Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins

Pombo, Marina A.; Zheng, Yi; Fernández-Pozo, Noé; Dunham, Diane; Fei, Zhangjun; Martin, Gregory B.

doi:10.1186/preaccept-1479195265134573

Cited by 21 publications

(35 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fni3) and UBC13-2 were shown previously to catalyze exclusively the unconventional, Lys-63-linked ubiquitination and to be required for immunityassociated PCD induced by Fen and several other ETI elicitors (Mural et al, 2013). More recently, two gene expression profiling studies of tomato immunity against Pst using high-throughput RNA sequencing identified multiple Flagellin-induced repressed by effectors genes and genes induced specifically during ETI, among which UBC12, UBC13, UBC13-2, UBC25, and UBC28 were found to be induced significantly during ETI, and UBC25 also was induced significantly in PTI (Rosli et al, 2013;Pombo et al, 2014). These findings not only corroborate the discovery that tomato UBC13 (Fni3) and UBC13-2 play an important role in ETI (Mural et al, 2013) but also suggest that tomato E2s other than the group III members, such as UBC25, also may play an important role in plant immunity.…”

Section: Discussionmentioning

confidence: 99%

“…The identification of UBC11, UBC12, UBC13, UBC13-2, UBC25, UBC28, UBC29, UBC39, and UBC40 in either PTI and/or ETI in this and previous studies warrants further investigation of them in plant immunity (Mural et al, 2013;Rosli et al, 2013;Pombo et al, 2014). Since the connections of these E2s with E3 ligases in plant immunity have not been established, screening for and characterization of E3 ligases that work with these E2s in PTI and/or ETI and subsequently pinpointing and characterizing the substrates they modify should be the next experiments in elucidating the roles of E2s in the plant immune system.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

et al. 2016

View full text Add to dashboard Cite

Of the three classes of enzymes involved in ubiquitination, ubiquitin-conjugating enzymes (E2) have been often incorrectly considered to play merely an auxiliary role in the process, and few E2 enzymes have been investigated in plants. To reveal the role of E2 in plant innate immunity, we identified and cloned 40 tomato genes encoding ubiquitin E2 proteins. Thioester assays indicated that the majority of the genes encode enzymatically active E2. Phylogenetic analysis classified the 40 tomato E2 enzymes into 13 groups, of which members of group III were found to interact and act specifically with AvrPtoB, a Pseudomonas syringae pv tomato effector that uses its ubiquitin ligase (E3) activity to suppress host immunity. Knocking down the expression of group III E2 genes in Nicotiana benthamiana diminished the AvrPtoB-promoted degradation of the Fen kinase and the AvrPtoB suppression of host immunity-associated programmed cell death. Importantly, silencing group III E2 genes also resulted in reduced pattern-triggered immunity (PTI). By contrast, programmed cell death induced by several effector-triggered immunity elicitors was not affected on group III-silenced plants. Functional characterization suggested redundancy among group III members for their role in the suppression of plant immunity by AvrPtoB and in PTI and identified UBIQUITIN-CONJUGATING11 (UBC11), UBC28, UBC29, UBC39, and UBC40 as playing a more significant role in PTI than other group III members. Our work builds a foundation for the further characterization of E2s in plant immunity and reveals that AvrPtoB has evolved a strategy for suppressing host immunity that is difficult for the plant to thwart.Ubiquitination as a major posttranslational modification of proteins in eukaryotes has emerged in recent years as an important regulatory mechanism underlying plant innate immunity Fu et al., 2012;Marino et al., 2012;Li et al., 2014). The ubiquitination process involves a consecutive, threestep enzymatic cascade that is catalyzed by three different classes of enzymes: ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. The first step of the process activates ubiquitin, a highly conserved 76-amino acid protein, in an ATP-dependent manner by attaching ubiquitin to an E1 enzyme. The activated ubiquitin is then transferred from the E1 to the Cys residue at the active site of an E2 conjugating enzyme. An E3 ligase then recruits the substrate protein to the E2 to transfer the ubiquitin molecule from E2 to the substrate. Through the action of E1, E2, and E3, ubiquitin is covalently attached usually to the Lys residue of a substrate through an isopeptide bond (Hershko and Ciechanover, 1998). Of the three enzymes involved in ubiquitination, E3 ubiquitin ligases have been the focus of many studies due to their key role in determining substrate specificity for the ubiquitination

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

et al. 2016

View full text Add to dashboard Cite

show abstract

“…A VIGS forward screen in N. benthamiana for PTI genes revealed surprisingly few essential genes and no silver‐bullet candidates for the PTI‐protected state (Chakravarthy et al ., ). However, RNA‐seq transcription profiling aimed at distinguishing PTI and ETI responses of tomato to DC3000 derivatives revealed enrichment for genes associated with the phenylpropanoid pathway in the PTI‐specific set (Pombo et al ., ). Phenylpropanoid pathway genes were similarly found in a transcriptome study of PTI genes in tobacco (Szatmari et al ., ), and the N. benthamiana VIGS screen identified the CA4H gene which plays a role in phenylpropanoid biosynthesis (Chakravarthy et al ., ).…”

Section: Defence Subversion and Other Processes Promoting Pathogenesimentioning

confidence: 97%

Defining essential processes in plant pathogenesis with Pseudomonas syringae pv. tomato DC3000 disarmed polymutants and a subset of key type III effectors

Wei

Collmer

2018

Molecular Plant Pathology

View full text Add to dashboard Cite

Pseudomonas syringae pv. tomato DC3000 and its derivatives cause disease in tomato, Arabidopsis and Nicotiana benthamiana. The primary virulence factors include a repertoire of 29 effector proteins injected into plant cells by the type III secretion system and the phytotoxin coronatine. The complete repertoire of effector genes and key coronatine biosynthesis genes have been progressively deleted and minimally reassembled to reconstitute basic pathogenic ability in N. benthamiana, and in Arabidopsis plants that have mutations in target genes that mimic effector actions. This approach and molecular studies of effector activities and plant immune system targets have highlighted a small subset of effectors that contribute to essential processes in pathogenesis. Most notably, HopM1 and AvrE1 redundantly promote an aqueous apoplastic environment, and AvrPtoB and AvrPto redundantly block early immune responses, two conditions that are sufficient for substantial bacterial growth in planta. In addition, disarmed DC3000 polymutants have been used to identify the individual effectors responsible for specific activities of the complete repertoire and to more effectively study effector domains, effector interplay and effector actions on host targets. Such work has revealed that AvrPtoB suppresses cell death elicitation in N. benthamiana that is triggered by another effector in the DC3000 repertoire, highlighting an important aspect of effector interplay in native repertoires. Disarmed DC3000 polymutants support the natural delivery of test effectors and infection readouts that more accurately reveal effector functions in key pathogenesis processes, and enable the identification of effectors with similar activities from a broad range of other pathogens that also defeat plants with cytoplasmic effectors.

show abstract

“…NormFinder uses a model‐based approach allowing intra‐ and inter‐group comparisons of the obtained Ct values, and it provides a ranking of the candidate reference genes based on the estimated standard deviations. Recent studies have proposed different reference genes for expression studies during tomato ( Solanum lycopersicum ) development (Expósito‐Rodríguez, Borges, Borges‐Pérez, & Pérez, ) and tomato–pathogen interactions (Fradin et al., ; Müller et al., ; Pombo et al., ). Primer pairs for ten of these genes—four classical housekeeping genes, such as elongation factor EF1‐ α and ATPase (Expósito‐Rodríguez et al., ; Pombo et al., ), and six newly suggested ones (Müller et al., ; Pombo et al., )—were selected and evaluated in tomato–grey mould interaction.…”

Section: Introductionmentioning

confidence: 99%

“…tomato interaction. The pathogen–leaf infiltrations were performed on whole plants from which leaf samples were harvested at 3, 6, 9 and 12 hrs postinoculation (hpi) (Pombo et al., ). Primers amplifying importin β (primer set IMP‐β), PHD finger family protein (PHD), cytochrome c oxidase subunit (COX), polyribonucleotide 5′‐hydroxyl‐kinase (CLP1) and U6 snRNA‐associated Sm‐like protein LSm7 (LSM7) were used in a tomato (cv.…”

Section: Introductionmentioning

confidence: 99%

Expression of tomato reference genes using established primer sets: Stability across experimental set‐ups

Rezzonico

Nicot²,

Fahrentrapp

2017

Journal of Phytopathology

View full text Add to dashboard Cite

Reliable reference genes are critical for relative quantification using quantitative real‐time PCR (qPCR). Ten tomato genes (Solanum lycopersicum) and their respective primer sets, which have been used over the last 6 years as references in expression studies, were evaluated for their performance using leaf tissue samples grown under semi‐controlled conditions and infected with grey mould (Botrytis cinerea) or late blight (Phytophthora infestans). The target genes coding for U6 snRNA‐associated Sm‐like protein LSm7, calcineurin B‐like protein and V‐type proton ATPase were the most stable expressed of all the genes tested in three experimental repetitions. Evaluation of candidate reference genes with geNorm and NormFinder softwares yielded the lowest mean values for their respective primer sets LSM7, SlCBL1 and SlATPase, suggesting stable expression. However, SlATPase primer set revealed a comparably high intra‐group variation and was thus not considered further. In follow‐up experiments with P. infestans, the geNorm and NormFinder values of primer sets LSM7 and SlCBL1 were even lower, indicating the stability of their expression also under these conditions. Primer efficiency differed by ‐18 to +5 percentage points from values presented in the literature. Our findings show that a reference primer set which delivers the best results in one system may be outperformed by another under different experimental conditions, thus recommending a reassessment of both expression stability and qPCR efficiency whenever the biological or technical experimental set‐up is changed. On the basis of our results, we recommend the use of LSM7 and SlCBL1 as reference primer sets for gene expression studies on plant tissue derived from open or semi‐controlled conditions.

show abstract

Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins

Cited by 21 publications

References 58 publications

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

Defining essential processes in plant pathogenesis with Pseudomonas syringae pv. tomato DC3000 disarmed polymutants and a subset of key type III effectors

Expression of tomato reference genes using established primer sets: Stability across experimental set‐ups

Contact Info

Product

Resources

About