scholarly journals Roq1 confers resistance to Xanthomonas, Pseudomonas syringae and Ralstonia solanacearum in tomato

2019 ◽  
Author(s):  
Nicholas C. Thomas ◽  
Connor G. Hendrich ◽  
Upinder S. Gill ◽  
Caitilyn Allen ◽  
Samuel F. Hutton ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Ralstonia Solanacearum ◽  
Plant Pathogens ◽  
Field Trials ◽  
Current Control ◽  
Effector Proteins ◽  
Effective Control ◽  
Crop Species ◽  
Xanthomonas Perforans ◽  
Pathogen Effector

AbstractXanthomonas species, Pseudomonas syringae and Ralstonia solanacearum are bacterial plant pathogens that cause significant yield loss in many crop species. Current control methods for these pathogens are insufficient but there is significant potential for generating new disease-resistant crop varieties. Plant immune receptors encoded by nucleotide-binding, leucine-rich repeat (NLR) genes typically confer resistance to pathogens that produce a cognate elicitor, often an effector protein secreted by the pathogen to promote virulence. The diverse sequence and presence / absence variation of pathogen effector proteins within and between pathogen species usually limits the utility of a single NLR gene to protecting a plant from a single pathogen species or particular strains. The NLR protein Recognition of XopQ 1 (Roq1) was recently identified from the plant Nicotiana benthamiana and mediates perception of the effector proteins XopQ and HopQ1 from Xanthomonas and P. syringae respectively. Unlike most recognized effectors, alleles of XopQ/HopQ1 are highly conserved and present in most plant pathogenic strains of Xanthomonas and P. syringae. A homolog of XopQ/HopQ1, named RipB, is present in many R. solanacearum strains. We found that Roq1 also mediates perception of RipB and confers immunity to Xanthomonas, P. syringae, and R. solanacearum when expressed in tomato. Strong resistance to Xanthomonas perforans was observed in three seasons of field trials with both natural and artificial inoculation. The Roq1 gene can therefore be used to provide safe, economical and effective control of these pathogens in tomato and other crop species and reduce or eliminate the need for traditional chemical controls.SummaryA single immune receptor expressed in tomato confers strong resistance to three different bacterial diseases.

The role of oomycete effectors in plant - pathogen interactions

2010 ◽  
Vol 37 (10) ◽  
pp. 919 ◽  
Author(s):  
Adrienne R. Hardham ◽  
David M. Cahill
Keyword(s):  
Plant Cell ◽  
Plant Pathogens ◽  
Plant Defence ◽  
Effector Proteins ◽  
Plant Structure ◽  
Cell Wall Degrading Enzymes ◽  
Cell Cytoplasm ◽  
Diverse Range ◽  
Successful Infection ◽  
Pathogen Effector

Plants constantly come into contact with a diverse range of microorganisms that are potential pathogens, and they have evolved multi-faceted physical and chemical strategies to inhibit pathogen ingress and establishment of disease. Microbes, however, have developed their own strategies to counteract plant defence responses. Recent research on plant–microbe interactions has revealed that an important part of the infection strategies of a diverse range of plant pathogens, including bacteria, fungi and oomycetes, is the production of effector proteins that are secreted by the pathogen and that promote successful infection by manipulating plant structure and metabolism, including interference in plant defence mechanisms. Pathogen effector proteins may function either in the extracellular spaces within plant tissues or within the plant cell cytoplasm. Extracellular effectors include cell wall degrading enzymes and inhibitors of plant enzymes that attack invading pathogens. Intracellular effectors move into the plant cell cytoplasm by as yet unknown mechanisms where, in incompatible interactions, they may be recognised by plant resistance proteins but where, in compatible interactions, they may suppress the plant’s immune response. This article presents a brief overview of our current understanding of the nature and function of effectors produced by oomycete plant pathogens.

scholarly journals Strain-Level Identification of Bacterial Tomato Pathogens Directly from Metagenomic Sequences

2020 ◽  
Vol 110 (4) ◽  
pp. 768-779 ◽  
Author(s):  
Marco E. Mechan Llontop ◽  
Parul Sharma ◽  
Marcela Aguilera Flores ◽  
Shu Yang ◽  
Jill Pollok ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Strain Level ◽  
Third Party ◽  
Metagenomic Sequencing ◽  
Microbial Identification ◽  
Xanthomonas Perforans ◽  
Field Samples ◽  
Group 2 ◽  
Level Identification

Routine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technologies (ONT) MinION sequencer for metagenomic sequencing of tomato plants either artificially inoculated with a known strain of the bacterial speck pathogen Pseudomonas syringae pv. tomato or collected in the field and showing bacterial spot symptoms caused by one of four Xanthomonas species. After species-level identification via ONT’s WIMP software and the third-party tools Sourmash and MetaMaps, we used Sourmash and MetaMaps with a custom database of representative genomes of bacterial tomato pathogens to attempt strain-level identification. In parallel, each metagenome was assembled and the longest contigs were used as query with the genome-based microbial identification Web service LINbase. Both the read-based and assembly-based approaches correctly identified P. syringae pv. tomato strain T1 in the artificially inoculated samples. The pathogen strain in most field samples was identified as a member of Xanthomonas perforans group 2. This result was confirmed by whole genome sequencing of colonies isolated from one of the samples. Although in our case metagenome-based pathogen identification at the strain level was achieved, caution still must be exercised in interpreting strain-level results because of the challenges inherent to assigning reads to specific strains and the error rate of nanopore sequencing.

scholarly journals Functional Characterization of Key Residues in Regulatory Proteins HrpG and HrpV of Pseudomonas syringae pv. tomato DC3000

2017 ◽  
Vol 30 (8) ◽  
pp. 656-665 ◽  
Author(s):  
Milija Jovanovic ◽  
Christopher Waite ◽  
Ellen James ◽  
Nicholas Synn ◽  
Timothy Simpson ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Functional Characterization ◽  
Direct Interaction ◽  
Negative Control ◽  
Effector Proteins ◽  
Tomato Dc3000 ◽  
Sequence Alignments ◽  
Group I ◽  
Σ Factor

The plant pathogen Pseudomonas syringae pv. tomato DC3000 uses a type III secretion system (T3SS) to transfer effector proteins into the host. The expression of T3SS proteins is controlled by the HrpL σ factor. Transcription of hrpL is σ54-dependent and bacterial enhancer-binding proteins HrpR and HrpS coactivate the hrpL promoter. The HrpV protein imposes negative control upon HrpR and HrpS through direct interaction with HrpS. HrpG interacts with HrpV and relieves such negative control. The sequence alignments across Hrp group I-type plant pathogens revealed conserved HrpV and HrpG amino acids. To establish structure–function relationships in HrpV and HrpG, either truncated or alanine substitution mutants were constructed. Key functional residues in HrpV and HrpG are found within their C-terminal regions. In HrpG, L101 and L105 are indispensable for the ability of HrpG to directly interact with HrpV and suppress HrpV-dependent negative regulation of HrpR and HrpS. In HrpV, L108 and G110 are major determinants for interactions with HrpS and HrpG. We propose that mutually exclusive binding of HrpS and HrpG to the same binding site of HrpV governs a transition from negative control to activation of the HrpRS complex leading to HrpL expression and pathogenicity of P. syringae.

Isolation of Ralstonia solanacearum hrpB constitutive mutants and secretion analysis of hrpB-regulated gene products that share homology with known type III effectors and enzymes

Microbiology ◽  
2005 ◽  
Vol 151 (9) ◽  
pp. 2873-2884 ◽  
Author(s):  
Naoyuki Tamura ◽  
Yukio Murata ◽  
Takafumi Mukaihara
Keyword(s):  
Pseudomonas Syringae ◽  
Ralstonia Solanacearum ◽  
Type Iii Secretion ◽  
Effector Proteins ◽  
Gene Products ◽  
Nudix Hydrolase ◽  
Type Iii Effectors ◽  
Type Iii ◽  
Extracellular Secretion ◽  
Culture Supernatants

The Hrp type III secretion system (TTSS) is essential for the pathogenicity of the Gram-negative plant pathogen Ralstonia solanacearum. To examine the secretion of type III effector proteins via the Hrp TTSS, a screen was done of mutants constitutively expressing the hrpB gene, which encodes an AraC-type transcriptional activator for the hrp regulon. A mutant was isolated that in an hrp-inducing medium expresses several hrpB-regulated genes 4·9–83-fold higher than the wild-type. R. solanacearum Hrp-secreted outer proteins PopA and PopC were secreted at high levels into the culture supernatants of the hrpB constitutive (hrpB c) mutant. Using hrpB c mutants, the extracellular secretion of several hrpB-regulated (hpx) gene products that share homology with known type III effectors and enzymes was examined. Hpx23, Hpx24 and Hpx25, which are similar in sequence to Pseudomonas syringae pv. tomato effector proteins HopPtoA1, HolPtoR and HopPtoD1, are also secreted via the Hrp TTSS in R. solanacearum. The secretion of two hpx gene products that share homology with known enzymes, glyoxalase I (Hpx19) and Nudix hydrolase (Hpx26), was also examined. Hpx19 is accumulated inside the cell, but interestingly, Hpx26 is secreted outside the cell as an Hrp-secreted outer protein, suggesting that Hpx19 functions intracellularly but Hpx26 is a novel effector protein of R. solanacearum.

scholarly journals The type III effector HopF2Pto targets Arabidopsis RIN4 protein to promote Pseudomonas syringae virulence

2010 ◽  
Vol 107 (5) ◽  
pp. 2349-2354 ◽  
Author(s):  
Mike Wilton ◽  
Rajagopal Subramaniam ◽  
James Elmore ◽  
Corinna Felsensteiner ◽  
Gitta Coaker ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Immunity ◽  
Effector Proteins ◽  
Type Iii ◽  
Pathogen Effector ◽  
Effector Triggered Immunity ◽  
Type Iii Secretion Effector ◽  
Virulence Target

Plant immunity can be induced by two major classes of pathogen-associated molecules. Pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs) are conserved molecular components of microbes that serve as “non-self” features to induce PAMP-triggered immunity (PTI). Pathogen effector proteins used to promote virulence can also be recognized as “non-self” features or induce a “modified-self” state that can induce effector-triggered immunity (ETI). The Arabidopsis protein RIN4 plays an important role in both branches of plant immunity. Three unrelated type III secretion effector (TTSE) proteins from the phytopathogen Pseudomonas syringae, AvrRpm1, AvrRpt2, and AvrB, target RIN4, resulting in ETI that effectively restricts pathogen growth. However, no pathogenic advantage has been demonstrated for RIN4 manipulation by these TTSEs. Here, we show that the TTSE HopF2Pto also targets Arabidopsis RIN4. Transgenic plants conditionally expressing HopF2Pto were compromised for AvrRpt2-induced RIN4 modification and associated ETI. HopF2Pto interfered with AvrRpt2-induced RIN4 modification in vitro but not with AvrRpt2 activation, suggestive of RIN4 targeting by HopF2Pto. In support of this hypothesis, HopF2Pto interacted with RIN4 in vitro and in vivo. Unlike AvrRpm1, AvrRpt2, and AvrB, HopF2Pto did not induce ETI and instead promoted P. syringae growth in Arabidopsis. This virulence activity was not observed in plants genetically lacking RIN4. These data provide evidence that RIN4 is a major virulence target of HopF2Pto and that a pathogenic advantage can be conveyed by TTSEs that target RIN4.

scholarly journals Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruth Kristianingsih ◽  
Dan MacLean
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Plant Pathogens ◽  
De Novo ◽  
Chemical Properties ◽  
Effector Proteins ◽  
Global Food Security ◽  
Pathogen Effector ◽  
Biological Insight

Abstract Background Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de novo from sequence is difficult because of the heterogeneity of the sequences. We hypothesised that deep learning classifiers based on Convolutional Neural Networks would be able to identify effectors and deliver new insights. Results We created a training set of manually curated effector sequences from PHI-Base and used these to train a range of model architectures for classifying bacteria, fungal and oomycete sequences. The best performing classifiers had accuracies from 93 to 84%. The models were tested against popular effector detection software on our own test data and data provided with those models. We observed better performance from our models. Specifically our models showed greater accuracy and lower tendencies to call false positives on a secreted protein negative test set and a greater generalisability. We used GRAD-CAM activation map analysis to identify the sequences that activated our CNN-LSTM models and found short but distinct N-terminal regions in each taxon that was indicative of effector sequences. No motifs could be observed in these regions but an analysis of amino acid types indicated differing patterns of enrichment and depletion that varied between taxa. Conclusions Small training sets can be used effectively to train highly accurate and sensitive deep learning models without need for the operator to know anything other than sequence and without arbitrary decisions made about what sequence features or physico-chemical properties are important. Biological insight on subsequences important for classification can be achieved by examining the activations in the model

scholarly journals Accurate plant pathogen effector protein classification ab initio with deepredeff, an ensemble of convolutional neural networks

2020 ◽  
Author(s):  
Ruth Kristianingsih ◽  
Dan MacLean
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Plant Pathogens ◽  
De Novo ◽  
R Package ◽  
Effector Proteins ◽  
Global Food Security ◽  
Pathogen Effector ◽  
Detection Software ◽  
Map Analysis

Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de novo from sequence is difficult because of the heterogeneity of the sequences. We hypothesised that deep learning classifiers based on Convolutional Neural Networks would be able to identify effectors and deliver new insights. We built a training set of manually curated effector sequences from PHI-Base and used these to train a range of model architectures for classifying bacteria, fungal and oomycete sequences. The best performing classifiers had accuracies from 93 % to 84 %. The models were tested against popular effector detection software on our own test data and data provided with those models. We observed better performance from our models. Specifically our models showed greater accuracy and lower tendencies to call false positives on a secreted protein negative test set and a greater generalisability. We used GRAD-CAM activation map analysis to identify the sequences that activated our CNN-LSTM models and found short but distinct N-terminal regions in each taxon that was indicative of effector sequences. No motifs could be observed in these regions but an analysis of amino acid types indicated differing patterns of enrichment and depletion that varied between taxa. We have produced an R package that will allow others to make easy effector predictions using our models.

scholarly journals Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

2019 ◽  
Author(s):  
Marco E. Mechan Llontop ◽  
Parul Sharma ◽  
Marcela Aguilera Flores ◽  
Shu Yang ◽  
Jill Pollock ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Strain Level ◽  
Third Party ◽  
Metagenomic Sequencing ◽  
Microbial Identification ◽  
Xanthomonas Perforans ◽  
Field Samples ◽  
Group 2 ◽  
Level Identification

AbstractRoutine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technologies (ONT) MinION™ sequencer for metagenomic sequencing of tomato plants either artificially inoculated with a known strain of the bacterial speck pathogenPseudomonas syringaepv.tomato(Pto), or collected in the field and showing bacterial spot symptoms caused by either one of fourXanthomonasspecies. After species-level identification using ONT’s WIMP software and the third party tools Sourmash and MetaMaps, we used Sourmash and MetaMaps with a custom database of representative genomes of bacterial tomato pathogens to attempt strain-level identification. In parallel, each metagenome was assembled and the longest contigs were used as query with the genome-based microbial identification Web service LINbase. Both the read-based and assembly-based approaches correctly identifiedPtostrain T1 in the artificially inoculated samples. The pathogen strain in most field samples was identified as a member ofXanthomonas perforansgroup 2. This result was confirmed by whole genome sequencing of colonies isolated from one of the samples. Although in our case, metagenome-based pathogen identification at the strain-level was achieved, caution still needs to be exerted when interpreting strain-level results because of the challenges inherent to assigning reads to specific strains and the error rate of nanopore sequencing.

scholarly journals Identification and Functional Analysis of Type III Effector Proteins in Mesorhizobium loti

2010 ◽  
Vol 23 (2) ◽  
pp. 223-234 ◽  
Author(s):  
Shin Okazaki ◽  
Saori Okabe ◽  
Miku Higashi ◽  
Yoshikazu Shimoda ◽  
Shusei Sato ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Rhizobium Leguminosarum ◽  
Plant Pathogens ◽  
Effector Proteins ◽  
Sequence Motif ◽  
Shikimate Kinase ◽  
Model Legume ◽  
Type Iii Effector ◽  
Mesorhizobium Loti ◽  
Type Iii

Mesorhizobium loti MAFF303099, a microsymbiont of the model legume Lotus japonicus, possesses a cluster of genes (tts) that encode a type III secretion system (T3SS). In the presence of heterologous nodD from Rhizobium leguminosarum and a flavonoid naringenin, we observed elevated expression of the tts genes and secretion of several proteins into the culture medium. Inoculation experiments with wild-type and T3SS mutant strains revealed that the presence of the T3SS affected nodulation at a species level within the Lotus genus either positively (L. corniculatus subsp. frondosus and L. filicaulis) or negatively (L. halophilus and two other species). By inoculating L. halophilus with mutants of various type III effector candidate genes, we identified open reading frame mlr6361 as a major determinant of the nodulation restriction observed for L. halophilus. The predicted gene product of mlr6361 is a protein of 3,056 amino acids containing 15 repetitions of a sequence motif of 40 to 45 residues and a shikimate kinase-like domain at its carboxyl terminus. Homologues with similar repeat sequences are present in the hypersensitive-response and pathogenicity regions of several plant pathogens, including strains of Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas species. These results suggest that L. halophilus recognizes Mlr6361 as potentially pathogen derived and subsequently halts the infection process.

scholarly journals Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa Seeds

2020 ◽  
Vol 8 (8) ◽  
pp. 1137 ◽  
Author(s):  
Patricia MB Saint-Vincent ◽  
Mary Ridout ◽  
Nancy L. Engle ◽  
Travis J. Lawrence ◽  
Meredith L. Yeary ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Virulence Factors ◽  
Host Response ◽  
Plant Pathogens ◽  
Populus Trichocarpa ◽  
Bacterial Pathogen ◽  
Effector Proteins ◽  
Agricultural Crop ◽  
Pseudomonas Syringae Pathovars ◽  
Woody Host

Pseudomonas syringae is a ubiquitous plant pathogen, infecting both woody and herbaceous plants and resulting in devastating agricultural crop losses. Characterized by a remarkable specificity for plant hosts, P. syringae pathovars utilize a number of virulence factors including the type III secretion system and effector proteins to elicit disease in a particular host species. Here, two Pseudomonas syringae strains were isolated from diseased Populustrichocarpa seeds. The pathovars were capable of inhibiting poplar seed germination and were selective for the Populus genus. Sequencing of the newly described organisms revealed similarity to phylogroup II pathogens and genomic regions associated with woody host-associated plant pathogens, as well as genes for specific virulence factors. The host response to infection, as revealed through metabolomics, is the induction of the stress response through the accumulation of higher-order salicylates. Combined with necrosis on leaf surfaces, the plant appears to quickly respond by isolating infected tissues and mounting an anti-inflammatory defense. This study improves our understanding of the initial host response to epiphytic pathogens in Populus and provides a new model system for studying the effects of a bacterial pathogen on a woody host plant in which both organisms are fully genetically sequenced.

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