Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge

AbstractPlants rely on (in)direct detection of bacterial pathogens through plasma membrane-localized and intracellular receptor proteins. Surface pattern-recognition receptors (PRRs) participate in the detection of microbe-associated molecular patterns (MAMPs) and are required for the activation of pattern-triggered immunity (PTI). Pathogenic bacteria, such as Pseudomonas syringae pv. tomato (Pst) deploys ~ 30 effector proteins into the plant cell that contribute to pathogenicity. Resistant plants are capable of detecting the presence or activity of effectors and mount another response termed effector-triggered immunity (ETI). In order to investigate the involvement of tomato’s long non-coding RNAs (lncRNAs) in the immune response against Pst, we used RNA-seq data to predict and characterize those that are transcriptionally active in leaves challenged with a large set of treatments. Our prediction strategy was validated by sequence comparison with tomato lncRNAs described in previous works and by an alternative approach (RT-qPCR). Early PTI (30 min), late PTI (6 h) and ETI (6 h) differentially expressed (DE) lncRNAs were identified and used to perform a co-expression analysis including neighboring (± 100 kb) DE protein-coding genes. Some of the described networks could represent key regulatory mechanisms of photosynthesis, PRR abundance at the cell surface and mitigation of oxidative stress, associated to tomato-Pst pathosystem.

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XopC and XopJ, Two Novel Type III Effector Proteinsfrom Xanthomonas campestris pv.vesicatoria

Journal of Bacteriology ◽

10.1128/jb.185.24.7092-7102.2003 ◽

2003 ◽

Vol 185 (24) ◽

pp. 7092-7102 ◽

Cited By ~ 65

Author(s):

Laurent Noël ◽

Frank Thieme ◽

Jana Gäbler ◽

Daniela Büttner ◽

Ulla Bonas

Keyword(s):

Pseudomonas Syringae ◽

Plant Cell ◽

Type Iii Secretion ◽

Xanthomonas Campestris ◽

Pathogenic Bacteria ◽

Effector Proteins ◽

Type Iii ◽

Genome Wide ◽

A Genome ◽

Xanthomonas Campestris Pv.Vesicatoria

ABSTRACT Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm.

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BAK1 Is Not a Target of the Pseudomonas syringae Effector AvrPto

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-04-10-0096 ◽

2011 ◽

Vol 24 (1) ◽

pp. 100-107 ◽

Cited By ~ 49

Author(s):

Tingting Xiang ◽

Na Zong ◽

Jie Zhang ◽

Jinfeng Chen ◽

Mingsheng Chen ◽

...

Keyword(s):

Cell Surface ◽

Immune Responses ◽

Pseudomonas Syringae ◽

Plant Cell ◽

Crucial Role ◽

Pathogenic Bacteria ◽

Effector Proteins ◽

Receptor Like Kinase ◽

Receptor Kinases ◽

New Evidence

Plant cell surface-localized receptor kinases such as FLS2, EFR, and CERK1 play a crucial role in detecting invading pathogenic bacteria. Upon stimulation by bacterium-derived ligands, FLS2 and EFR interact with BAK1, a receptor-like kinase, to activate immune responses. A number of Pseudomonas syringae effector proteins are known to block immune responses mediated by these receptors. Previous reports suggested that both FLS2 and BAK1 could be targeted by the P. syringae effector AvrPto to inhibit plant defenses. Here, we provide new evidence further supporting that FLS2 but not BAK1 is targeted by AvrPto in plants. The AvrPto-FLS2 interaction prevented the phosphorylation of BIK1, a downstream component of the FLS2 pathway.

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Identification of Novel Type III Secretion Effectors in Xanthomonas oryzae pv. oryzae

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-22-1-0096 ◽

2009 ◽

Vol 22 (1) ◽

pp. 96-106 ◽

Cited By ~ 71

Author(s):

Ayako Furutani ◽

Minako Takaoka ◽

Harumi Sanada ◽

Yukari Noguchi ◽

Takashi Oku ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Type Iii Secretion ◽

Pathogenic Bacteria ◽

Regulatory Protein ◽

Effector Proteins ◽

Xanthomonas Oryzae ◽

Dependent Manner ◽

Plant Pathogenic Bacteria ◽

Type Iii ◽

Genes Encoding

Many gram-negative bacteria secrete so-called effector proteins via a type III secretion (T3S) system. Through genome screening for genes encoding potential T3S effectors, 60 candidates were selected from rice pathogen Xanthomonas oryzae pv. oryzae MAFF311018 using these criteria: i) homologs of known T3S effectors in plant-pathogenic bacteria, ii) genes with expression regulated by hrp regulatory protein HrpX, or iii) proteins with N-terminal amino acid patterns associated with T3S substrates of Pseudomonas syringae. Of effector candidates tested with the Bordetella pertussis calmodulin-dependent adenylate cyclase reporter for translocation into plant cells, 16 proteins were translocated in a T3S system-dependent manner. Of these 16 proteins, nine were homologs of known effectors in other plant-pathogenic bacteria and seven were not. Most of the effectors were widely conserved in Xanthomonas spp.; however, some were specific to X. oryzae. Interestingly, all these effectors were expressed in an HrpX-dependent manner, suggesting coregulation of effectors and the T3S system. In X. campestris pv. vesicatoria, HpaB and HpaC (HpaP in X. oryzae pv. oryzae) have a central role in recruiting T3S substrates to the secretion apparatus. Secretion of all but one effector was reduced in both HpaB– and HpaP– mutant strains, indicating that HpaB and HpaP are widely involved in efficient secretion of the effectors.

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The small molecule Zaractin activates ZAR1-mediated immunity in Arabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2116570118 ◽

2021 ◽

Vol 118 (47) ◽

pp. e2116570118

Author(s):

Derek Seto ◽

Madiha Khan ◽

D. Patrick Bastedo ◽

Alexandre Martel ◽

Trinh Vo ◽

...

Keyword(s):

Immune System ◽

Pseudomonas Syringae ◽

Small Molecule ◽

Nucleotide Binding ◽

Infection Process ◽

Effector Proteins ◽

Cellular Proteins ◽

Leucine Rich Repeat ◽

Effector Triggered Immunity ◽

Immune Pathway

Pathogenic effector proteins use a variety of enzymatic activities to manipulate host cellular proteins and favor the infection process. However, these perturbations can be sensed by nucleotide-binding leucine-rich-repeat (NLR) proteins to activate effector-triggered immunity (ETI). Here we have identified a small molecule (Zaractin) that mimics the immune eliciting activity of the Pseudomonas syringae type III secreted effector (T3SE) HopF1r and show that both HopF1r and Zaractin activate the same NLR-mediated immune pathway in Arabidopsis. Our results demonstrate that the ETI-inducing action of pathogenic effectors can be harnessed to identify synthetic activators of the eukaryotic immune system.

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Identification and Functional Analysis of AopN, an Acidovorax Citrulli Effector that Induces Programmed Cell Death in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms21176050 ◽

2020 ◽

Vol 21 (17) ◽

pp. 6050 ◽

Cited By ~ 1

Author(s):

Xiaoxiao Zhang ◽

Mei Zhao ◽

Jie Jiang ◽

Linlin Yang ◽

Yuwen Yang ◽

...

Keyword(s):

Functional Analysis ◽

Cell Death ◽

Programmed Cell Death ◽

Pathogenic Bacteria ◽

Plant Immunity ◽

Effector Proteins ◽

Economic Losses ◽

Homologous Protein ◽

Acidovorax Citrulli ◽

Effector Triggered Immunity

Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, seriously affects watermelon and other cucurbit crops, resulting in significant economic losses. However, the pathogenicity mechanism of A. citrulli is not well understood. Plant pathogenic bacteria often suppress the plant immune response by secreting effector proteins. Thus, identifying A. citrulli effector proteins and determining their functions may improve our understanding of the underlying pathogenetic mechanisms. In this study, a novel effector, AopN, which is localized on the cell membrane of Nicotiana benthamiana, was identified. The functional analysis revealed that AopN significantly inhibited the flg22-induced reactive oxygen species burst. AopN induced a programmed cell death (PCD) response. Unlike its homologous protein, the ability of AopN to induce PCD was dependent on two motifs of unknown functions (including DUP4129 and Cpta_toxin), but was not dependent on LXXLL domain. More importantly, the virulence of the aopN mutant of A. citrulli in N. benthamiana significantly decreased, indicating that it was a core effector. Further analysis revealed that AopN interacted with watermelon ClHIPP and ClLTP, which responds to A. citrulli strain Aac5 infection at the transcription level. Collectively, these findings indicate that AopN suppresses plant immunity and activates the effector-triggered immunity pathway.

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Effects of galU Mutation on Pseudomonas syringae–Plant Interactions

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-23-9-1184 ◽

2010 ◽

Vol 23 (9) ◽

pp. 1184-1196 ◽

Cited By ~ 15

Author(s):

Wen-Ling Deng ◽

Yuan-Chun Lin ◽

Rong-Hwa Lin ◽

Chia-Fong Wei ◽

Yi-Chiao Huang ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Type Iii Secretion ◽

Pathogenic Bacteria ◽

Capsular Polysaccharides ◽

Uridine Diphosphate ◽

Plant Interactions ◽

In Planta ◽

Animal Pathogens ◽

Diphosphate Glucose ◽

Molecular Patterns

Bacterial galU coding for a uridine diphosphate-glucose pyrophosphorylase plays an important role in carbohydrates biosynthesis, including synthesis of lipopolysaccharides (LPS), membrane-derived oligosaccharides, and capsular polysaccharides. In this study, we characterized the galU mutant of Pseudomonas syringae pv. syringae 61 (Psy61), a necrotizing plant pathogen whose pathogenicity depends on a functional type III secretion system (T3SS), and showed that the Psy61 galU mutant had reduced biofilm formation ability, was nonmotile, and had an assembled T3SS structure but failed to elicit hypersensitive response in resistant plants and necrotic lesions in susceptible plants. Moreover, the defective LPS and other pathogen-associated molecular patterns (PAMPs) on the surface of the Psy61 galU mutant were capable of inducing PAMP-triggered immunity, which severely compromised the ability of the Psy61 galU mutant to survive in planta. Our results demonstrated that the complete LPS protected plant-pathogenic bacteria from host innate immunity, similar to what was found in animal pathogens, prior to the translocation of T3S effectors and bacterial multiplication.

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0904739107 ◽

2010 ◽

Vol 107 (5) ◽

pp. 2349-2354 ◽

Cited By ~ 92

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.

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The HopZ Family of Pseudomonas syringae Type III Effectors Require Myristoylation for Virulence and Avirulence Functions in Arabidopsis thaliana

Journal of Bacteriology ◽

10.1128/jb.01702-07 ◽

2008 ◽

Vol 190 (8) ◽

pp. 2880-2891 ◽

Cited By ~ 68

Author(s):

Jennifer D. Lewis ◽

Wasan Abada ◽

Wenbo Ma ◽

David S. Guttman ◽

Darrell Desveaux

Keyword(s):

Arabidopsis Thaliana ◽

Pseudomonas Syringae ◽

Hypersensitive Response ◽

Pathogenic Bacteria ◽

Functional Characterization ◽

Defense Responses ◽

Effector Proteins ◽

Type Iii Effectors ◽

Type Iii ◽

Virulence Protein

ABSTRACT Pseudomonas syringae utilizes the type III secretion system to translocate effector proteins into plant cells, where they can contribute to the pathogen's ability to infect and cause disease. Recognition of these effectors by resistance proteins induces defense responses that typically include a programmed cell death reaction called the hypersensitive response. The YopJ/HopZ family of type III effector proteins is a common family of effector proteins found in animal- and plant-pathogenic bacteria. The HopZ family in P. syringae includes HopZ1aPsyA2, HopZ1bPgyUnB647, HopZ1cPmaE54326, HopZ2Ppi895A and HopZ3PsyB728a. HopZ1a is predicted to be most similar to the ancestral hopZ allele and causes a hypersensitive response in multiple plant species, including Arabidopsis thaliana. Therefore, it has been proposed that host defense responses have driven the diversification of this effector family. In this study, we further characterized the hypersensitive response induced by HopZ1a and demonstrated that it is not dependent on known resistance genes. Further, we identified a novel virulence function for HopZ2 that requires the catalytic cysteine demonstrated to be required for protease activity. Sequence analysis of the HopZ family revealed the presence of a predicted myristoylation sequence in all members except HopZ3. We demonstrated that the myristoylation site is required for membrane localization of this effector family and contributes to the virulence and avirulence activities of HopZ2 and HopZ1a, respectively. This paper provides insight into the selective pressures driving virulence protein evolution by describing a detailed functional characterization of the diverse HopZ family of type III effectors with the model plant Arabidopsis.

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Molecular characterization of HEXOKINASE1 in plant innate immunity

Applied Biological Chemistry ◽

10.1186/s13765-020-00560-8 ◽

2020 ◽

Vol 63 (1) ◽

Author(s):

Wu Jing ◽

Shahab Uddin ◽

Rupak Chakraborty ◽

Duong Thu Van Anh ◽

Donah Mary Macoy ◽

...

Keyword(s):

Immune Responses ◽

Pseudomonas Syringae ◽

Glucose Sensor ◽

Plant Immunity ◽

Interacting Protein ◽

Bacterial Populations ◽

Effector Triggered Immunity ◽

Callose Formation ◽

Molecular Patterns

AbstractHexokinase1 (HXK1) is an Arabidopsis glucose sensor that has a variety of roles during plant growth and devlopment, including during germination, flowering, and senescence. HXK1 also acts as a positive regulator of plant immune responses. Previous research suggested that HXK1 might influence plant immune responses via responses to glucose. Plant immune responses are governed by two main pathways: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI involves the recognition of Pathogen-Associated Molecular Patterns (PAMPs) and leads to increased callose formation and accumulation of pathogenesis response (PR) proteins. ETI acts in response to effectors secreted by Gram-negative bacteria. During ETI, the membrane-localized protein RPM1-interacting protein 4 (RIN4) becomes phosphorylated in reponse to interactions with effectors and mediates the downstream response. In this study, the effects of glucose on plant immune responses against infection with Pseudomonas syringae pv. tomato DC3000 and other P. syringae strains were investigated in the presence and absence of HXK1. Infiltration of leaves with glucose prior to infection led to decreases in bacterial populations and reductions in disease symptoms in wild-type Arabidopsis plants, indicating that glucose plays a role in plant immunity. Both PTI and ETI responses were affected. However, these effects were not observed in a hxk1 mutant, indicating that the effects of glucose on plant immune responses were mediated by HXK1-related pathways.

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Receptors in the induction of the plant innate immunity

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-07-20-0173-cr ◽

2021 ◽

Author(s):

Tian-Ying Yu ◽

Meng-Kun Sun ◽

Li-Kun Liang

Keyword(s):

Immune Responses ◽

Innate Immune System ◽

Effector Proteins ◽

Innate Immune ◽

Leucine Rich Repeat ◽

Nucleotide Binding Domain ◽

Effector Triggered Immunity ◽

Growth Development ◽

Immune Pathway ◽

Molecular Patterns

Plants adjust amplitude and duration of immune responses via different strategies to maintain growth, development and resistance to pathogens. Pathogen-associated molecular patterns (PAMPs)-triggered immunity (PTI) and effector-triggered immunity (ETI) play vital roles. PRRs (pattern recognition receptors), comprising a large number of receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), recognize related ligands and trigger immunity. PTI is the first layer of the innate immune system, and it recognizes PAMPs at plasma membrane to prevent infection. However, pathogens exploit effector proteins to bypass or directly inhibit the PTI immune pathway. Consistently, plants have evolved intracellular nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to detect pathogenic effectors and trigger a hypersensitive response to activate ETI. PTI and ETI work together to protect plants from infection of virus and other pathogens. Diverse receptors and the corresponding ligands, especially several pairs of well-studied receptors and ligands in PTI immunity, are reviewed to illustrate the dynamic process of PTI response here.

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