genes was identified as the N resistance gene by sequence analysis of three mutant alleles and by transgenic expression. We isolated homologous genes from two flax lines containing the N1 or N2 specificities and from flax lines carrying no N locus resistance specificities. Analysis of shared polymorphisms among this set of 18 N locus sequences revealed three groups of genes with independent lineages. Sequence exchanges have only occurred between genes within each group, but not between groups. Two of the groups contain only one sequence from each haplotype and probably represent orthologous genes. However, the third group contains two genes from each haplotype. We suggest that the re-assortment of variation by recombination/gene conversion at this locus is limited by the degree of sequence identity between genes.     

Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease

Plant-pathogen co-evolutionary selection processes are continuous, complex and occur across many spatial and temporal scales. Comprehensive studies of the flax-flax rust pathosystem have led to the postulation of the gene-for-gene model, a genetic paradigm describing recognition events between host disease resistance proteins and pathogen effector proteins. The identification of directly interacting fungal effector proteins and plant disease resistance proteins in this pathosystem has facilitated the study of both the physical nature of these interactions and the evolutionary forces that have resulted in a molecular arms race between these organisms. The flax-flax rust pathosystem has also been detailed on the scale of interacting populations, and the integration of molecular- and population-scale datasets represents a unique opportunity to further our understanding of many poorly understood facets of host-pathogen dynamics. In this article, we discuss recent developments and insights in the flax-flax rust pathosystem and their implications for both long-term co-evolutionary dynamics in natural settings, as well as short-term co-evolutionary dynamics in agro-ecosystems.     

Changes in the transcription pattern of flax cotyledons after inoculation with flax rust

The rate of ³²P incorporation into RNA fractions of flax cotyledons (Linum usitatissimum L. var. Bison) was found to increase two- to three-fold by 48h after inoculation with flax rust [Melampsora lini (Pers.) Lev., race no. 3]. This was accompanied by a change in the nucleotide composition of the newly transcribed sodium chloride-soluble RNA fraction. A comparison of the nucleotide composition of the RNA synthesized in the host–parasite complex at different stages of development indicated the preferential synthesis of one or more molecular species of RNA with a high A+U/G+C ratio at a relatively early stage of infection. Treatment of healthy plants with indol-3-ylacetic acid also resulted in a substantial stimulation in the rate of ³²P incorporation into RNA but this was not accompanied by a detectable change in the nucleotide ratios of the newly synthesized RNA. These results suggest that the synthesis of one of more additional RNA species or the augmented synthesis of certain species of RNA may be a specific phenomenon elicited by host–pathogen interaction.     

Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity

The gene-for-gene mechanism of plant disease resistance involves direct or indirect recognition of pathogen avirulence (Avr) proteins by plant resistance (R) proteins. Flax rust (Melampsora lini) AvrL567 avirulence proteins and the corresponding flax (Linum usitatissimum) L5, L6, and L7 resistance proteins interact directly. We determined the three-dimensional structures of two members of the AvrL567 family, AvrL567-A and AvrL567-D, at 1.4- and 2.3-A resolution, respectively. The structures of both proteins are very similar and reveal a beta-sandwich fold with no close known structural homologs. The polymorphic residues in the AvrL567 family map to the surface of the protein, and polymorphisms in residues associated with recognition differences for the R proteins lead to significant changes in surface chemical properties. Analysis of single amino acid substitutions in AvrL567 proteins confirm the role of individual residues in conferring differences in recognition and suggest that the specificity results from the cumulative effects of multiple amino acid contacts. The structures also provide insights into possible pathogen-associated functions of AvrL567 proteins, with nucleic acid binding activity demonstrated in vitro. Our studies provide some of the first structural information on avirulence proteins that bind directly to the corresponding resistance proteins, allowing an examination of the molecular basis of the interaction with the resistance proteins as a step toward designing new resistance specificities.     

Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination

Multiple alleles controlling different gene-for-gene flax rust resistance specificities occur at the L locus of flax. At least three distinct regions can be recognized in the predicted protein products: the Toll/interleukin-1 receptor homology (TIR) region, a nucleotide binding site (NBS) region, and a leucine-rich repeat (LRR) region. Replacement of the TIR-encoding region of the L6 allele with the corresponding regions of L2 or LH by recombination changed the specificity of the allele from L6 to L7. Replacement of the TIR and most of the NBS-encoding region of L10 with the equivalent region of L2 or L9 generated recombinant alleles having a novel specificity. However, replacement of the L10 TIR-encoding region with the TIR-encoding region of L2 gave rise to an allele with no detectable specificity. These data indicate that non-LRR regions can determine specificity differences between allelic gene products and that functional specificity involves interactions between coadapted polymorphic regions in the protein products of the alleles. Evidence for the action of diversifying selection on the TIR region is observed.     

Isolation of a flax (Linum usitatissimum) gene induced during susceptible infection by flax rust (Melampsora lini)

In a susceptible infection of flax ( Linum usitatissimum ), the obligate rust pathogen ( Melampsora lini ) can grow in the leaf without triggering the hypersensitive resistance response. The rust establishes specialized structures (haustoria) in plant mesophyll cells and induces changes in plant subcellular organization. Subtraction hybridization methods were used to isolate cDNA clones of mRNAs that have altered expression in infected leaves. Most of the cDNAs recovered were of fungal origin, but one clone, pFIS1 ( f lax i nducible s equence No. 1), recovered from several independent experiments, was a plant-specified mRNA that showed a 10-fold increase in steady-state levels during susceptible growth. The increase in fis1 mRNA levels was not seen in the resistant reaction (hypersensitive reaction) and the predicted protein sequence (551 amino acids with a predicted molecular weight of 61 kDa) has no similarity to known pathogenesis-related proteins. Searches of sequence data bases showed that fis1 encodes a protein which contains amino acid sequence motifs that are conserved in all previously characterized aldehyde dehydrogenases.