Plants and Microbes
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PLoS Pathogens: Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity

PLoS Pathogens: Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity | Plants and Microbes | Scoop.it

Plants have evolved pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) to protect themselves from infection by diverse pathogens. Avirulence (Avr) effectors that trigger plant ETI as a result of recognition by plant resistance (R) gene products have been identified in many plant pathogenic oomycetes and fungi. However, the virulence functions of oomycete and fungal Avr effectors remain largely unknown. Here, we combined bioinformatics and genetics to identify Avr3b, a new Avr gene from Phytophthora sojae, an oomycete pathogen that causes soybean root rot. Avr3b encodes a secreted protein with the RXLR host-targeting motif and C-terminal W and Nudix hydrolase motifs. Some isolates of P. sojae evade perception by the soybean R gene Rps3b through sequence mutation in Avr3b and lowered transcript accumulation. Transient expression of Avr3b in Nicotiana benthamiana increased susceptibility to P. capsici and P. parasitica, with significantly reduced accumulation of reactive oxygen species (ROS) around invasion sites. Biochemical assays confirmed that Avr3b is an ADP-ribose/NADH pyrophosphorylase, as predicted from the Nudix motif. Deletion of the Nudix motif of Avr3b abolished enzyme activity. Mutation of key residues in Nudix motif significantly impaired Avr3b virulence function but not the avirulence activity. Some Nudix hydrolases act as negative regulators of plant immunity, and thus Avr3b might be delivered into host cells as a Nudix hydrolase to impair host immunity. Avr3b homologues are present in several sequenced Phytophthora genomes, suggesting that Phytophthora pathogens might share similar strategies to suppress plant immunity.

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Twitter: "This has to count as the most beautiful thesis cover. Ever. Well done @xiaolin422 @VivianneTwit #apoplasticeffectors #plantpath #plantsci #Immunity" (2018)

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YouTube: Interview with Stella Cesari, 2017 New Phytologist Tansley Medal winner

"I have always been fascinated by how beautiful and diverse plants are." Stella Cesari is the winner of the 2017 New Phytologist Tansley Medal for excellence in plant science.

 

Read Stella's winning Tansley insight review here: https://doi.org/10.1111/nph.14877

 

Watch Stella present her research in this video: https://www.youtube.com/watch?v=c1OW_...

 

Find out more about the New Phytologist Tansley Medal: https://newphytologist.org/tansleymedal

 

Stella Cesari was speaking to Mike Whitfield. Recording and editing by Leeds Media Services: http://leedsmediaservices.co.uk/

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Resource: Plant Genome Editing Database (2018)

Resource: Plant Genome Editing Database (2018) | Plants and Microbes | Scoop.it

The Plant Genome Editing Database currently provides information about plants that have been generated using the CRISPR/Cas9 technology in order to study economically important traits. Users begin by either choosing the species they are interested in and browsing the list of genes that carry mutations or searching the database using specific gene identifiers (e.g., Solyc05g053230). Information provided includes the transformation experiment, the name of the transformed plant variety, the DNA construct used including the guide RNA sequence and primers used to characterize resulting mutations, and details about the mutant plant line including the altered sequence, whether it is heterozygous or homozygous, and any phenotypes that have been observed. Users are encouraged to make information available about their own CRISPR-generated plant lines and details are provided about how data can be submitted for inclusion in the database.

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MPMI: Subfamily-specific specialization of RGH1/MLA immune receptors in wild barley (2018)

MPMI: Subfamily-specific specialization of RGH1/MLA immune receptors in wild barley (2018) | Plants and Microbes | Scoop.it

The barley disease resistance (R) gene locus Mildew Locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis hordei (Bgh) and has been introgressed into modern cultivars from diverse germplasms, including the wild relative Hordeum spontaneum. Known Mla disease resistance specificities to Bgh appear to encode allelic variants of the R Gene Homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. We here sequenced and assembled the transcriptomes of 50 H. spontaneum accessions representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, linked neither to geographic origin nor population structure and could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil signaling domains that are both capable of eliciting cell death. The presence of positively selected sites, located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both coiled-coil signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the population. Unexpectedly, known MLA receptor variants that confer Bghresistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially as adaptation to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor.

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bioRxiv: Sulfated RaxX, which represents an unclassified group of ribosomally synthesized post-translationally modified peptides, binds a host immune receptor (2018)

bioRxiv: Sulfated RaxX, which represents an unclassified group of ribosomally synthesized post-translationally modified peptides, binds a host immune receptor (2018) | Plants and Microbes | Scoop.it

The rice immune receptor XA21 is activated by the sulfated microbial peptide RaxX (required for activation of XA21-mediated immunity X) produced by Xanthomonas oryzae pv. oryzae (Xoo). Mutational studies and targeted proteomics revealed that RaxX is processed and secreted by the protease/transporter RaxB, whose function can be partially fulfilled by a noncognate peptidase-containing transporter B (PctB). RaxX is cleaved at a Gly-Gly motif, yielding a mature peptide that retains the necessary elements for RaxX function as an immunogen and host peptide hormone mimic. These results indicate that RaxX is a founding member of a previously unclassified and understudied group of tyrosine sulfated RiPPs (ribosomally synthesized, post-translationally modified peptides). We further demonstrate that sulfated RaxX directly binds XA21 with high affinity. This work reveals a complete, previously uncharacterized biological process: bacterial RiPP biosynthesis, secretion, binding to a eukaryotic receptor and triggering of a robust host immune response.

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PLoS Genetics: The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates (2018)

PLoS Genetics: The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates (2018) | Plants and Microbes | Scoop.it

Author summary Plants are constantly exposed to a multitude of potential pathogens but remain immune to most of these due to a multilayered immune system. Pathogens have specialized by adapting to certain host plants and their defense barriers. Most of our understanding of plant-pathogen interactions stems from these highly specialized interactions, because they are characterized by qualitative interactions (resistant or susceptible). It has generally been assumed that the genetic and molecular basis of resistance to non-adapted pathogens is fundamentally different, as either no variation exists in a species (complete immunity) or variation encompasses only early pathogen invasion (colonization), but not full susceptibility. We have studied the interaction between the agronomically important fungal stripe rust pathogen (Puccinia striiformis) of wheat and barley with the wild grass species Brachypodium distachyon. Rust infections consist of two stages: colonization of plant tissues followed by a reproductive phase. We identified natural variation for the degree of P. striiformis colonization in different B. distachyon accessions and dissected the genetic architecture controlling resistance at this infection stage. QTLs conferring resistance possessed several characteristics similar to adapted host systems, indicating that resistance to adapted and non-adapted pathogens are not intrinsically different.


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Molecular Plant Pathology: Recognition of lettuce downy mildew effector BLR38 in Lactuca serriola LS102 requires two unlinked loci (2018)

Molecular Plant Pathology: Recognition of lettuce downy mildew effector BLR38 in Lactuca serriola LS102 requires two unlinked loci (2018) | Plants and Microbes | Scoop.it

Plant pathogenic oomycetes secrete effector proteins to suppress host immune responses. Resistance genes may recognize effectors and activate immunity, which is often associated with a hypersensitive response (HR). Transient expression of effectors in plant germplasm and screening for HR has proven a powerful tool in the identification of new resistance genes. In this study, fourteen effectors from the lettuce downy mildew Bremia lactucae race Bl:24 were screened for HR induction in over 150 lettuce accessions. Three effectors ‐ BLN06, BLR38 and BLR40 – were recognized in specific lettuce lines. Recognition of effector BLR38 in Lactuca serriola LS102 did not co‐segregate with resistance against race Bl:24 but was linked to resistance against multiple other B. lactucae races. Two unlinked loci are both required for effector recognition and are located near known major resistance clusters. Gene dosage affects the intensity of the BLR38‐triggered HR but is of minor importance for disease resistance.

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Sci Reports: CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus (2018)

Sci Reports: CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus (2018) | Plants and Microbes | Scoop.it

The rice blast fungus Magnaporthe oryzae is the most serious pathogen of cultivated rice and a significant threat to global food security. To accelerate targeted mutation and specific genome editing in this species, we have developed a rapid plasmid-free CRISPR-Cas9-based genome editing method. We show that stable expression of Cas9 is highly toxic to Moryzae. However efficient gene editing can be achieved by transient introduction of purified Cas9 pre-complexed to RNA guides to form ribonucleoproteins (RNPs). When used in combination with oligonucleotide or PCR-generated donor DNAs, generation of strains with specific base pair edits, in-locus gene replacements, or multiple gene edits, is very rapid and straightforward. We demonstrate a co-editing strategy for the creation of single nucleotide changes at specific loci. Additionally, we report a novel counterselection strategy which allows creation of precisely edited fungal strains that contain no foreign DNA and are completely isogenic to the wild type. Together, these developments represent a scalable improvement in the precision and speed of genetic manipulation in Moryzae and are likely to be broadly applicable to other fungal species.


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Twitter Archive: #ICPP2018 International Congress of Plant Pathology, Boston, July/August 2018

Twitter Archive: #ICPP2018 International Congress of Plant Pathology, Boston, July/August 2018 | Plants and Microbes | Scoop.it

Download #ICPP2018 Twitter archive as a PDF file [~290 Mb].

 

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Robin Choudhury's #sketchnotes at #ICPP2018 the International Congress of Plant Pathology, Boston, July/August 2018

Robin Choudhury's #sketchnotes at #ICPP2018 the International Congress of Plant Pathology, Boston, July/August 2018 | Plants and Microbes | Scoop.it

Robin Choudhury @rob_choudhury AMAZING #sketchnotes at #ICPP2018. Click here to get the entire set.

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bioRxiv: Convergent evolution of effector protease recognition by Arabidopsis and barley (2018)

bioRxiv: Convergent evolution of effector protease recognition by Arabidopsis and barley (2018) | Plants and Microbes | Scoop.it

The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense responses in diverse barley cultivars. We show also that barley contains two PBS1 orthologs, that their products are cleaved by AvrPphB, and that the barley AvrPphB response maps to a single locus containing a nucleotide-binding leucine-rich repeat (NLR) gene, which we termed AvrPphB Resistance 1 (Pbr1). Transient co-expression of PBR1 with wild-type AvrPphB, but not a protease inactive mutant, triggered defense responses, indicating that PBR1 detects AvrPphB protease activity. Additionally, PBR1 co-immunoprecipitated with barley and N. benthamiana PBS1 proteins, suggesting mechanistic similarity to detection by RPS5. Lastly, we determined that wheat cultivars also recognize AvrPphB protease activity and contain a Pbr1 ortholog. Phylogenetic analyses showed however that Pbr1 is not orthologous to RPS5. Our results indicate that the ability to recognize AvrPphB evolved convergently, and imply that selection to guard PBS1-like proteins is ancient. Also, the results suggest that PBS1-based decoys may be used to engineer protease effector recognition-based resistance in barley and wheat.

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Annual Reviews of Phytopathology: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018)

Annual Reviews of Phytopathology: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018) | Plants and Microbes | Scoop.it

Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.


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bioRxiv: CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus (2018)

bioRxiv: CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus (2018) | Plants and Microbes | Scoop.it

The rice blast fungus Magnaporthe oryzae is the most serious pathogen of cultivated rice and a significant threat to global food security. To accelerate targeted mutation and specific gene editing in this species, we have developed a rapid plasmid-free CRISPR-Cas9-based gene editing method. It has previously been reported in M. oryzae that transformation with plasmids expressing Cas9 can generate specific mutations using sgRNAs, directing the endonuclease to specific genes. We show, however, that expression of Cas9 is highly toxic to M. oryzae, rendering this approach impractical. We demonstrate that using purified Cas9 pre-complexed to RNA guides to form ribonucleoproteins (RNPs), provides an alternative and very effective gene editing procedure. When used in combination with oligonucleotide or PCR-generated donor DNAs, generation of strains with specific base pair edits, in-locus gene replacements, or multiple gene edits, is very rapid and straightforward. Additionally, we report a novel counterselection strategy which allows creation of precisely edited fungal strains that contain no foreign DNA and are completely isogenic to the wild type. Together, these developments represent a scalable improvement in the precision and speed of genetic manipulation in M. oryzae and are likely to be broadly applicable to other fungal species.

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YouTube: #Future-ready: Harnessing Plant-Microbe Systems | Naweed Naqvi | TEDxYouth@AIS (2018)

While making the roadmap ”wish-list” for the future, the last item, “food”, set the plant biologist in Dr. Naweed Naqvi thinking about what could be the major challenges faced by food crops or plants in general, in the future. In this talk, he speaks about how we can engineer precision plant-immunity by studying the defence pathways of rice, a simple, but powerful crop. Naweed Naqvi obtained his PhD from the Maharaja Sayajirao University of Baroda (India) and the International Rice Research Institute (IRRI, Philippines) in 1995. He worked as a Rockefeller Foundation Fellow at IRRI until 1997, when he moved to the Institute of Molecular Agrobiology, Singapore for a postdoctoral stint in eukaryotic cell division. He subsequently started his independent research group at IMA focusing primarily on Fungal Pathogenesis. He joined the Temasek Life Sciences Laboratory as a Senior Scientist in 2002, and serves as an Adjunct Professor at the National University of Singapore This talk was given at a TEDx event using the TED conference format but independently organized by a local community. Click here to edit the contentClick here to edit the content

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PNAS: Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces (2018)

PNAS: Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces (2018) | Plants and Microbes | Scoop.it

The structurally conserved but sequence-unrelated MAX (Magnaporthe oryzae avirulence and ToxB-like) effectors AVR1-CO39 and AVR-PikD from the blast fungus M. oryzae are recognized by the rice nucleotide-binding domain and leucine-rich repeat proteins (NLRs) RGA5 and Pikp-1, respectively. This involves, in both cases, direct interaction of the effector with a heavy metal-associated (HMA) integrated domain (ID) in the NLR. Here, we solved the crystal structures of a C-terminal fragment of RGA5 carrying the HMA ID (RGA5_S), alone, and in complex with AVR1-CO39 and compared it to the structure of the Pikp1HMA/AVR-PikD complex. In both complexes, HMA ID/MAX effector interactions involve antiparallel alignment of β-sheets from each partner. However, effector-binding occurs at different surfaces in Pikp1HMA and RGA5HMA, indicating that these interactions evolved independently by convergence of these two MAX effectors to the same type of plant target proteins. Interestingly, the effector-binding surface in RGA5HMA overlaps with the surface that mediates RGA5HMA self-interaction. Mutations in the HMA-binding interface of AVR1-CO39 perturb RGA5HMA-binding, in vitro and in vivo, and affect the recognition of M. oryzae in a rice cultivar containing Pi-CO39. Our study provides detailed insight into the mechanisms of effector recognition by NLRs, which has substantial implications for future engineering of NLRs to expand their recognition specificities. In addition, we propose, as a hypothesis for the understanding of effector diversity, that in the structurally conserved MAX effectors the molecular mechanism of host target protein-binding is conserved rather than the host target proteins themselves.

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Current Biology: FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana (2018)

Current Biology: FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana (2018) | Plants and Microbes | Scoop.it

Bacterial pathogens use effectors and phytotoxins to facilitate infection of host plants. Coronatine (COR) is one of the phytotoxins produced in bacterial pathogens, such as Pseudomonas syringae pv. tomato DC3000 (pst DC3000). COR structurally and functionally mimics the active form of the plant hormone jasmonic acid (JA), JA-isoleucine (JA-Ile), and can hijack the host JA-signaling pathway to achieve host disease susceptibility [ 1 ]. COR utilizes the transcription factor MYC2, a master regulator of JA signaling, to activate NAC transcription factors, which functions to inhibit accumulation of salicylic acid (SA) and thus compromise host immunity [ 2 ]. It has been demonstrated that SA can antagonize JA signaling through NONEXPRESSOR of PATHOGENESIS-RELATED GENE1 (NPR1) [ 3 ] and downstream transcription factors TGAs [ 4 ] and WRKYs [ 5 , 6 ]. However, the detailed mechanism by which host plants counteract COR-mediated susceptibility is largely unknown. Here, we show that the receptor kinase FERONIA (FER) functions to inhibit JA and COR signaling by phosphorylating and destabilizing MYC2, thereby positively regulating immunity. Conversely, the peptide ligand RALF23 acts through FER to stabilize MYC2 and elevate JA signaling, negatively contributing to plant immunity. Our results establish the RALF23-FER-MYC2 signaling module and provide a previously unknown mechanism by which host plants utilize FER signaling to counteract COR-mediated host disease susceptibility.

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Plant J: The truncated NLR protein TIR‐NBS13 is a MOS6/IMPORTIN‐α3 interaction partner required for plant immunity (2017)

Plant J: The truncated NLR protein TIR‐NBS13 is a MOS6/IMPORTIN‐α3 interaction partner required for plant immunity (2017) | Plants and Microbes | Scoop.it

Importin‐α proteins mediate the translocation of nuclear localization signal (NLS)‐containing proteins from the cytoplasm into the nucleus through nuclear pore complexes (NPCs). Genetically, Arabidopsis IMPORTIN‐α3/MOS6 (MODIFIER OF SNC1, 6) is required for basal plant immunity and constitutive disease resistance activated in the autoimmune mutant snc1 (suppressor of npr1‐1, constitutive 1), suggesting that MOS6 plays a role in the nuclear import of proteins involved in plant defense signaling. Here, we sought to identify and characterize defense‐regulatory cargo proteins and interaction partners of MOS6. We conducted both in silico database analyses and affinity purification of functional epitope‐tagged MOS6 from pathogen‐challenged stable transgenic plants coupled with mass spectrometry. We show that among the 13 candidate MOS6 interactors we selected for further functional characterization, the TIR‐NBS‐type protein TN13 is required for resistance against Pseudomonas syringae pv. tomato (Pst) DC3000 lacking the type‐III effector proteins AvrPto and AvrPtoB. When expressed transiently in N. benthamianaleaves, TN13 co‐immunoprecipitates with MOS6, but not with its closest homolog IMPORTIN‐α6, and localizes to the endoplasmic reticulum (ER), consistent with a predicted N‐terminal transmembrane domain in TN13. Our work uncovered the truncated NLR protein TN13 as a component of plant innate immunity that selectively binds to MOS6/IMPORTIN‐α3 in planta. We speculate that the release of TN13 from the ER membrane in response to pathogen stimulus, and its subsequent nuclear translocation, is important for plant defense signal transduction.Click here to edit the content

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#TwitterWisdom "I'm not a fan of the persistent PAMP-triggered (PTI) vs. effector-triggered immunity (ETI) nomenclature... #plantpath #plantsci" (2018)

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Talking Biotech: Winning the disease resistance 'arms race' against plant pathogens to ensure food security (2018)

Talking Biotech: Winning the disease resistance 'arms race' against plant pathogens to ensure food security (2018) | Plants and Microbes | Scoop.it

Plant disease resistance is a complicated arms race between the plant and pathogens. Bacteria, viruses and fungi evolve in lock-step with plants, creating new ways to overcome new disease resistance strategies. Resistance to disease has a foundation in the gene-for-gene model, a model that hypothesizes that plants and pathogens have a molecular relationship with each other that mediates pathogenicity.

 

Today’s podcast features Drs. Lida Derevnina and Chih-Hang Wu, postdoctoral researchers with Sophien Kamoun (@KamounLab) at the Sainsbury Laboratory (@TheSainsburyLab) in Norwich, England. They describe the new thinking of disease resistance as a number of complex layers that integrates many gene-for-gene interactions with other mechanisms in mediating plant defense.

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PNAS: Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors (2018)

PNAS: Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors (2018) | Plants and Microbes | Scoop.it

Plant intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors often function in pairs to detect pathogen effectors and activate defense. The Arabidopsis RRS1-R–RPS4 NLR pair recognizes the bacterial effectors AvrRps4 and PopP2 via an integrated WRKY transcription factor domain in RRS1-R that mimics the effector’s authentic targets. How the complex activates defense upon effector recognition is unknown. Deletion of the WRKY domain results in an RRS1 allele that triggers constitutive RPS4-dependent defense activation, suggesting that in the absence of effector, the WRKY domain contributes to maintaining the complex in an inactive state. We show the WRKY domain interacts with the adjacent domain 4, and that the inactive state of RRS1 is maintained by WRKY–domain 4 interactions before ligand detection. AvrRps4 interaction with the WRKY domain disrupts WRKY–domain 4 association, thus derepressing the complex. PopP2-triggered activation is less easily explained by such disruption and involves the longer C-terminal extension of RRS1-R. Furthermore, some mutations in RPS4 and RRS1 compromise PopP2 but not AvrRps4 recognition, suggesting that AvrRps4 and PopP2 derepress the complex differently. Consistent with this, a “reversibly closed” conformation of RRS1-R, engineered in a method exploiting the high affinity of colicin E9 and Im9 domains, reversibly loses AvrRps4, but not PopP2 responsiveness. Following RRS1 derepression, interactions between domain 4 and the RPS4 C-terminal domain likely contribute to activation. Simultaneous relief of autoinhibition and activation may contribute to defense activation in many immune receptors.


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New York Times: Watch Plants Light Up When They Get Attacked (2018)

New York Times: Watch Plants Light Up When They Get Attacked (2018) | Plants and Microbes | Scoop.it

Plants have no eyes, no ears, no mouth and no hands. They do not have a brain or a nervous system. Muscles? Forget them. They’re stuck where they started, soaking up the sun and sucking up nutrients from the soil. And yet, when something comes around to eat them, they sense it.

And they fight back.


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Jean-Michel Ané's curator insight, September 13, 10:01 PM

Awesome research from @SimonGilroy

Zanarick's curator insight, September 15, 9:44 AM
This is cool how the plant try’s to heal itself.
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Nature Communications: An effector from the Huanglongbing-associated pathogen targets citrus proteases (2018)

Nature Communications: An effector from the Huanglongbing-associated pathogen targets citrus proteases (2018) | Plants and Microbes | Scoop.it

The citrus industry is facing an unprecedented challenge from Huanglongbing (HLB). All cultivars can be affected by the HLB-associated bacterium ‘Candidatus Liberibacter asiaticus’ (CLas) and there is no known resistance. Insight into HLB pathogenesis is urgently needed in order to develop effective management strategies. Here, we use Sec-delivered effector 1 (SDE1), which is conserved in all CLas isolates, as a molecular probe to understand CLas virulence. We show that SDE1 directly interacts with citrus papain-like cysteine proteases (PLCPs) and inhibits protease activity. PLCPs are defense-inducible and exhibit increased protein accumulation in CLas-infected trees, suggesting a role in citrus defense responses. We analyzed PLCP activity in field samples, revealing specific members that increase in abundance but remain unchanged in activity during infection. SDE1-expressing transgenic citrus also exhibit reduced PLCP activity. These data demonstrate that SDE1 inhibits citrus PLCPs, which are immune-related proteases that enhance defense responses in plants.

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bioRxiv: Re-annotated Nicotiana benthamiana gene models for enhanced proteomics and reverse genetics (2018)

bioRxiv: Re-annotated Nicotiana benthamiana gene models for enhanced proteomics and reverse genetics (2018) | Plants and Microbes | Scoop.it

Nicotiana benthamiana is an important model organism and representative of the Solanaceae (Nightshade) family. N. benthamiana has a complex ancient allopolyploid genome with 19 chromosomes, and an estimated genome size of 3.1Gb. Several draft assemblies of the N. benthamiana genome have been generated, however, many of the gene-models in these draft assemblies appear incorrect. Here we present a nearly non-redundant database of improved N. benthamiana gene-models based on gene annotations from well-annotated genomes in the Nicotiana genus. We show that the new predicted proteome is more complete than the previous proteomes and more sensitive and accurate in proteomics applications, while maintaining a reasonable low gene number (~43,000). As a proof-of-concept we use this proteome to compare the leaf extracellular (apoplastic) proteome to a total extract of leaves. Several gene families are more abundant in the apoplast. For one of these apoplastic protein families, the subtilases, we present a phylogenetic analysis illustrating the utility of this database. Besides proteome annotation, this database will aid the research community with improved target gene selection for genome editing and off-target prediction for gene silencing.

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Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018)

Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018) | Plants and Microbes | Scoop.it

Accelerated adaptive evolution is a hallmark of plant–pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.


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bioRxiv: Tracking disease resistance deployment in potato breeding by enrichment sequencing (2018)

bioRxiv: Tracking disease resistance deployment in potato breeding by enrichment sequencing (2018) | Plants and Microbes | Scoop.it

Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans)gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

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