ORCID Profile
0000-0003-0620-5923
Current Organisations
University of Michigan
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CSIRO
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Publisher: Wiley
Date: 28-02-2012
Publisher: Wiley
Date: 2007
DOI: 10.1111/J.1364-3703.2006.00375.X
Abstract: SUMMARY The flax rust resistance gene L, a nucleotide binding site, leucine-rich repeat (NBS-LRR) class of plant resistance gene, has 12 characterized alleles with different gene-for-gene resistance specificities. Here the specificities of presumptive L1, L5, L8 and L11 genomic clones are confirmed by transgenic expression. L6 and L11 differ by 33 amino acids, 32 in the LRR region and one in the C-terminal non-LRR region, and recognize unrelated avirulence proteins, AvrL567 and AvrL11, respectively. To analyse the specificity differences, 13 L6L11 recombinant genes were constructed in vitro and tested in transgenic flax for resistance to F2 progeny of rust strain CH5, in which the unlinked avirulence genes AvrL567 and AvrL11 segregate. The data show that the single C-terminal non-LRR region polymorphism is not involved in L6-L11 specificity differences, that polymorphisms necessary for specificity are spread throughout the LRR region and that some polymorphisms essential for L11 are not essential for L6. Seven 'null' recombinants expressed no resistance when tested with CH5-derived rusts. These were tested for new resistance specificities by inoculation with a strain of rust, Bs-1, which is distantly related to CH5 and which potentially carries a different range of avirulence specificities. The 'null' recombinant L6L11RV, which differs from L6 and L11 by its susceptibility to CH5, was resistant to strain Bs-1. The specificity difference is due to a reduction in the number of AvrL567 variants recognized by L6L11RV compared with L6 and not due to recognition of an unrelated Avr gene product in strain Bs-1.
Publisher: Proceedings of the National Academy of Sciences
Date: 03-02-2017
Abstract: Toll/interleukin-1 receptor/resistance protein (TIR) domains are present in plant and animal innate immunity receptors and appear to play a scaffold function in defense signaling. In both systems, self-association of TIR domains is crucial for their function. In plants, the TIR domain is associated with intracellular immunity receptors, known as nucleotide-binding oligomerization domain-like receptors (NLRs). Previous studies from several plant NLRs have identified two distinct interfaces that are required for TIR:TIR dimerization in different NLRs. We show that the two interfaces previously identified are both important for self-association and defense signaling of multiple TIR–NLR proteins. Collectively, this work suggests that there is a common mechanism of TIR domain self-association in signaling across the TIR–NLR class of receptor proteins.
Publisher: Humana Press
Date: 2011
DOI: 10.1007/978-1-61737-998-7_8
Abstract: The haustorium is a distinguishing feature of biotrophic plant pathogens. Several highly erged -pathogen classes have independently evolved haustoria, suggesting that they represent an effective adaptation for growing within living plant tissue. Despite their clear importance in biotrophy, they have been difficult to study due to the close association of biotrophic pathogens with their host and the inability to produce haustoria in vitro. These drawbacks have been circumvented in the study of rust fungi by the development of a haustoria isolation technique. The strong binding of the lectin concanavalin A (ConA) to rust haustoria allows these structures to be purified from infected plant tissue by affinity chromatography on a ConA-Sepharose macrobead column. The isolation process results in substantial yields of intact haustoria that retain their cytoplasmic contents, making them amenable to experimentation. The construction of cDNA libraries from isolated rust haustoria and their subsequent sequence analysis have provided significant insight into haustoria function at a molecular level, revealing important roles in nutrient acquisition and the delivery of pathogenicity effector proteins. The generation of a rust haustorium-specific cDNA library is described in this chapter.
Publisher: Elsevier BV
Date: 07-2001
Publisher: Public Library of Science (PLoS)
Date: 12-12-2019
Publisher: American Society for Microbiology
Date: 07-03-2018
Abstract: Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae , is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype ersity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed ergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae . IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae , which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae , resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic ersity in populations of P. coronata f. sp. avenae .
Publisher: Scientific Societies
Date: 12-2022
DOI: 10.1094/MPMI-08-22-0167-SC
Abstract: Functional characterization of effector proteins of fungal obligate biotrophic pathogens, especially confirmation of avirulence (Avr) properties, has been notoriously difficult, due to the experimental intractability of many of these organisms. Previous studies in wheat have shown promising data suggesting the type III secretion system (T3SS) of bacteria may be a suitable surrogate for delivery and detection of Avr properties of fungal effectors. However, these delivery systems were tested in the absence of confirmed Avr effectors. Here, we tested two previously described T3SS-mediated delivery systems for their suitability when delivering two confirmed Avr effectors from two fungal pathogens of wheat, Puccinia graminis f. sp. tritici and Magnaporthe oryzae pathotype tritici. We showed that both effectors (AvrSr50 and AvrRmg8) were unable to elicit a hypersensitive response on wheat seedlings with the corresponding resistance gene when expressed by the Pseudomonas fluorescens “Effector to Host Analyser” (EtHAn) system. Furthermore, we found the utility of Burkholderia glumae for screening Avr phenotypes is severely limited, as the wild-type strain elicits nonhost cell death in multiple wheat accessions. These results provide valuable insight into the suitability of these systems for screening fungal effectors for Avr properties that may help guide further development of surrogate bacterial delivery systems in wheat. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Publisher: Frontiers Media SA
Date: 24-11-2014
Publisher: Elsevier BV
Date: 08-2020
Publisher: Wiley
Date: 13-11-2009
Publisher: Frontiers Media SA
Date: 26-05-2020
Publisher: Elsevier BV
Date: 06-2022
DOI: 10.1016/J.PBI.2022.102210
Abstract: Filamentous plant pathogens cause disease in numerous economically important crops. These pathogens secrete virulence proteins, termed effectors, that modulate host cellular processes and promote infection. Plants have evolved immunity receptors that detect effectors and activate defence pathways, resulting in resistance to the invading pathogen. This leads to an evolutionary arms race between pathogen and host that is characterised by highly erse effector repertoires in plant pathogens. Here, we review the recent advances in understanding host-pathogen co-evolution provided by the structural determination of effectors alone, and in complex with immunity receptors. We highlight the use of recent advances in structural prediction within this field and its role for future development of designer resistance proteins.
Publisher: Oxford University Press (OUP)
Date: 04-2007
DOI: 10.1111/J.1574-6968.2007.00684.X
Abstract: A major insight that has emerged in the study of haustoria-forming plant pathogens over the last few years is that these eukaryotic biotrophs deliver suites of secreted proteins into host cells during infection. This insight has largely derived from successful efforts to identify avirulence (Avr) genes and their products from these pathogens. These Avr genes, identified from a rust and a powdery mildew fungus and three oomycete species, encode small proteins that are recognized by resistance proteins in the host plant cytoplasm, suggesting that they are transported inside plant cells during infection. These Avr proteins probably represent ex les of fungal and oomycete effector proteins with important roles in subverting host cell biology during infection. In this respect, they represent a new opportunity to understand the basis of disease caused by these biotrophic pathogens. Elucidating how these pathogen proteins gain entry into plant cells and their biological function will be key questions for future research.
Publisher: Elsevier BV
Date: 08-2000
DOI: 10.1016/S1369-5266(00)00080-7
Abstract: Gene-for-gene plant disease resistance involves two basic processes: perception of pathogen attack, followed by responses to limit disease. Perception involves receptors with high degrees of specificity for pathogen strains, which are encoded by disease resistance genes. Large repertoires of distantly related resistance (R) genes with erse recognitional specificities are found within a single plant species. The generation of R-gene polymorphism involves gene duplication, followed by DNA-sequence ergence by point mutation, and by deletion and duplication of intragenic DNA repeats encoding blocks of leucine-rich elements. Recombination between related genes reassorts this variation to further ersify gene sequences. Pathogen pressure selects functional resistance specificities and results in the maintenance of R-gene ersity. Recent genome-sequence data reveal that the NBS-LRR (i.e. nucleotide-binding site-leucine-rich repeat) class of R genes represents as much as 1% of the Arabidopsis genome. Experimental data have shown that the LRR has a role in determination of specificity. Mutation experiments, in which R-gene signaling has been dissociated from specificity in constitutive signal mutants, have provided the potential for non-specific resistance to be expressed from pathogen-infection-induced promoters in transgenic plants.
Publisher: Frontiers Media SA
Date: 09-2014
Publisher: Wiley
Date: 23-02-2022
DOI: 10.1111/NPH.18011
Abstract: Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic ersity of the stem rust ( Puccinia graminis f. sp. tritici ( Pgt )) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site‐directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino‐acid variation involving a single substitution of the AvrSr50 surface‐exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate‐binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
Publisher: Wiley
Date: 08-12-2022
Abstract: Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high‐quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi‐C data to assemble a gigabase‐sized fungal pathogen, Puccinia polysora f.sp . zeae , to haplotype‐phased and chromosome‐scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga‐scale fungi assembled to chromosome level. Transcript‐based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype‐specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome‐size expansion and copy number increasing of species‐specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine‐time‐point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a “two‐speed genome” evolution in P. polysora . Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC , indicating the ongoing virulence to evade recognition by RppC , a major resistance gene in Chinese corn cultivars. The high‐quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora .
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-04-2014
Abstract: Certain pathogen effectors are detected in plants by cytoplasmic receptors. First solving the crystal structures of Arabidopsis receptors, Williams et al. (p. 299 see the Perspective by Nishimura and Dangl ) discovered that in the resting state, the structures form a heterodimer that readies the complex for effector binding and keeps the signaling domains from firing too early. Once the pathogen effector binds, the structure of the complex shifts such that the signaling domains can form a homodimer to initiate downstream signaling. Similarities between these plant-pathogen receptors and Toll-like receptors in animals suggest the molecular mechanisms may translate broadly.
Publisher: Proceedings of the National Academy of Sciences
Date: 06-06-2006
Abstract: Plant resistance proteins (R proteins) recognize corresponding pathogen avirulence (Avr) proteins either indirectly through detection of changes in their host protein targets or through direct R–Avr protein interaction. Although indirect recognition imposes selection against Avr effector function, pathogen effector molecules recognized through direct interaction may overcome resistance through sequence ersification rather than loss of function. Here we show that the flax rust fungus AvrL567 genes, whose products are recognized by the L5, L6, and L7 R proteins of flax, are highly erse, with 12 sequence variants identified from six rust strains. Seven AvrL567 variants derived from Avr alleles induce necrotic responses when expressed in flax plants containing corresponding resistance genes ( R genes), whereas five variants from avr alleles do not. Differences in recognition specificity between AvrL567 variants and evidence for ersifying selection acting on these genes suggest they have been involved in a gene-specific arms race with the corresponding flax R genes. Yeast two-hybrid assays indicate that recognition is based on direct R–Avr protein interaction and recapitulate the interaction specificity observed in planta . Biochemical analysis of Escherichia coli -produced AvrL567 proteins shows that variants that escape recognition nevertheless maintain a conserved structure and stability, suggesting that the amino acid sequence differences directly affect the R–Avr protein interaction. We suggest that direct recognition associated with high genetic ersity at corresponding R and Avr gene loci represents an alternative outcome of plant–pathogen coevolution to indirect recognition associated with simple balanced polymorphisms for functional and nonfunctional R and Avr genes.
Publisher: Scientific Societies
Date: 08-2023
Publisher: Springer Science and Business Media LLC
Date: 09-11-2015
DOI: 10.1038/NG.3439
Abstract: As there are numerous pathogen species that cause disease and limit yields of crops, such as wheat (Triticum aestivum), single genes that provide resistance to multiple pathogens are valuable in crop improvement. The mechanistic basis of multi-pathogen resistance is largely unknown. Here we use comparative genomics, mutagenesis and transformation to isolate the wheat Lr67 gene, which confers partial resistance to all three wheat rust pathogen species and powdery mildew. The Lr67 resistance gene encodes a predicted hexose transporter (LR67res) that differs from the susceptible form of the same protein (LR67sus) by two amino acids that are conserved in orthologous hexose transporters. Sugar uptake assays show that LR67sus, and related proteins encoded by homeoalleles, function as high-affinity glucose transporters. LR67res exerts a dominant-negative effect through heterodimerization with these functional transporters to reduce glucose uptake. Alterations in hexose transport in infected leaves may explain its ability to reduce the growth of multiple biotrophic pathogen species.
Publisher: Public Library of Science (PLoS)
Date: 26-06-2013
Publisher: Frontiers Media SA
Date: 08-01-2015
Publisher: Springer Science and Business Media LLC
Date: 04-01-2021
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/AR07055
Abstract: The continued deployment of resistance genes in Australian wheat varieties plays a crucial role in the prevention of crop losses as a result of rust infection. Resistance genes in plants act as an immune system by recognising specific components of the rust pathogen, encoded by avirulence (Avr) genes, and initiating defence responses. Recent advances in the model rust species, Mel sora lini, which infects cultivated flax (Linum usitatissimum), has led to the identification of several avirulence genes. These encode secreted proteins that are expressed in haustoria, specialised rust structures that penetrate the host cell wall. The AvrL567, AvrM, AvrP4, and AvrP123 proteins are recognised when expressed intracellularly in resistant plants, and the AvrL567 proteins interact directly with the corresponding L5 and L6 cytoplasmic resistance proteins. These observations imply that rusts deliver a range of small effector proteins directly into the plant cytoplasm, which are likely to perform key functions in facilitating pathogen infection. The plants’ resistance protein system has evolved to recognise the presence of these effectors during infection. Selection imposed by host resistance genes has led to the ersification of flax rust Avr genes to escape recognition. Nevertheless, virulent strains of flax rust retain variant forms of the Avr genes, suggesting that they have a positive fitness value to the pathogen. This knowledge is now being applied to develop screens for avirulence and pathogenicity-related proteins from important rust pathogens of wheat.
Publisher: Oxford University Press (OUP)
Date: 18-02-2004
DOI: 10.1105/TPC.020040
Publisher: Wiley
Date: 11-05-2018
DOI: 10.1111/MPP.12682
Publisher: Springer Science and Business Media LLC
Date: 26-10-2023
Publisher: Scientific Societies
Date: 02-2022
DOI: 10.1094/MPMI-08-21-0201-R
Abstract: Many fungi and oomycete species are devasting plant pathogens. These eukaryotic filamentous pathogens secrete effector proteins to facilitate plant infection. Fungi and oomycete pathogens have erse infection strategies and their effectors generally do not share sequence homology. However, they occupy similar host environments, either the plant apoplast or plant cytoplasm, and, therefore, may share some unifying properties based on the requirements of these host compartments. Here, we exploit these biological signals and present the first classifier (EffectorP 3.0) that uses two machine-learning models: one trained on apoplastic effectors and one trained on cytoplasmic effectors. EffectorP 3.0 accurately predicts known apoplastic and cytoplasmic effectors in fungal and oomycete secretomes with low estimated false-positive rates of 3 and 8%, respectively. Cytoplasmic effectors have a higher proportion of positively charged amino acids, whereas apoplastic effectors are enriched for cysteine residues. The combination of fungal and oomycete effectors in training leads to a higher number of predicted cytoplasmic effectors in biotrophic fungi. EffectorP 3.0 expands predicted effector repertoires beyond small, cysteine-rich secreted proteins in fungi and RxLR-motif containing secreted proteins in oomycetes. We show that signal peptide prediction is essential for accurate effector prediction, because EffectorP 3.0 recognizes a cytoplasmic signal also in intracellular, nonsecreted proteins. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Publisher: Annual Reviews
Date: 08-09-2007
DOI: 10.1146/ANNUREV.PHYTO.45.062806.094331
Abstract: Genetic studies of the flax-flax rust interaction led to the formulation of the gene-for-gene hypothesis and identified resistance genes (R) in the host plant and pathogenicity genes, including avirulence (Avr) and inhibitor of avirulence genes (I), in the rust pathogen. R genes have now been cloned from four of the five loci in flax and all encode proteins of the Toll, Interleukin-1 receptor, R gene-nucleotide binding site-leucine-rich repeat (TIR-NBS-LRR) class. Avr genes have been cloned from four loci in flax rust and encode small secreted proteins with no between locus similarity and no close homologs in current data bases. It is postulated that Avr proteins enter the host cell, have virulence effector functions, and in resistant host genotypes, are recognized by direct and specific interaction with host R proteins, leading to activation of rust resistance defense responses. Direct interaction between R and Avr proteins is the basis of gene-for-gene specificity in the flax-flax rust system and both R and Avr genes have the signatures of ersifying selection, suggesting the existence of a coevolutionary arms race between the host plant and its obligate rust pathogen.
Publisher: Oxford University Press (OUP)
Date: 2001
DOI: 10.1105/TPC.13.1.163
Abstract: At least six rust resistance specificities (P and P1 to P5) map to the complex P locus in flax. The P2 resistance gene was identified by transposon tagging and transgenic expression. P2 is a member of a small multigene family and encodes a protein with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains and an N-terminal Toll/interleukin-1 receptor (TIR) homology domain, as well as a C-terminal non-LRR (CNL) domain of approximately 150 amino acids. A related CNL domain was detected in almost half of the predicted Arabidopsis TIR-NBS-LRR sequences, including the RPS4 and RPP1 resistance proteins, and in the tobacco N protein, but not in the flax L and M proteins. Presence or absence of this domain defines two subclasses of TIR-NBS-LRR resistance genes. Truncations of the P2 CNL domain cause loss of function, and evidence for ersifying selection was detected in this domain, suggesting a possible role in specificity determination. A spontaneous rust-susceptible mutant of P2 contained a G-->E amino acid substitution in the GLPL motif, which is conserved in the NBS domains of plant resistance proteins and the animal cell death control proteins APAF-1 and CED4, providing direct evidence for the importance of this motif in resistance gene function. A P2 homologous gene isolated from a flax line expressing the P resistance specificity encodes a protein with only 10 amino acid differences from the P2 protein. Chimeric gene constructs indicate that just six of these amino acid changes, all located within the predicted beta-strand/beta-turn motif of four LRR units, are sufficient to alter P2 to the P specificity.
Publisher: Cold Spring Harbor Laboratory
Date: 29-04-2023
DOI: 10.1101/2023.04.28.538616
Abstract: Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance ( R ) gene cloning and stacking has accelerated in recent years 1-3 , the identification of corresponding avirulence ( Avr ) genes in many pathogens is h ered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts for rapid identification of interacting R / Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust ( Puccinia graminis f. sp. tritici ) by screening a designed library of putative effectors against in idual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution by genotype surveillance and optimise R gene deployment and stacking strategies. This screening platform is broadly applicable to many crop pathogens, whilst also adaptable for screening genes involved in other protoplast-selectable traits.
Publisher: Elsevier BV
Date: 08-2007
DOI: 10.1016/J.MIB.2007.05.015
Abstract: Five unrelated avirulence (Avr) gene families have been cloned from flax rust and barley powdery mildew, fungal pathogens that make close contact with living host plant cells using specialized feeding structures called haustoria. Transgenic expression studies indicate Avr proteins are recognized by disease resistance (R) proteins within host cells, which suggests that Avr proteins are transported via an as yet unidentified route from the fungus to the host during infection. Recognition of flax rust AvrL567 proteins is by direct R-Avr protein interaction. Virulence effector functions have been demonstrated for barley powdery mildew Avr proteins Avra10 and Avrk1. Mildew resistance triggered by Avra10 in barley involves association of the cognate barley R protein Mla10 and transcriptional repressor proteins, including HvWRKY2, in the host nucleus. High litude defence gene expression has a dual dependence on transcriptional de-repression induced by specific R-Avr protein recognition and additionally, activation signals initiated by host perception of general pathogen molecules.
Publisher: International Union of Crystallography (IUCr)
Date: 28-09-2013
Publisher: Public Library of Science (PLoS)
Date: 09-01-2014
Publisher: Wiley
Date: 2010
Publisher: Springer Science and Business Media LLC
Date: 22-07-2021
DOI: 10.1038/S41477-021-00971-5
Abstract: Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved
Publisher: Springer Science and Business Media LLC
Date: 2002
Abstract: We previously characterized LePRK1 and LePRK2, pollen-specific receptor kinases from tomato (Muschietti et al., 1998). Here we identify a similar receptor kinase from maize, ZmPRK1, that is also specifically expressed late in pollen development, and a third pollen receptor kinase from tomato, LePRK3. LePRK3 is less similar to LePRK1 and LePRK2 than either is to each other. We used immunolocalization to show that all three LePRKs localize to the pollen tube wall, in partially overlapping but distinct patterns. We used RT-PCR and degenerate primers to clone homologues of the tomato kinases from other Solanaceae. We deduced features diagnostic of pollen receptor kinases and used these criteria to identify family members in the Arabidopsis database. RT-PCR confirmed pollen expression for five of these Arabidopsis candidates two of these are clearly homologues of LePRK3. Our results reveal the existence of a distinct pollen-specific receptor kinase gene family whose members are likely to be involved in perceiving extracellular cues during pollen tube growth.
Publisher: Proceedings of the National Academy of Sciences
Date: 07-10-2013
Abstract: Fungal and oomycete pathogens cause devastating diseases in crop plants and facilitate infection by delivering effector molecules into the plant cell. The secreted effector protein AvrM from flax rust, a fungal pathogen that infects flax plants, internalizes into host cells in the absence of the pathogen, binds to phosphoinositides, and is recognized directly by the resistance protein M in flax to initiate effector-triggered immunity. We describe the crystal structure of AvrM and identify functionally important surface regions in the protein, which advances our understanding of the molecular mechanisms underlying how effectors enter host cells and how they are detected by the plant immune system.
Publisher: Research Square Platform LLC
Date: 31-10-2022
DOI: 10.21203/RS.3.RS-2208386/V1
Abstract: Most resistance genes thus far isolated from wheat have a very limited number of functional alleles, with the exception of the powdery mildew PM3 resistance locus. Here we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9 , representing the largest multi-allelic rust resistance locus in common wheat. The seven previously reported resistance alleles ( Sr9a , Sr9b , Sr9d , Sr9e , Sr9f , Sr9g , and Sr9h ) at the locus were characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation were used to confirm Sr9b , two haplotypes of Sr9e ( Sr9e_h1 , Sr9e_h2 ), Sr9g , and Sr9h . Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing a previously unreported motif at their N termini and an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differed from SR9B by a single amino acid. SR9B and SR9G resistance proteins were also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences.
Publisher: Informa UK Limited
Date: 22-03-2010
Publisher: Elsevier BV
Date: 08-2009
DOI: 10.1016/J.PBI.2009.05.004
Abstract: Plant-pathogen interactions involve processes of pathogen offence, host defence and pathogen counter-attack that are commonly played out using molecules secreted by hosts and pathogens. Secreted pathogen molecules involved in these events, referred to as 'effectors', function either in the plant extracellular space (apoplast) or inside of plant cells after translocation from the pathogen. These molecules have evolved as virulence factors that can be detected by polymorphic host resistance proteins. Advances are being made in the identification and in understanding the evolution of effectors and of host uptake signals used by eukaryotic effectors to enter host cells.
Publisher: Elsevier BV
Date: 09-2000
DOI: 10.1016/S1360-1385(00)01694-0
Abstract: We are gaining an understanding of the molecular basis of resistance specificity and of the natural processes that generate different specificities. This is a prerequisite for the genetic engineering of new plant disease-resistance genes to control diseases for which naturally occurring resistance is inadequate. DNA sequence analysis indicates that point mutation, recombination and selection can generate and maintain the high levels of polymorphism observed in resistance genes. Comparisons of closely related resistance proteins indicate that specificity can be determined by variation in at least two regions. One of these contains leucine-rich repeats, which are a common feature of most resistance proteins.
Publisher: Springer Science and Business Media LLC
Date: 29-06-1999
Publisher: The Royal Society
Date: 20-05-2009
Abstract: Pathogen genes involved in interactions with their plant hosts are expected to evolve under positive Darwinian selection or balancing selection. In this study a single copy avirulence gene, AvrP4 , in the plant pathogen Mel sora lini , was used to investigate the evolution of such a gene across species. Partial translation elongation factor 1-alpha sequences were obtained to establish phylogenetic relationships among the Mel sora species. We lified AvrP4 homologues from species pathogenic on hosts from different plant families and orders, across the inferred phylogeny. Translations of the AvrP4 sequences revealed a predicted signal peptide and towards the C-terminus of the protein, six identically spaced cysteines were identified in all sequences. Maximum likelihood analysis of synonymous versus non-synonymous substitution rates indicated that positive selection played a role in the evolution of the gene during the ersification of the genus. Fourteen codons under significant positive selection reside in the C-terminal 28 amino acid region, suggesting that this region interacts with host molecules in most sequenced accessions. Selection pressures on the gene may be either due to the pathogenicity or avirulence function of the gene or both.
Publisher: Cold Spring Harbor Laboratory
Date: 28-01-2022
DOI: 10.1101/2022.01.26.477636
Abstract: Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with non-haploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the two nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae ( Pca ). This resource complements two previous released partially phased genome references of Pca , which display virulence traits absent in the isolate of historic race 203 (isolate Pca 203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca 203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca 203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina , the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca 203 reference marks the third fully-phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these three Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
Publisher: Springer Science and Business Media LLC
Date: 22-08-2016
Publisher: Frontiers Media SA
Date: 24-02-2016
Publisher: Oxford University Press (OUP)
Date: 05-1995
DOI: 10.1104/PP.108.1.427
Publisher: Proceedings of the National Academy of Sciences
Date: 17-10-2016
Abstract: Plants and animals use intracellular immunity receptors, known as nucleotide-binding oligomerization domain-like receptors (NLRs), to defend themselves against invading microbes. In this study, we report the solution structure of the N-terminal coiled-coil (CC) domain from the wheat stem rust resistance protein Sr33. Remarkably, this structure differs substantially from the published crystal structure of the equivalent region from the orthologous barley powdery mildew resistance protein MLA10. Using a structural, biophysical, and functional approach, we compare the Sr33 CC domain with other structurally defined NLR CC domains. Collectively, this work redefines our current understanding of the structure and function of plant NLR CC domains, which has significant implications for future studies into this important class of defense receptors.
Publisher: Cold Spring Harbor Laboratory
Date: 29-09-2023
Publisher: Annual Reviews
Date: 25-08-2021
DOI: 10.1146/ANNUREV-PHYTO-020620-121149
Abstract: Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
Publisher: Cold Spring Harbor Laboratory
Date: 03-08-2023
DOI: 10.1101/2023.08.02.551391
Abstract: Plant Toll/interleukin-1 receptor/resistance protein (TIR) type nucleotide-binding and leucine-rich repeat immune receptors (NLRs) require Enhanced Disease Susceptibility 1 (EDS1) family proteins and the helper NLRs NRG1 and ADR1 for immune activation. TIR signalling domains possess NADase activity, producing NAM and v-cADPR from NAD + in vitro . However, after TIR activation different small non-cyclic signalling molecules have been detected bound to EDS1/SAG101 and EDS1/PAD4 heterodimers. These molecules have not been detected in in vitro assays or as free molecules in planta and it is not clear how they are delivered to the EDS1 complexes. Here we investigate physical and functional interactions between TIR signalling domains, EDS1 family proteins and helper NLRs to clarify these signalling transduction pathways. We show that the Nb EDS1- Nb SAG101b- Nb NRG1 signalling pathway in N. benthamiana is necessary and sufficient for cell death signalling induced by six different TIR-containing NLRs from a range of plant species, suggesting this module is likely a universal requirement for TIR-NLR mediated cell death in N. benthamiana . We also find that TIR domains physically interact with Nb EDS1, Nb PAD4 and Nb SAG101 in planta , independently of each other. We also find evidence for direct interaction of Nb NRG1 with Nb SAG101b via its C-terminal EP domain, but not with other EDS1 family members. These data suggest a model in which physical interaction between activated TIRs and EDS1 signalling complexes facilitates efficient transfer of low abundance products of TIR catalytic activity directly to EDS1 heterocomplexes. The interaction could also alter TIR catalytic activity to favor production of the ligands recognised by EDS1/SAG101 and EDS1/PAD4.
Publisher: Springer Science and Business Media LLC
Date: 25-03-2022
DOI: 10.1186/S13059-022-02658-2
Abstract: Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false-positive signals. We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false-positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30–40 times using HiFi sequencing is required for phasing of the leaf rust genome, with 0.7% heterozygosity, and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.
Publisher: Wiley
Date: 10-08-2009
DOI: 10.1111/J.1469-8137.2009.02922.X
Abstract: Many biotrophic fungal and oomycete pathogens share a common infection process involving the formation of haustoria, which penetrate host cell walls and form a close association with plant membranes. Recent studies have identified a class of pathogenicity effector proteins from these pathogens that is transferred into host cells from haustoria during infection. This insight stemmed from the identification of avirulence (Avr) proteins from these pathogens that are recognized by intracellular host resistance (R) proteins. Oomycete effectors contain a conserved translocation motif that directs their uptake into host cells independently of the pathogen, and is shared with the human malaria pathogen. Genome sequence information indicates that oomycetes may express several hundred such host‐translocated effectors. Elucidating the transport mechanism of fungal and oomycete effectors and their roles in disease offers new opportunities to understand how these pathogens are able to manipulate host cells to establish a parasitic relationship and to develop new disease‐control measures.
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.TPLANTS.2018.05.009
Abstract: Innate immunity in land plants mostly relies on a repertoire of NLR (nucleotide-binding, leucine-rich repeat) receptors. Gao et al. show that evolutionary assembly of the core building blocks of NLRs occurred in the ancestors of early plants and trace the ersification of NLR subclasses in green algae and mosses.
Publisher: Wiley
Date: 12-04-2016
DOI: 10.1111/MPP.12385
Publisher: Public Library of Science (PLoS)
Date: 13-07-2017
Publisher: Cold Spring Harbor Laboratory
Date: 24-09-2023
Publisher: Public Library of Science (PLoS)
Date: 28-05-2015
Publisher: International Union of Crystallography (IUCr)
Date: 23-02-2007
Publisher: Springer Science and Business Media LLC
Date: 05-1996
DOI: 10.1007/BF00021786
Abstract: This work presents a mechanistic study of the electrochemical synthesis of magnetite nanoparticles (NPs) based on the analysis of the electrochemical impedance spectroscopy (EIS) technique. After a discussion of the mechanisms reported in the literature, three models are devised and a prediction of their EIS spectra is presented. The approach consisted of the simulation of EIS spectra as a tool for assessing model validity, as EIS allows to characterize the relaxation of adsorbed intermediates. The comparison between the simulated impedance spectra and the experimental results shows that the mechanisms proposed to date do not explain all of the experimental results. Thus, a new model is proposed, in which up to three adsorbed intermediate species are involved. This model accounts for the number of loops found in experimental impedance data. The closest approximation of the features found in the experimental spectra by this proposed model suggests a better representation of the reaction mechanism within the evaluated potential range.
Publisher: Wiley
Date: 09-2001
DOI: 10.1046/J.1365-313X.2001.01114.X
Abstract: 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.
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2017
DOI: 10.1101/192435
Abstract: A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here we present a diploidaware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long-reads using the FALCON-Unzip assembler. RNA-seq datasets were used to infer high quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high inter-haplotype ersity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When investigating genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors, and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales . In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. Current representations of eukaryotic microbial genomes are haploid, hiding the genomic ersity intrinsic to diploid and polyploid life forms. This hidden ersity contributes to the organism’s evolutionary potential and ability to adapt to stress conditions. Yet it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which leads to allelic variation and the presence of genes lacking allelic counterparts. Non-allelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic ersity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Publisher: Wiley
Date: 23-05-2007
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2023
Publisher: Oxford University Press (OUP)
Date: 2016
DOI: 10.1105/TPC.15.00303
Publisher: American Association for the Advancement of Science (AAAS)
Date: 16-12-2016
Abstract: Plants respond to pathogen infection by relocalizing sugar from bacterial colonization sites
Publisher: Springer Science and Business Media LLC
Date: 30-11-2015
Abstract: We identify the wheat stem rust resistance gene Sr50 (using physical mapping, mutation and complementation) as homologous to barley Mla, encoding a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity different from Sr31 and other genes on rye chromosome 1RS, and is effective against the broadly virulent Ug99 race lineage. Extensive haplotype ersity at the rye Sr50 locus holds promise for mining effective resistance genes.
Publisher: Frontiers Media SA
Date: 25-11-2014
Publisher: Humana Press
Date: 2014
DOI: 10.1007/978-1-62703-986-4_21
Abstract: Large numbers of candidate effectors are being identified by genome sequencing of fungal pathogens and in planta expression studies. These effectors are both a boon and a curse for pathogens as they modulate the host cellular environment or suppress defense response to allow fungal growth as well as become targets of plant resistance (R) proteins. Recognition of a fungal effector by a plant R protein triggers a hypersensitive reaction (HR) leading to death of plant cells in and around the infection site, thus preventing further proliferation of the pathogen. Such HR induction has been used as an indicator of effector activity in functional assays of candidate effectors in dicots based on Agrobacterium-mediated transient expression. However, the Agrobacterium assay is not functional in cereal leaves. We therefore have adapted an alternative assay based on effector protein delivery using the type III secretion system (T3SS) of a non-pathogenic Pseudomonas spp. for use in wheat and other cereals. Here, we describe protocols for delivery of effector proteins into wheat and barley cells using the AvrRpm1 T3SS signal in the engineered non-pathogenic Pseudomonas fluorescens strain Effector-to-Host Analyzer (EtHAn). For ease of making expression clones we have generated the GATEWAY cloning compatible vectors. A calmodulin-dependent adenylate cyclase (Cya) reporter protein can be used as an effective marker for fusion protein delivery into wheat and barley by this system.
Publisher: Elsevier BV
Date: 02-2006
DOI: 10.1016/J.TPLANTS.2005.12.008
Abstract: Recent advances in cloning avirulence genes from a rust fungus and three oomycete species have provided the novel insight that these eukaryotic plant pathogens deliver small proteins into the host cell cytoplasm where they are recognized by resistance proteins. Anne Rehmany et al. have recently identified a potential host-targeting signal in oomycete avirulence proteins from Hyaloperonospora parasitica, Phytophthora sojae and Phytophthora infestans that might be involved in transporting proteins into the host cell. This signal is surprisingly similar to the host targeting signal used by the malaria pathogen Plasmodium fulciparum to target virulence proteins to the mammalian host cell.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2010
DOI: 10.1038/NRG2812
Abstract: Plants are engaged in a continuous co-evolutionary struggle for dominance with their pathogens. The outcomes of these interactions are of particular importance to human activities, as they can have dramatic effects on agricultural systems. The recent convergence of molecular studies of plant immunity and pathogen infection strategies is revealing an integrated picture of the plant-pathogen interaction from the perspective of both organisms. Plants have an amazing capacity to recognize pathogens through strategies involving both conserved and variable pathogen elicitors, and pathogens manipulate the defence response through secretion of virulence effector molecules. These insights suggest novel biotechnological approaches to crop protection.
Publisher: Springer Science and Business Media LLC
Date: 14-10-2022
Publisher: Wiley
Date: 29-08-2010
Publisher: Wiley
Date: 16-11-2017
DOI: 10.1111/MPP.12597
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/AR06151
Abstract: Although chemical control is available for rust diseases in wheat, economic and environmental factors favour genetic solutions. Maintenance and improvement of levels of resistance and durability of the genetic control of the 3 wheat rust diseases will occur with the application of DNA markers for pyramiding resistance genes. Information about the molecular basis of rust resistance, including durable, adult-plant resistance, coming from studies in model species such as flax and flax rust and from studies of wheat and barley, will provide knowledge for new biotechnological approaches to rust resistance. Increasing cereal gene sequence data will improve the efficiency of cloning disease resistance genes and, together with the rapid progress in understanding the molecular basis of rust resistance, will make it possible to construct transgenic plants with multiple rust resistance genes at a single locus, which will provide efficient breeding and increased durability of rust resistance.
Publisher: International Union of Crystallography (IUCr)
Date: 26-11-2011
DOI: 10.1107/S1744309111037675
Abstract: The flax rust effector AvrM is a secreted protein of unknown fold that is recognized by the M resistance protein in flax. In order to investigate the structural basis of the AvrM–M interaction and possible virulence-associated functions of AvrM, the C-terminal domains of two different AvrM variants (AvrM-A and avrM) were crystallized. Crystals of native AvrM-A were obtained using pentaerythritol ethoxylate (15/4 EO/OH) as a precipitant and diffracted X-rays to 2.9 Å resolution. Selenomethionine-derivative crystals of similar quality were obtained using PEG 1500 as a precipitant. Both the native and selenomethionine-labelled AvrM-A crystals had symmetry of space group C 222 1 with eight molecules in the asymmetric unit. Crystals of avrM had symmetry of space group P 2 1 2 1 2 1 and diffracted X-rays to 2.7 Å resolution. Initial AvrM-A phases were calculated using the single-wavelength anomalous dispersion (SAD) method and a partial model was built. Phases for avrM were obtained by molecular replacement using the partial AvrM-A model.
Publisher: Springer Science and Business Media LLC
Date: 07-11-2019
DOI: 10.1038/S41467-019-12927-7
Abstract: Parasexuality contributes to ersity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici ( Pgt ), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt , with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic ersity and facilitate the emergence of new lineages in asexual fungal populations.
Publisher: Springer Science and Business Media LLC
Date: 04-2000
Publisher: Scientific Societies
Date: 06-2005
DOI: 10.1094/MPMI-18-0570
Abstract: 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 (Mel sora 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).
Publisher: Wiley
Date: 22-06-2007
DOI: 10.1111/J.1364-3703.2007.00405.X
Abstract: Mel sora lini, while of economic importance as the causal agent of rust disease of flax and linseed, has for several decades been the 'model' rust species with respect to genetic studies of avirulence/virulence. Studies by Harold Flor demonstrated that single pairs of allelic genes determine the avirulence/virulence phenotype on host lines with particular resistance genes and led him to propose his famous 'gene-for-gene' hypothesis. Flor's inheritance studies, together with those subsequently carried out by others, also revealed that, in some cases, an inhibitor gene pair and an avirulence/virulence gene pair interact to determine the infection outcome on host lines with particular resistance genes. Recently, avirulence/virulence genes at four loci, AvrL567, AvrM, AvrP4 and AvrP/AvrP123, have been cloned. All encode novel, small, secreted proteins that are recognized inside plant cells. Yeast two-hybrid studies have shown that the AvrL567 proteins interact directly with the resistance gene protein. The molecular basis of Flor's gene-for-gene relationship has now been elucidated for six interacting gene pairs: those involving resistance genes L5, L6, L7, M, P and P2, where both the resistance gene and the corresponding avirulence gene have been cloned. In other inheritance studies it has been shown that M. lini does not possess a (+) and (-) mating system, but may possess a two factor system. Double-stranded (ds) RNA molecules occur in many strains of M. lini: examination of the progeny of one strain that possesses 11 dsRNA molecules revealed that they fall into three transmission units, designated L, A and B. The L unit consists of a single large dsRNA of 5.2 kbp while the A and B units each consist of five dsRNAs in the size range 1.1-2.8 kbp. The three units have different sexual and asexual transmission characteristics. The L unit is encapsidated in a virus-like particle, whereas the other units are not encapsidated. The population and coevolutionary aspects of M. lini on a wild, native Australian host species, Linum marginale, have been extensively investigated. A recent molecular analysis revealed that the M. lini isolates from L. marginale fall into two distinct lineages, one of which is apparently hybrid between two erse genomes. Isolates in this lineage are largely fixed for heterozygosity, which suggests that sexual recombination does not occur in this lineage.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-12-2017
Abstract: The fungal pathogen Ug99 (named for its identification in Uganda in 1999) threatens wheat crops worldwide. Ug99 can kill entire fields of wheat and is undeterred by many of the disease-resistance genes that otherwise protect wheat crops. Two papers describe two peptides secreted by the fungus as it attacks the wheat (see the Perspective by Moscou and van Esse). Chen et al. show that fungal AvrSr50 binds to the plant's immune receptor Sr50, and Salcedo et al. show that fungal AvrSr35 binds to Sr35. Successful binding activates the plant's immune defenses. Removing or inactivating these Avr effectors leaves the plant defenseless and susceptible to disease. Science , this issue p. 1607 , p. 1604 see also p. 1541
Publisher: American Association for the Advancement of Science (AAAS)
Date: 16-08-2013
Abstract: Recently, Ug99, a particularly devastating strain of wheat stem rust fungus, has emerged, which could potentially threaten food security. Now, two genes have been cloned that offer resistance to Ug99. Saintenac et al. (p. 783 , published online 27 June) cloned Sr35 from Triticum monococcum , a diploid wheat species not often cultivated. Periyannan et al. (p. 786 , published online 27 June) cloned Sr33 from Aegilops tauschii , a diploid wild grass that contributed to the hexaploid genome of cultivated wheat. The genes both encode proteins that show features typical of other disease resistance proteins and offer opportunities to slow the pace of Ug99 progression.
Publisher: Springer Science and Business Media LLC
Date: 16-03-2017
DOI: 10.1038/SREP44598
Abstract: Pathogens secrete effector proteins and many operate inside plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. For 107 eukaryotic effectors, LOCALIZER outperforms other methods and predicts a previously unrecognized chloroplast transit peptide for the ToxA effector, which we show translocates into tobacco chloroplasts. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. LOCALIZER is available at localizer.csiro.au/ .
Publisher: Scientific Societies
Date: 03-2014
DOI: 10.1094/MPMI-07-13-0187-FI
Abstract: Large numbers of candidate effectors from fungal pathogens are being identified through whole-genome sequencing and in planta expression studies. Although Agrobacterium-mediated transient expression has enabled high-throughput functional analysis of effectors in dicot plants, this assay is not effective in cereal leaves. Here, we show that a nonpathogenic Pseudomonas fluorescens engineered to express the type III secretion system (T3SS) of P. syringae and the wheat pathogen Xanthomonas translucens can deliver fusion proteins containing T3SS signals from P. syringae (AvrRpm1) and X. c estris (AvrBs2) avirulence (Avr) proteins, respectively, into wheat leaf cells. A calmodulin-dependent adenylate cyclase reporter protein was delivered effectively into wheat and barley by both bacteria. Absence of any disease symptoms with P. fluorescens makes it more suitable than X. translucens for detecting a hypersensitive response (HR) induced by an effector protein with avirulence activity. We further modified the delivery system by removal of the myristoylation site from the AvrRpm1 fusion to prevent its localization to the plasma membrane which could inhibit recognition of an Avr protein. Delivery of the flax rust AvrM protein by the modified delivery system into transgenic tobacco leaves expressing the corresponding M resistance protein induced a strong HR, indicating that the system is capable of delivering a functional rust Avr protein. In a preliminary screen of effectors from the stem rust fungus Puccinia graminis f. sp. tritici, we identified one effector that induced a host genotype-specific HR in wheat. Thus, the modified AvrRpm1:effector–Pseudomonas fluorescens system is an effective tool for large-scale screening of pathogen effectors for recognition in wheat.
Publisher: Wiley
Date: 15-12-2018
DOI: 10.1111/NPH.14946
Abstract: The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate between these localizations. We present ApoplastP, the first method for predicting whether an effector or plant protein localizes to the apoplast. ApoplastP uncovers features of apoplastic localization common to both effectors and plant proteins, namely depletion in glutamic acid, acidic amino acids and charged amino acids and enrichment in small amino acids. ApoplastP predicts apoplastic localization in effectors with a sensitivity of 75% and a false positive rate of 5%, improving the accuracy of cysteine-rich classifiers by > 13%. ApoplastP does not depend on the presence of a signal peptide and correctly predicts the localization of unconventionally secreted proteins. The secretomes of fungal saprophytes as well as necrotrophic, hemibiotrophic and extracellular fungal pathogens are enriched for predicted apoplastic proteins. Rust pathogens have low proportions of predicted apoplastic proteins, but these are highly enriched for predicted effectors. ApoplastP pioneers apoplastic localization prediction using machine learning. It will facilitate functional studies and will be valuable for predicting if an effector localizes to the apoplast or if it enters plant cells.
Publisher: Annual Reviews
Date: 04-08-2017
DOI: 10.1146/ANNUREV-PHYTO-080516-035250
Abstract: The first plant disease resistance (R) genes were identified and cloned more than two decades ago. Since then, many more R genes have been identified and characterized in numerous plant pathosystems. Most of these encode members of the large family of intracellular NLRs (NOD-like receptors), which also includes animal immune receptors. New discoveries in this expanding field of research provide new elements for our understanding of plant NLR function. But what do we know about plant NLR function today? Genetic, structural, and functional analyses have uncovered a number of commonalities and differences in pathogen recognition strategies as well as how NLRs are regulated and activate defense signaling, but many unknowns remain. This review gives an update on the latest discoveries and breakthroughs in this field, with an emphasis on structural findings and some comparison to animal NLRs, which can provide additional insights and paradigms in plant NLR function.
Publisher: Oxford University Press (OUP)
Date: 03-1999
DOI: 10.1105/TPC.11.3.495
Abstract: 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.
Publisher: Frontiers Media SA
Date: 07-01-2016
Publisher: Elsevier BV
Date: 05-2003
DOI: 10.1016/S0960-9822(03)00321-X
Abstract: A plant protein RIN4 is targeted and modified by bacterial pathogens as part of the disease process. At least two host resistance proteins monitor this pathogen interference and trigger the plant's defence responses.
Publisher: International Union of Crystallography (IUCr)
Date: 30-10-2013
Publisher: Elsevier BV
Date: 08-2012
DOI: 10.1016/J.PBI.2012.05.003
Abstract: Both mutualistic and biotrophic pathogenic fungi rely on living host plants for growth and reproduction and must modify host cell structure and function for successful infection. The deployment of a erse set of secreted virulence determinants referred to as 'effectors', many of which are directly delivered into the host cell, is postulated to be the key to host infection. This review provides a snapshot of the current progress in fungal effector biology. Recent genome sequencing of rust and powdery mildew obligate biotrophs has provided insight into the repertoires of potential effectors of these highly specialised pathogens. Identification of the first host-translocated effectors from mutualistic fungi has revealed that these fungi also manipulate host cells through effectors. The biological activities of some fungal effectors are just beginning to be revealed, while much uncertainty still surrounds the mechanisms of transport into host cells.
Publisher: Oxford University Press (OUP)
Date: 10-2019
Abstract: Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of Ph (“Ph560”) using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of Ph-infected host tissues and homology to proteins from four other Puccinia species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains, Ph612, Ph626, Ph608 and Ph584, which are considered to be simple mutational derivatives of Ph560 with added virulence to one or two of three barley leaf rust resistance genes (viz. Rph3, Rph13 and Rph19). To identify candidate genes for the corresponding avirulence genes AvrRph3, AvrRph13 and AvrRph19, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for AvrRph13, AvrRph3 and AvrRph19, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence.
Publisher: American Society for Microbiology
Date: 07-03-2018
Abstract: A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N 50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype ersity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales . In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic ersity intrinsic to diploid and polyploid life forms. This hidden ersity contributes to the organism’s evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic ersity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
Publisher: Elsevier BV
Date: 12-2009
DOI: 10.1016/J.SEMCDB.2009.04.010
Abstract: As in nearly every discipline of plant biology, new insights are constantly changing our understanding of plant immunity. It is now clear that plant immunity is controlled by two layers of inducible responses: basal responses triggered by conserved microbial features and specific responses triggered by gene-for-gene recognition of pathogen effector proteins by host resistance (R) proteins. The nucleotide-binding domain leucine-rich repeat (NB-LRR) class of R proteins plays a major role in the combat against a wide range of plant pathogens. The variation that has been generated and is maintained within these conserved proteins has ersified their specificity, subcellular localisations, activation and recognition mechanisms, allowing them to specifically adapt to different plant-pathogen interaction systems. This review addresses recent advances in the molecular role of NB-LRR proteins in pathogen recognition and activation of plant defence responses.
Publisher: Oxford University Press (OUP)
Date: 02-12-2005
Abstract: Rust fungi, obligate biotrophs that cause disease and yield losses in crops such as cereals and soybean (Glycine max), obtain nutrients from the host through haustoria, which are specialized structures that develop within host cells. Resistance of flax (Linum usitatissimum) to flax rust (Mel sora lini) involves the induction of a hypersensitive cell death response at haustoria formation sites, governed by gene-for-gene recognition between host resistance and pathogen avirulence genes. We identified genes encoding haustorially expressed secreted proteins (HESPs) by screening a flax rust haustorium-specific cDNA library. Among 429 unigenes, 21 HESPs were identified, one corresponding to the AvrL567 gene. Three other HESPs cosegregated with the independent AvrM, AvrP4, and AvrP123 loci. Expression of these genes in flax induced resistance gene–mediated cell death with the appropriate specificity, confirming their avirulence activity. AvrP4 and AvrP123 are Cys-rich proteins, and AvrP123 contains a Kazal Ser protease inhibitor signature, whereas AvrM contains no Cys residues. AvrP4 and AvrM induce cell death when expressed intracellularly, suggesting their translocation into plant cells during infection. However, secreted AvrM and AvrP4 also induce necrotic responses, with secreted AvrP4 more active than intracellular AvrP4, possibly as a result of enhanced formation of endoplasmic reticulum–dependent disulfide bonds. Addition of an endoplasmic reticulum retention signal inhibited AvrM-induced necrosis, suggesting that both AvrM and AvrP4 can reenter the plant cell after secretion in the absence of the pathogen.
Publisher: Public Library of Science (PLoS)
Date: 28-12-2020
DOI: 10.1371/JOURNAL.PGEN.1009291
Abstract: Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae ( Pca ), which causes crown rust disease in oat ( Avena sativa ) s led from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide ersity patterns at a single Avr locus corresponding to Pc38 , Pc39 , Pc55 , Pc63 , Pc70 , and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
Publisher: Scientific Societies
Date: 08-2011
Abstract: Resistance (R) proteins are key regulators of the plant innate immune system and are capable of pathogen detection and activation of the hypersensitive cell death immune response. To understand the molecular mechanism of R protein activation, we undertook a phenotypic and biochemical study of the flax nucleotide binding (NB)-ARC leucine-rich repeat protein, M. Using Agrobacterium-mediated transient expression in flax cotyledons, site-directed mutations of key residues within the P-loop, kinase 2, and MHD motifs within the NB-ARC domain of M were shown to affect R protein function. When purified using a yeast expression system and assayed for ATP and ADP, these mutated proteins exhibited marked differences in the quantity and identity of the bound nucleotide. ADP was bound to recombinant wild-type M protein, while the nonfunctional P-loop mutant did not have any nucleotides bound. In contrast, ATP was bound to an autoactive M protein mutated in the highly conserved MHD motif. These data provide direct evidence supporting a model of R protein function in which the “off” R protein binds ADP and activation of R protein defense signaling involves the exchange of ADP for ATP.
Publisher: CSIRO Publishing
Date: 2009
DOI: 10.1071/FP08320
Abstract: The outcome of infection of in idual plants by pathogenic organisms is governed by complex interactions between the host and pathogen. These interactions are the result of long-term co-evolutionary processes involving selection and counterselection between plants and their pathogens. These processes are ongoing, and occur at many spatio-temporal scales, including genes and gene products, cellular interactions within host in iduals, and the dynamics of host and pathogen populations. However, there are few systems in which host–pathogen interactions have been studied across these broad scales. In this review, we focus on research to elucidate the structure and function of plant resistance and pathogen virulence genes in the flax-flax rust interaction, and also highlight complementary co-evolutionary studies of a related wild plant–pathogen interaction. The confluence of these approaches is beginning to shed new light on host–pathogen molecular co-evolution in natural environments.
Publisher: Springer Science and Business Media LLC
Date: 15-09-2021
DOI: 10.1186/S12915-021-01123-Z
Abstract: Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici ( Pgt ), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly erse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally ersified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5′ uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5′ adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation.
Publisher: Proceedings of the National Academy of Sciences
Date: 19-08-2011
Publisher: Proceedings of the National Academy of Sciences
Date: 24-07-2020
Abstract: Animal NLRs form wheel-like structures called inflammasomes upon perception of pathogen-associated molecules. The induced proximity of the signaling domains at the center of the wheel is hypothesized to recruit caspases for the first step of immune signal transduction. We expressed a plant-animal NLR fusion to demonstrate that induced proximity of TIR signaling domains from plant NLRs is sufficient to activate plant immune signaling. This demonstrates that a signaling-competent inflammasome can be formed from known, minimal components. The intrinsic NADase activity of plant TIRs is necessary for immune signaling, but fusions to a bacterial or a mammalian TIR domain with NADase activity, which also lead to accumulation of NAD + hydrolysis products (e.g. cyclic ADP-ribose), were unable to activate immune signaling.
Publisher: Portland Press Ltd.
Date: 09-2022
DOI: 10.1042/EBC20210072
Abstract: Plants deploy extracellular and intracellular immune receptors to sense and restrict pathogen attacks. Rapidly evolving pathogen effectors play crucial roles in suppressing plant immunity but are also monitored by intracellular nucleotide-binding, leucine-rich repeat immune receptors (NLRs), leading to effector-triggered immunity (ETI). Here, we review how NLRs recognize effectors with a focus on direct interactions and summarize recent research findings on the signalling functions of NLRs. Coiled-coil (CC)-type NLR proteins execute immune responses by oligomerizing to form membrane-penetrating ion channels after effector recognition. Some CC-NLRs function in sensor–helper networks with the sensor NLR triggering oligomerization of the helper NLR. Toll/interleukin-1 receptor (TIR)-type NLR proteins possess catalytic activities that are activated upon effector recognition-induced oligomerization. Small molecules produced by TIR activity are detected by additional signalling partners of the EDS1 lipase-like family (enhanced disease susceptibility 1), leading to activation of helper NLRs that trigger the defense response.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-08-2019
Abstract: One way that plants respond to pathogen infection is by sacrificing the infected cells. The nucleotide-binding leucine-rich repeat immune receptors responsible for this hypersensitive response carry Toll/interleukin-1 receptor (TIR) domains. In two papers, Horsefield et al. and Wan et al. report that these TIR domains cleave the metabolic cofactor nicotinamide adenine dinucleotide (NAD + ) as part of their cell-death signaling in response to pathogens. Similar signaling links mammalian TIR-containing proteins to NAD + depletion during Wallerian degeneration of neurons. Science , this issue p. 793 , p. 799
Publisher: Proceedings of the National Academy of Sciences
Date: 23-08-2016
Abstract: Stem rust caused by the fungus Puccinia graminis f. sp. tritici ( Pgt ) remains the major disease threat to wheat production. The Sr33 and Sr50 resistance proteins protect wheat against a broad spectrum of field isolates of Pgt and are closely related to the barley powdery mildew-resistance protein MLA10. Like MLA10, Sr33 and Sr50 possess signaling N-terminal domains that self-associate in planta and initiate cell-death signaling from the cytosol. However, Sr33 induces disease-resistance signaling from the cytosol but not from the nucleus of wheat cells, suggesting cytosolic activation of both cell death and stem rust resistance.
Publisher: Oxford University Press (OUP)
Date: 24-07-2009
Publisher: Springer Science and Business Media LLC
Date: 07-06-2021
DOI: 10.1038/S41467-021-23738-0
Abstract: The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61 , with both genes independently introduced as alien chromosome introgressions from tall wheat grass ( Thinopyrum ponticum ). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability.
Publisher: Humana Press
Date: 2014
Publisher: American Association for the Advancement of Science (AAAS)
Date: 10-12-2010
Abstract: Pathogen genes that shut down specific host plant immune responses are highly ergent and have evolved rapidly to accommodate adaptation.
Publisher: Elsevier BV
Date: 04-1996
DOI: 10.1016/S0092-8674(00)81090-9
Abstract: Copper radical alcohol oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens, are attractive for the production of fragrant fatty aldehydes. With the initial objective to investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum, and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture in the absence of any plant-biomass mimicking compounds to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29 to 52% of which were carbohydrate-active enzymes (CAZymes), including a wide ersity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11, AA12, AA13, and AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were thus expressed in Pichia pastoris, and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C
Publisher: Wiley
Date: 05-10-2010
Publisher: Public Library of Science (PLoS)
Date: 29-11-2012
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/FP10072
Abstract: Plant pathogenic biotrophic fungi are able to grow within living plant tissue due to the action of secreted pathogen proteins known as effectors that alter the response of plant cells to pathogens. The discovery and identification of these proteins has greatly expanded with the sequencing and annotation of fungal pathogen genomes. Studies to characterise effector function have revealed that a subset of these secreted pathogen proteins interact with plant proteins within the host cytoplasm. This review focuses on the effectors of intracellular biotrophic and hemibiotrophic fungal plant pathogens and summarises advances in understanding the roles of these proteins in disease and in elucidating the mechanism of fungal effector uptake into host cells.
Publisher: Scientific Societies
Date: 2010
Abstract: In plant immunity, recognition of pathogen effectors by plant resistance proteins leads to the activation of plant defenses and a localized cell death response. The AvrM effector from flax rust is a small secreted protein that is recognized by the M resistance protein in flax. Here, we investigate the mechanism of M–AvrM recognition and show that these two proteins directly interact in a yeast two-hybrid assay, and that this interaction correlates with the recognition specificity observed for each of the different AvrM variants. We further characterize this interaction by demonstrating that the C-terminal domain of AvrM is required for M-dependent cell death, and show that this domain also interacts with the M protein in yeast. We investigate the role of C-terminal differences among the different AvrM proteins for their involvement in this interaction and establish that M recognition is hindered by an additional 34 amino acids present at the C terminus of several AvrM variants. Structural characterization of recombinant AvrM-A protein revealed a globular C-terminal domain that dimerizes.
Publisher: Wiley
Date: 23-09-2010
Publisher: Elsevier BV
Date: 10-2011
Publisher: Springer Berlin Heidelberg
Date: 23-08-2011
Publisher: Oxford University Press (OUP)
Date: 22-06-2022
DOI: 10.1093/G3JOURNAL/JKAC149
Abstract: Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
Publisher: Hindawi Limited
Date: 14-09-2011
Publisher: Wiley
Date: 02-02-2023
DOI: 10.1111/NPH.18727
Abstract: To infect plants, pathogenic fungi secrete small proteins called effectors. Here, we describe the catalytic activity and potential virulence function of the Nudix hydrolase effector AvrM14 from the flax rust fungus ( Mel sora lini ). We completed extensive in vitro assays to characterise the enzymatic activity of the AvrM14 effector. Additionally, we used in planta transient expression of wild‐type and catalytically dead AvrM14 versions followed by biochemical assays, phenotypic analysis and RNA sequencing to unravel how the catalytic activity of AvrM14 impacts plant immunity. AvrM14 is an extremely selective enzyme capable of removing the protective 5′ cap from mRNA transcripts in vitro . Homodimerisation of AvrM14 promoted biologically relevant mRNA cap cleavage in vitro and this activity was conserved in related effectors from other Mel sora spp. In planta expression of wild‐type AvrM14, but not the catalytically dead version, suppressed immune‐related reactive oxygen species production, altered the abundance of some circadian‐rhythm‐associated mRNA transcripts and reduced the hypersensitive cell‐death response triggered by the flax disease resistance protein M1. To date, the decapping of host mRNA as a virulence strategy has not been described beyond viruses. Our results indicate that some fungal pathogens produce Nudix hydrolase effectors with in vitro mRNA‐decapping activity capable of interfering with plant immunity.
Publisher: EMBO
Date: 14-07-2014
Abstract: Plant resistance proteins of the class of nucleotide‐binding and leucine‐rich repeat domain proteins ( NB ‐ LRR s) are immune sensors which recognize pathogen‐derived molecules termed avirulence ( AVR ) proteins. We show that RGA 4 and RGA 5, two NB ‐ LRR s from rice, interact functionally and physically to mediate resistance to the fungal pathogen Magnaporthe oryzae and accomplish different functions in AVR recognition. RGA 4 triggers an AVR ‐independent cell death that is repressed in the presence of RGA 5 in both rice protoplasts and Nicotiana benthamiana . Upon recognition of the pathogen effector AVR ‐Pia by direct binding to RGA 5, repression is relieved and cell death occurs. RGA 4 and RGA 5 form homo‐ and hetero‐complexes and interact through their coiled‐coil domains. Localization studies in rice protoplast suggest that RGA 4 and RGA 5 localize to the cytosol. Upon recognition of AVR ‐Pia, neither RGA 4 nor RGA 5 is re‐localized to the nucleus. These results establish a model for the interaction of hetero‐pairs of NB ‐ LRR s in plants: RGA 4 mediates cell death activation, while RGA 5 acts as a repressor of RGA 4 and as an AVR receptor.
Publisher: Oxford University Press (OUP)
Date: 09-2007
Abstract: 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 (Mel sora 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-Å resolution, respectively. The structures of both proteins are very similar and reveal a β-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 in idual 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.
Publisher: American Association for Cancer Research (AACR)
Date: 11-09-2023
DOI: 10.1158/2159-8290.CD-23-0131
Abstract: H3K27M-mutant diffuse midline glioma (DMG) patients have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/CSF correlate s les from patients treated in two completed multi-site clinical studies. Patients treated with ONC201 following initial radiation but prior to recurrence demonstrated a median overall survival of 21.7 months, while those treated after recurrence had a median overall survival of 9.3 months. Radiographic response was associated with increased expression of key tricarboxylic acid cycle-related genes in baseline tumor sequencing. ONC201 treatment increased 2-hydroxyglutarate levels in cultured H3K27M-DMG cells and patient CSF s les. This corresponded with increases in repressive H3K27me3 in vitro and in human tumors accompanied by epigenetic downregulation of cell cycle regulation and neuro-glial differentiation genes. Overall, ONC201 demonstrates efficacy in H3K27M-DMG by disrupting integrated metabolic and epigenetic pathways and reversing pathognomonic H3K27me3 reduction.
Publisher: Informa UK Limited
Date: 10-2010
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.CHOM.2019.07.020
Abstract: Plant innate immunity is triggered via direct or indirect recognition of pathogen effectors by the NLR family immune receptors. Mechanistic understanding of plant NLR function has relied on structural information from in idual NLR domains and inferences from studies on animal NLRs. Recent reports of the cryo-EM structures of the Arabidopsis plant immune receptor ZAR1 in monomeric inactive and transition states, as well as the active oligomeric state or the "resistosome," have afforded a quantum leap in our understanding of how plant NLRs function. In this Review, we outline the recent structural findings and examine their implications for the activation of plant immune receptors more broadly. We also discuss how NLR signaling in plants, as illustrated by the ZAR1 structure, is analogous to innate immune receptor signaling mechanisms across kingdoms, drawing particular attention to the concept of signaling by cooperative assembly formation.
Publisher: Wiley
Date: 15-11-2018
DOI: 10.1111/MPP.12749
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-05-2009
Abstract: Many biotrophic fungal and oomycete plant pathogens deliver effector proteins directly into host cells during infection. Recent advances are revealing the extensive effector repertoires of these pathogens and are beginning to shed light on how they manipulate host cells to establish a parasitic relationship. Surprisingly, oomycete effectors seem to share a common uptake system with those from the human malaria pathogen. The current explosion of information is opening new research avenues in molecular plant pathology and is providing new opportunities to limit the impact of plant disease on food production.
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.TPLANTS.2017.09.018
Abstract: Wu and co-workers show how a network of sensor and helper NOD-like receptor proteins (NLRs) act together to confer robust resistance to erse plant pathogens.
Publisher: International Union of Crystallography (IUCr)
Date: 22-01-2011
Publisher: Oxford University Press (OUP)
Date: 08-2000
Abstract: 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 ersifying selection on the TIR region is observed.
Publisher: Public Library of Science (PLoS)
Date: 11-09-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 02-05-2011
Abstract: Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Mel sora larici - populina , the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici , the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici . Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
Publisher: Elsevier BV
Date: 03-2011
Location: United States of America
Location: Australia
No related grants have been discovered for Peter Dodds.