Helper NLRs Nrc2 and Nrc3 act codependently with Prf/Pto and activate MAPK signaling to induce immunity in tomato

Plant intracellular immune receptors, primarily nucleotide-binding, leucine-rich repeat proteins (NLRs), detect pathogen effector proteins and activate NLR-triggered immunity (NTI). Recently, 'sensor' NLRs have been reported to function with 'helper' NLRs to activate immunity. We investigated the role of two helper NLRs, Nrc2 and Nrc3, on immunity in tomato to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) mediated by the sensor NLR Prf and the Pto kinase. An nrc2/nrc3 mutant no longer activated Prf/Pto-mediated NTI to Pst containing the effectors AvrPto and AvrPtoB. An nrc3 mutant showed intermediate susceptibility between wild-type plants and a Prf mutant, while an nrc2 mutant developed only mild disease. These observations indicate that Nrc2 and Nrc3 act additively in Prf-/Pto-mediated immunity. We examined at what point Nrc2 and Nrc3 act in the Prf/Pto-mediated immune response. In the nrc2/3 mutant, programmed cell death (PCD) normally induced by constitutively active variants of AvrPtoB, Pto, or Prf was abolished, but that induced by M3Kα or Mkk2 was not. PCD induced by a constitutively active Nrc3 was also abolished in a Nicotiana benthamiana line with reduced expression of Prf. MAPK activation triggered by expression of AvrPto in the wild-type tomato plants was completely abolished in the nrc2/3 mutant. These results indicate that Nrc2 and Nrc3 act with Prf/Pto and upstream of MAPK signaling. Nrc2 and Nrc3 were not required for PCD triggered by Ptr1, another sensor NLR-mediating Pst resistance, although these helper NLRs do appear to be involved in resistance to certain Pst race 1 strains.

Ptr1 and ZAR1 immune receptors confer overlapping and distinct bacterial pathogen effector specificities

Some nucleotide-binding and leucine-rich repeat receptors (NLRs) indirectly detect pathogen effectors by monitoring their host targets. In Arabidopsis thaliana, RIN4 is targeted by multiple sequence-unrelated effectors and activates immune responses mediated by RPM1 and RPS2. These effectors trigger cell death in Nicotiana benthamiana, but the corresponding NLRs have yet not been identified. To identify N. benthamiana NLRs (NbNLRs) that recognize Arabidopsis RIN4-targeting effectors, we conducted a rapid reverse genetic screen using an NbNLR VIGS library. We identified that the N. benthamiana homolog of Ptr1 (Pseudomonas tomato race 1) recognizes the Pseudomonas effectors AvrRpt2, AvrRpm1, and AvrB. We demonstrated that recognition of the Xanthomonas effector AvrBsT and the Pseudomonas effector HopZ5 is conferred independently by the N. benthamiana homolog of Ptr1 and ZAR1. Interestingly, the recognition of HopZ5 and AvrBsT is contributed unequally by Ptr1 and ZAR1 in N. benthamiana and Capsicum annuum. In addition, we showed that the RLCK XII family protein JIM2 is required for the NbZAR1-dependent recognition of AvrBsT and HopZ5. The recognition of sequence-unrelated effectors by NbPtr1 and NbZAR1 provides an additional example of convergently evolved effector recognition. Identification of key components involved in Ptr1 and ZAR1-mediated immunity could reveal unique mechanisms of expanded effector recognition.

Loss-of-function mutations in WRKY22 and WRKY25 impair stomatal-mediated immunity and PTI and ETI responses against Pseudomonas syringae pv. tomato

Plants defend themselves against pathogens using a two-layered immune system. The first response, pattern-triggered immunity (PTI), is activated upon recognition of microbe-associated molecular patterns (MAMPs). Virulent bacteria such as Pseudomonas syringae pv. tomato (Pst), deliver effector proteins into the plant cell to promote susceptibility. However, some plants possess resistance (R) proteins that recognize specific effectors leading to the activation of the second response, effector-triggered immunity (ETI). Resistant tomatoes such as Río Grande-PtoR recognize two Pst effectors (AvrPto and AvrPtoB) through the host Pto/Prf complex and activate ETI. We previously showed that the transcription factors (TF) WRKY22 and WRKY25 are positive regulators of plant immunity against bacterial and potentially non-bacterial pathogens in Nicotiana benthamiana. Here, the CRISPR-Cas9 technique was used to develop three knockout tomato lines for either one or both TFs. The single and double mutants were all compromised in Pto/Prf-mediated ETI and had a weaker PTI response. The stomata apertures in all of the mutant lines did not respond to darkness or challenge with Pst DC3000. The WRKY22 and WRKY25 proteins both localize in the nucleus, but we found no evidence of a physical interaction between them. The WRKY22 TF was found to be involved in the transcriptional regulation of WRKY25, supporting the idea that they are not functionally redundant. Together, our results indicate that both WRKY TFs play a role in modulating stomata and are positive regulators of plant immunity in tomato.

Tomato receptor-like cytoplasmic kinase Fir1 is involved in flagellin signaling and preinvasion immunity

Detection of bacterial flagellin by the tomato (Solanum lycopersicum) receptors Flagellin sensing 2 (Fls2) and Fls3 triggers activation of pattern-triggered immunity (PTI). We identified the tomato Fls2/Fls3-interacting receptor-like cytoplasmic kinase 1 (Fir1) protein that is involved in PTI triggered by flagellin perception. Fir1 localized to the plasma membrane and interacted with Fls2 and Fls3 in yeast (Saccharomyces cerevisiae) and in planta. CRISPR/Cas9-generated tomato fir1 mutants were impaired in several immune responses induced by the flagellin-derived peptides flg22 and flgII-28, including resistance to Pseudomonas syringae pv. tomato (Pst) DC3000, production of reactive oxygen species, and enhanced PATHOGENESIS-RELATED 1b (PR1b) gene expression, but not MAP kinase phosphorylation. Remarkably, fir1 mutants developed larger Pst DC3000 populations than wild-type plants, whereas no differences were observed in wild-type and fir1 mutant plants infected with the flagellin deficient Pst DC3000ΔfliC. fir1 mutants failed to close stomata when infected with Pst DC3000 and Pseudomonas fluorescens and were more susceptible to Pst DC3000 than wild-type plants when inoculated by dipping, but not by vacuum-infiltration, indicating involvement of Fir1 in preinvasion immunity. RNA-seq analysis detected fewer differentially expressed genes in fir1 mutants and altered expression of jasmonic acid (JA)-related genes. In support of JA response deregulation in fir1 mutants, these plants were similarly susceptible to Pst DC3000 and to the coronatine-deficient Pst DC3118 strain, and more resistant to the necrotrophic fungus Botrytis cinerea following PTI activation. These results indicate that tomato Fir1 is required for a subset of flagellin-triggered PTI responses and support a model in which Fir1 negatively regulates JA signaling during PTI activation.

Tomato receptor-like cytoplasmic kinase Fir1 interacts with a negative regulator of jasmonic acid signaling

Plant cells detect potential pathogens through plasma membrane-localized pattern recognition receptors (PRRs) that recognize microbe-associated molecular patterns (MAMPs) and activate pattern-triggered immunity (PTI). PRR-mediated MAMP perception is linked to PTI signaling by receptor-like cytoplasmic kinases (RLCKs). In tomato, Flagellin-sensing 2 (Fls2)/Fls3 interacting RLCK 1 (Fir1) is involved in PTI triggered by flagellin perception. Fir1 is necessary for regulation of jasmonic acid (JA) signaling and is involved in pre-invasion immunity. We show that Fir1 physically interacts with JASMONATE-ZIM-DOMAIN PROTEIN 3 (JAZ3), a negative regulator of JA signaling. This finding suggests that Fir1 modulates JA signaling by regulating JAZ3.

Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae

Basic helix-loop-helix (bHLH) transcription factors constitute a superfamily in eukaryotes, but their roles in plant immunity remain largely uncharacterized. We found that the transcript abundance in tomato (Solanum lycopersicum) leaves of one bHLH transcription factor-encoding gene, negative regulator of resistance to DC3000 1 (Nrd1), increased significantly after treatment with the immunity-inducing flgII-28 peptide. Plants carrying a loss-of-function mutation in Nrd1 (Δnrd1) showed enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 although early pattern-triggered immunity responses, such as generation of reactive oxygen species and activation of mitogen-activated protein kinases after treatment with flagellin-derived flg22 and flgII-28 peptides, were unaltered compared to wild-type plants. RNA-sequencing (RNA-seq) analysis identified a gene, Arabinogalactan protein 1 (Agp1), whose expression is strongly suppressed in an Nrd1-dependent manner. Agp1 encodes an arabinogalactan protein, and overexpression of the Agp1 gene in Nicotiana benthamiana led to ∼10-fold less Pst growth compared to the control. These results suggest that the Nrd1 protein promotes tomato susceptibility to Pst by suppressing the defense gene Agp1. RNA-seq also revealed that the loss of Nrd1 function has no effect on the transcript abundance of immunity-associated genes, including AvrPtoB tomato-interacting 9 (Bti9), Cold-shock protein receptor (Core), Flagellin sensing 2 (Fls2), Flagellin sensing (Fls3), and Wall-associated kinase 1 (Wak1) upon Pst inoculation, suggesting that the enhanced immunity observed in the Δnrd1 mutants is due to the activation of key PRR signaling components as well as the loss of Nrd1-regulated suppression of Agp1.

The Emerging Role of PP2C Phosphatases in Tomato Immunity

The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants. [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.

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.

Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants

Prime editing is an adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase fusion and a guide RNA amended with template and primer binding site sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of prime editing in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for prime editing in dicots as well as monocots, their validation in Nicotiana benthamiana, rice, and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.

WRKY22 and WRKY25 transcription factors are positive regulators of defense responses in Nicotiana benthamiana

KEY MESSAGE

NbWRKY22 and NbWRKY25 are required for full activation of bacteria-associated pattern- and effector-triggered immunity as well as for the response to other non-bacterial defense elicitors. Plants defend themselves against pathogens using a two-layered immune system. Pattern-triggered immunity (PTI) can be activated upon recognition of epitopes from flagellin including flg22. Pseudomonas syringae pv. tomato (Pst) delivers effector proteins into the plant cell to promote host susceptibility. However, some plants express resistance (R) proteins that recognize specific effectors leading to the activation of effector-triggered immunity (ETI). Resistant tomato lines such as Rio Grande-PtoR (RG-PtoR) recognize two Pst effectors, AvrPto and AvrPtoB, and activate ETI through the Pto/Prf protein complex. Using RNA-seq, we identified two tomato WRKY transcription factor genes, SlWRKY22 and SlWRKY25, whose expression is increased during Pst-induced ETI. Silencing of the WRKY25/22 orthologous genes in Nicotiana benthamiana led to a delay in programmed cell death normally associated with AvrPto recognition or several non-bacterial effector/R protein pairs. An increase in disease symptoms was observed in silenced plants infiltrated with Pseudomonas syringae pv. tabaci expressing AvrPto or HopQ1-1. Expression of both tomato WRKY genes is also induced upon treatment with flg22 and callose deposition and cell death suppression assays in WRKY25/22-silenced N. benthamiana plants supported their involvement in PTI. Our results reveal an important role for two WRKYs as positive regulators of plant immunity against bacterial and potentially non-bacterial pathogens.

Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato

Plants have evolved a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI and ETI are functionally linked, but also have distinct characteristics. Unraveling how these immune systems coordinate plant responses against pathogens is crucial for understanding the regulatory mechanisms underlying plant defense. Here we report integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem with different Pst mutants that allow the dissection of PTI and ETI. A total of 225 proteins and 79 phosphopeptides differentially accumulated in tomato leaves during Pst infection. The abundances of many proteins and phosphoproteins changed during PTI or ETI, and some responses were triggered by both PTI and ETI. For most proteins, the ETI response was more robust than the PTI response. The patterns of protein abundance and phosphorylation changes revealed key regulators involved in Ca²⁺ signaling, mitogen-activated protein kinase cascades, reversible protein phosphorylation, reactive oxygen species (ROS) and redox homeostasis, transcription and protein turnover, transport and trafficking, cell wall remodeling, hormone biosynthesis and signaling, suggesting their common or specific roles in PTI and/or ETI. A NAC (NAM, ATAF, and CUC family) domain protein and lipid particle serine esterase, two PTI-specific genes identified from previous transcriptomic work, were not detected as differentially regulated at the protein level and were not induced by PTI. Based on integrative transcriptomics and proteomics data, as well as qRT-PCR analysis, several potential PTI and ETI-specific markers are proposed. These results provide insights into the regulatory mechanisms underlying PTI and ETI in the tomato-Pst pathosystem, and will promote future validation and application of the disease biomarkers in plant defense.

Ovulation and ovulation rate in ewes under grazing conditions: factors affecting the response to short-term supplementation

The relationships between ovulation rate and nutrition remain confused, probably because of uncontrolled variation in experimental conditions. To help resolve the problem, we analyzed data from 20 experiments conducted between 2002 and 2016, in Uruguay with grazing ewes. All experiments were carried out by a single laboratory under comparable conditions of experimental design and measured variables. The studies used a total of 3 720 ewes, of purebred Corriedale, Polwarth, or East Friesian x Polwarth genotypes. In all experiments, a control group grazed native pastures and extra nutrition was provided to the treatment groups using either improved pastures or supplements. Ovulation rate was measured by counting corpora lutea using laparoscopy or rectal ultrasound or by counting foetuses at ultrasound on day 45 of gestation. For statistical analysis, data were grouped according to nutritional treatment (control or supplemented) and, within these groups, type of supplement to provide energy or protein (protected or not from rumen degradation). Across all experiments, 92-99% of the ewes ovulated and the effects of diet, length of supplementation, and initial live weight and genotype are reported. Within diets, ovulation was most affected by overall energy intake during supplementation (P < 0.01). Ewes that grazed native pastures supplemented with protein supplements had higher ovulation rates (P < 0.05) than control ewes grazing only native pastures. The addition of tannins to the protein supplement, to protect it from degradation in the rumen, did not further increase the ovulation rate. In unsupplemented ewes that had access to legume pastures, ovulation rates did not increase when the legume pasture was rich in tannins although only ewes that grazed tanniniferous legumes had marginally higher ovulation rates than the control ewes (P < 0.05). When ewes grazing native pastures were supplemented with energy, their ovulation rate did not increase above those of nonsupplemented ewes. Live weight at the start of supplementation also affected ovulation rate. We conclude that ovulation was most affected by overall energy intake, whereas the factors that affected ovulation rate during short-tern nutritional supplementation were intake of protein from highly digested supplements or dietary protein protected from ruminal degradation.

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.

Arcuate nucleus kisspeptin response to increased nutrition in rams

Rams respond to acute nutritional supplementation by increasing the frequency of gonadotrophin-releasing hormone (GnRH) pulses. Kisspeptin neurons may mediate the effect of environmental cues on GnRH secretion, so we tested whether the ram response to nutrition involves activation of kisspeptin neurons in the arcuate nucleus (ARC), namely kisspeptin, neurokin B, dynorphin (KNDy) neurons. Rams were given extra lupin grain with their normal ration. Blood was sampled before feeding, and continued until animals were killed for collection of brain tissue at 2 or 11h after supplementation. In supplemented rams, LH pulse frequency increased after feeding, whereas control animals showed no change. Within the caudal ARC, there were more kisspeptin neurons in supplemented rams than in controls and a higher proportion of kisspeptin cells coexpressed Fos, regardless of the time the rams were killed. There were more Fos cells in the mid-ARC and mid-dorsomedial hypothalamus of the supplemented compared with control rams. No effect of nutrition was found on kisspeptin expression in the rostral or mid-ARC, or on GnRH expression in the preoptic area. Kisspeptin neurons in the caudal ARC appear to mediate the increase in GnRH and LH production due to acute nutritional supplementation, supporting the hypothesised role of the KNDy neurons as the pulse generator for GnRH.

Tomato Wall-Associated Kinase SlWak1 Depends on Fls2/Fls3 to Promote Apoplastic Immune Responses to Pseudomonas syringae

Wall-associated kinases (Waks) are important components of plant immunity against various pathogens, including the bacterium Pseudomonas syringae pv. tomato (Pst). However, the molecular mechanisms of their role(s) in plant immunity are largely unknown. In tomato (Solanum lycopersicum), wall-associated kinase 1 (SlWak1), has been implicated in pattern recognition receptor (PRR)-triggered immunity (PTI) because its transcript abundance increases significantly after treatment with the flagellin-derived, microbe-associated molecular patterns flg22 and flgII-28, which activate the PRRs Fls2 and Fls3, respectively. We generated two SlWak1 tomato mutants (Δwak1) using CRISPR/Cas9 gene editing technology and investigated the role of SlWak1 in tomato-Pst interactions. Late PTI responses activated in the apoplast by flg22 or flgII-28 were compromised in Δwak1 plants, but PTI at the leaf surface was unaffected. The Δwak1 plants developed fewer callose deposits than wild-type plants, but retained early PTI responses such as generation of reactive oxygen species and activation of mitogen-activated protein kinases upon exposure to flg22 and flgII-28. Induction of Wak1 gene expression by flg22 and flgII-28 was greatly reduced in a tomato mutant lacking Fls2 and Fls3, but induction of Fls3 gene expression by flgII-28 was unaffected in Δwak1 plants. After Pst inoculation, Δwak1 plants developed disease symptoms more slowly than Δfls2.1/2.2/3 mutant plants, although ultimately, both plants were similarly susceptible. SlWak1 coimmunoprecipitated with both Fls2 and Fls3, independently of flg22/flgII-28 or of BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE1. These observations suggest that SlWak1 acts in a complex with Fls2/Fls3 and is important at later stages of PTI in the apoplast.

Molecular Characterization of Differences between the Tomato Immune Receptors Flagellin Sensing 3 and Flagellin Sensing 2

Plants mount defense responses by recognizing indicators of pathogen invasion, including microbe-associated molecular patterns (MAMPs). Flagellin, from the bacterial pathogen Pseudomonas syringae pv. tomato (Pst), contains two MAMPs, flg22 and flgII-28, that are recognized by tomato (Solanum lycopersicum) receptors Flagellin sensing2 (Fls2) and Fls3, respectively, but to what degree each receptor contributes to immunity and whether they promote immune responses using the same molecular mechanisms are unknown. Here, we characterized CRISPR/Cas9-generated Fls2 and Fls3 tomato mutants and found that the two receptors contribute equally to disease resistance both on the leaf surface and in the apoplast. However, we observed striking differences in certain host responses mediated by the two receptors. Compared to Fls2, Fls3 mediated a more sustained production of reactive oxygen species and an increase in transcript abundance of 44 tomato genes, with two genes serving as specific reporters for the Fls3 pathway. Fls3 had greater in vitro kinase activity than Fls2 and could transphosphorylate a substrate. Using chimeric Fls2/Fls3 proteins, we found no evidence that a single receptor domain is responsible for the Fls3-sustained reactive oxygen species, suggesting involvement of multiple structural features or a nullified function of the chimeric construct. This work reveals differences in certain immunity outputs between Fls2 and Fls3, suggesting that they might use distinct molecular mechanisms to activate pattern-triggered immunity in response to flagellin-derived MAMPs.

Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species

The Ptr1 (Pseudomonas tomato race 1) locus in Solanum lycopersicoides confers resistance to strains of Pseudomonas syringae pv. tomato expressing AvrRpt2 and Ralstonia pseudosolanacearum expressing RipBN. Here we describe the identification and phylogenetic analysis of the Ptr1 gene. A single recombinant among 585 F2 plants segregating for the Ptr1 locus was discovered that narrowed the Ptr1 candidates to eight nucleotide-binding leucine-rich repeat protein (NLR)-encoding genes. From analysis of the gene models in the S. lycopersicoides genome sequence and RNA-Seq data, two of the eight genes emerged as the strongest candidates for Ptr1. One of these two candidates was found to encode Ptr1 based on its ability to mediate recognition of AvrRpt2 and RipBN when it was transiently expressed with these effectors in leaves of Nicotiana glutinosa. The ortholog of Ptr1 in tomato and in Solanum pennellii is a pseudogene. However, a functional Ptr1 ortholog exists in Nicotiana benthamiana and potato, and both mediate recognition of AvrRpt2 and RipBN. In apple and Arabidopsis, recognition of AvrRpt2 is mediated by the Mr5 and RPS2 proteins, respectively. Phylogenetic analysis places Ptr1 in a distinct clade compared with Mr5 and RPS2, and it therefore appears to have arisen by convergent evolution for recognition of AvrRpt2.

Generation and Molecular Characterization of CRISPR/Cas9-Induced Mutations in 63 Immunity-Associated Genes in Tomato Reveals Specificity and a Range of Gene Modifications

The CRISPR/Cas9 system is a powerful tool for targeted gene editing in many organisms including plants. However, most of the reported uses of CRISPR/Cas9 in plants have focused on modifying one or a few genes, and thus the overall specificity, types of mutations, and heritability of gene alterations remain unclear. Here, we describe the molecular characterization of 361 T0 transgenic tomato plants that were generated using CRISPR/Cas9 to induce mutations in 63 immunity-associated genes. Among the T0 transformed plants, 245 carried mutations (68%), with 20% of those plants being homozygous for the mutation, 30% being heterozygous, 32% having two different mutations (biallelic), and 18% having multiple mutations (chimeric). The mutations were predominantly short insertions or deletions, with 87% of the affected sequences being smaller than 10 bp. The majority of 1 bp insertions were A (50%) or T (29%). The mutations from the T0 generation were stably transmitted to later generations, although new mutations were detected in some T1 plants. No mutations were detected in 18 potential off-target sites among 144 plants. Our study provides a broad and detailed view into the effectiveness of CRISPR/Cas9 for genome editing in an economically important plant species.

Volatiles from Merino fleece evoke antennal and behavioural responses in the Australian sheep blow fly Lucilia cuprina

To identify flystrike-related volatile compounds in wool from Merino sheep, the attractiveness of wool to Lucilia cuprina Wiedmann (Diptera: Calliphoridae) was examined. First, a selection of wool samples guided by previous knowledge of sheep lines, predicted to be more susceptible or more resistant to flystrike, was tested. The attractiveness of the 10 samples selected was not associated with field susceptibility: two samples from the more resistant line were identified as most attractive and two samples from the more susceptible line were identified as least attractive, based on the behavioural assays with gravid flies. Comparison of the headspace volatiles of these samples, using solid phase microextraction and gas chromatography-mass spectrometry-electroantennographic detection, revealed octanal and nonanal to be present in the attractive wool samples that elicited responses from the fly antenna. Furthermore, the two compounds were not present in wool that was least attractive to L. cuprina. In laboratory bioassays, octanal and nonanal evoked antennal and behavioural responses in gravid L. cuprina, thus confirming their potential role as semiochemicals responsible for attracting L. cuprina to Merino sheep.

Mai1 Protein Acts Between Host Recognition of Pathogen Effectors and Mitogen-Activated Protein Kinase Signaling

The molecular mechanisms acting between host recognition of pathogen effectors by nucleotide-binding leucine-rich repeat receptor (NLR) proteins and mitogen-activated protein kinase (MAPK) signaling cascades are unknown. MAPKKKα (M3Kα) activates MAPK signaling leading to programmed cell death (PCD) associated with NLR-triggered immunity. We identified a tomato M3Kα-interacting protein, SlMai1, that has 80% amino acid identity with Arabidopsis brassinosteroid kinase 1 (AtBsk1). SlMai1 has a protein kinase domain and a C-terminal tetratricopeptide repeat domain that interacts with the kinase domain of M3Kα. Virus-induced gene silencing of Mai1 homologs in Nicotiana benthamiana increased susceptibility to Pseudomonas syringae and compromised PCD induced by four NLR proteins. PCD was restored by expression of a synthetic SlMai1 gene that resists silencing. Expression of AtBsk1 did not restore PCD in Mai1-silenced plants, suggesting SlMai1 is functionally divergent from AtBsk1. PCD caused by overexpression of M3Kα or MKK2 was unaffected by Mai1 silencing, suggesting Mai1 acts upstream of these proteins. Coexpression of Mai1 with M3Kα in leaves enhanced MAPK phosphorylation and accelerated PCD. These findings suggest Mai1 is a molecular link acting between host recognition of pathogens and MAPK signaling.

The Ptr1 Locus of Solanum lycopersicoides Confers Resistance to Race 1 Strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by Recognizing the Type III Effectors AvrRpt2 and RipBN

Race 1 strains of Pseudomonas syringae pv. tomato, which cause bacterial speck disease of tomato, are becoming increasingly common and no simply inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 P. syringae pv. tomato strains by detecting the activity of type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein, thereby activating RPS2-mediated immunity. Using site-directed mutagenesis of AvrRpt2, we found that, like RPS2, activation of Ptr1 requires AvrRpt2 proteolytic activity. Ptr1 also detected the activity of AvrRpt2 homologs from diverse bacteria, including one in Ralstonia pseudosolanacearum. The genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.

Natural variation for unusual host responses and flagellin-mediated immunity against Pseudomonas syringae in genetically diverse tomato accessions

The interaction between tomato and Pseudomonas syringae pv tomato (Pst) is a well-developed model for investigating the molecular basis of the plant immune system. There is extensive natural variation in Solanum lycopersicum (tomato) but it has not been fully leveraged to enhance our understanding of the tomato-Pst pathosystem. We screened 216 genetically diverse accessions of cultivated tomato and a wild tomato species for natural variation in their response to three strains of Pst. The host response to Pst was investigated using multiple Pst strains, tomato accessions with available genome sequences, reactive oxygen species (ROS) assays, reporter genes and bacterial population measurements. The screen uncovered a broad range of previously unseen host symptoms in response to Pst, and one of these, stem galls, was found to be simply inherited. The screen also identified tomato accessions that showed enhanced responses to flagellin in bacterial population assays and in ROS assays upon exposure to flagellin-derived peptides, flg22 and flgII-28. Reporter genes confirmed that the host responses were due primarily to pattern recognition receptor-triggered immunity. This study revealed extensive natural variation in tomato for susceptibility and resistance to Pst and will enable elucidation of the molecular mechanisms underlying these host responses.

PP2C phosphatase Pic1 negatively regulates the phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato

Plant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRRs) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato, two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a PP2C protein phosphatase, referred to as Pic1. An in vitro pull-down assay and in vivo split-luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233, and this phosphorylation was abolished in the presence of Pic1. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to Pic1 phosphatase activity, although it still interacted with Pic1. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. The expression of Pic1, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that Pic1 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.

Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana

RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to find and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identification of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research field. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infiltrated with Pseudomonas fluorescens, we identified and tested a set of 9 candidate reference genes. Using three different algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the first two is sufficient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.

Virus-induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana

Virus-induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lacking. Such a database would allow researchers to know the phenotype associated with the silencing of a large number of individual genes without experimentation. We have developed a VIGS phenomics and functional genomics database (VPGD) that has DNA sequence information derived from over 4,000 N. benthamiana VIGS clones along with the associated silencing phenotype for approximately 1,300 genes. The VPGD has a built-in BLAST search feature that provides silencing phenotype information of specific genes. In addition, a keyword-based search function could be used to find a specific phenotype of interest with the corresponding gene, including its Gene Ontology descriptions. Query gene sequences from other plant species that have not been used for VIGS can also be searched for their homologs and silencing phenotype in N. benthamiana. VPGD is useful for identifying gene function not only in N. benthamiana but also in related Solanaceae plants such as tomato and potato. The database is accessible at http://vigs.noble.org.

The Bacterial Effector AvrPto Targets the Regulatory Coreceptor SOBIR1 and Suppresses Defense Signaling Mediated by the Receptor-Like Protein Cf-4

Receptor-like proteins (RLPs) and receptor-like kinases (RLKs) are cell-surface receptors that are essential for detecting invading pathogens and subsequent activation of plant defense responses. RLPs lack a cytoplasmic kinase domain to trigger downstream signaling leading to host resistance. The RLK SOBIR1 constitutively interacts with the tomato RLP Cf-4, thereby providing Cf-4 with a kinase domain. SOBIR1 is required for Cf-4-mediated resistance to strains of the fungal tomato pathogen Cladosporium fulvum that secrete the effector Avr4. Upon perception of this effector by the Cf-4/SOBIR1 complex, the central regulatory RLK SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3a (SERK3a) is recruited to the complex and defense signaling is triggered. SOBIR1 is also required for RLP-mediated resistance to bacterial, fungal ,and oomycete pathogens, and we hypothesized that SOBIR1 is targeted by effectors of such pathogens to suppress host defense responses. In this study, we show that Pseudomonas syringae pv. tomato DC3000 effector AvrPto interacts with Arabidopsis SOBIR1 and its orthologs of tomato and Nicotiana benthamiana, independent of SOBIR1 kinase activity. Interestingly, AvrPto suppresses Arabidopsis SOBIR1-induced cell death in N. benthamiana. Furthermore, AvrPto compromises Avr4-triggered cell death in Cf-4-transgenic N. benthamiana, without affecting Cf-4/SOBIR1/SERK3a complex formation. Our study shows that the RLP coreceptor SOBIR1 is targeted by a bacterial effector, which results in compromised defense responses.

Detecting the interaction of peptide ligands with plant membrane receptors

The field of plant receptor biology has rapidly expanded in recent years, however the demonstration of direct interaction between receptor-ligand pairs remains a challenge. Click chemistry has revolutionized small molecule research but lacks popularity in plant research. Here we describe a method that tests for the direct physical interaction of a candidate receptor protein and a peptide ligand. This protocol describes the generation of the ligand probe, transient expression of a receptor protein, enrichment of membrane-bound receptors, photo-crosslinking and click chemistry-mediated reporter addition, and detection of the receptor-ligand complex. Copper-based click chemistry confers several advantages, including the versatility to use almost any azide-containing reporter molecule for detection or visualization of the complex and addition of the reporter molecule after receptor-ligand binding which reduces the need for bulky ligand modifications that could interfere with the interaction.

The Tomato Kinase Pti1 Contributes to Production of Reactive Oxygen Species in Response to Two Flagellin-Derived Peptides and Promotes Resistance to Pseudomonas syringae Infection

The Pti1 kinase was identified from a reverse genetic screen as contributing to pattern-triggered immunity (PTI) against Pseudomonas syringae pv. tomato (Pst). The tomato genome has two Pti1 genes, referred to as Pti1a and Pti1b. A hairpin-Pti1 (hpPti1) construct was developed and was used to generate two independent stable transgenic tomato lines that had reduced transcript abundance of both genes. In response to P. syringae pv. tomato inoculation, these hpPti1 plants developed more severe disease symptoms, supported higher bacterial populations, and had reduced transcript accumulation of PTI-associated genes, as compared with wild-type plants. In response to two flagellin-derived peptides, the hpPti1 plants produced lesser amounts of reactive oxygen species (ROS) but showed no difference in mitogen-activated protein kinase (MAPK). Synthetic Pti1a and Pti1b genes designed to avoid silencing were transiently expressed in the hpPti1 plants and restored the ability of the plants to produce wild-type levels of ROS. Our results identify a new component of PTI in tomato that, because it affects ROS production but not MAPK signaling, appears to act early in the immune response.

Pseudomonas syringae pv. tomato Strains from New York Exhibit Virulence Attributes Intermediate Between Typical Race 0 and Race 1 Strains

Bacterial speck disease, caused by Pseudomonas syringae pv. tomato, is a persistent problem for fresh-market tomato growers in New York. Race 0 strains of this pathogen express either or both of the type III effectors AvrPto or AvrPtoB, which are recognized by tomato varieties expressing the Pto resistance gene. Pto encodes a protein kinase that activates the host immune system, thereby inhibiting bacterial multiplication and preventing disease development. Race 1 P. syringae pv. tomato strains do not express these effectors and are virulent on tomato whether or not the variety expresses Pto. Very few fresh-market tomato varieties have the Pto gene. We collected six P. syringae pv. tomato strains from naturally infected tomato plants across New York in 2015 and characterized them for their virulence and for the presence of specific effectors. In experiments conducted in the greenhouse, all strains reached population sizes in Pto-expressing tomato leaves that were intermediate between typical race 0 and race 1 strains. This phenotype has not been observed previously and suggests that the strains are recognized by Pto but such recognition is compromised by another P. syringae pv. tomato factor. The strains were found to encode avrPto, which is transcribed and translated. They also express avrPtoB although, as reported for other P. syringae pv. tomato strains, protein expression for this effector was not detectable. Deletion of avrPto from a representative New York strain allowed it to reach high populations in Pto-expressing tomato varieties, without compromising its virulence on susceptible tomato plants. Collectively, our data suggest that introgression of the Pto gene into fresh-market tomato varieties could enhance protection against extant P. syringae pv. tomato strains.

Generation of a Collection of Mutant Tomato Lines Using Pooled CRISPR Libraries

The high efficiency of clustered regularly interspaced short palindromic repeats (CRISPR)-mediated mutagenesis in plants enables the development of high-throughput mutagenesis strategies. By transforming pooled CRISPR libraries into tomato (Solanum lycopersicum), collections of mutant lines were generated with minimal transformation attempts and in a relatively short period of time. Identification of the targeted gene(s) was easily determined by sequencing the incorporated guide RNA(s) in the primary transgenic events. From a single transformation with a CRISPR library targeting the immunity-associated leucine-rich repeat subfamily XII genes, heritable mutations were recovered in 15 of the 54 genes targeted. To increase throughput, a second CRISPR library was made containing three guide RNAs per construct to target 18 putative transporter genes. This resulted in stable mutations in 15 of the 18 targeted genes, with some primary transgenic plants having as many as five mutated genes. Furthermore, the redundancy in this collection of plants allowed for the association of aberrant T0 phenotypes with the underlying targeted genes. Plants with mutations in a homolog of an Arabidopsis (Arabidopsis thaliana) boron efflux transporter displayed boron deficiency phenotypes. The strategy described here provides a technically simple yet high-throughput approach for generating a collection of lines with targeted mutations and should be applicable to any plant transformation system.

Ser360 and Ser364 in the Kinase Domain of Tomato SlMAPKKKα are Critical for Programmed Cell Death Associated with Plant Immunity

SlMAPKKKα, a tomato (Solanum lycopersicum) mitogen-activated protein kinase kinase kinase, is a positive regulator of Pto-mediated effector-triggered immunity, which elicits programmed cell death (PCD) in plants. In this study, we examined whether putative phosphorylation sites in the conserved activation segment of the SlMAPKKKα kinase domain are critical for eliciting PCD. Three amino acids, threonine³⁵³, serine³⁶⁰ (Ser³⁶⁰), or serine³⁶⁴ (Ser³⁶⁴), in the conserved activation segment of SlMAPKKKα kinase domain were substituted to alanine (T353A, S360A, or S364A), and these variants were transiently expressed in tomato and Nicotiana benthamiana plants. Two alanine substitutions, S360A and S364A, completely abolished SlMAPKKKα PCD-eliciting activity in both plants, while T353A substitution did not affect its PCD-eliciting activity. SlMAPKKKα wild type and variant proteins accumulated to similar levels in plant leaves. However, SlMAPKKKα protein with the largest size was missed when either S360A or S364A substitutions were expressed, whereas proteins with the smaller masses were more accumulated than those of full-length of SIMAPKKKα and T353A. These results suggest that phosphorylation of SlMAPKKKα at Ser³⁶⁰ and Ser³⁶⁴ is critical for PCD elicitation in plants.

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

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.

Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system

Plants and animals detect the presence of potential pathogens through the perception of conserved microbial patterns by cell surface receptors. Certain solanaceous plants, including tomato, potato and pepper, detect flgII-28, a region of bacterial flagellin that is distinct from that perceived by the well-characterized FLAGELLIN-SENSING 2 receptor. Here we identify and characterize the receptor responsible for this recognition in tomato, called FLAGELLIN-SENSING 3. This receptor binds flgII-28 and enhances immune responses leading to a reduction in bacterial colonization of leaf tissues. Further characterization of FLS3 and its signalling pathway could provide new insights into the plant immune system and transfer of the receptor to other crop plants offers the potential of enhancing resistance to bacterial pathogens that have evolved to evade FLS2-mediated immunity.

Natural Variation in Tomato Reveals Differences in the Recognition of AvrPto and AvrPtoB Effectors from Pseudomonas syringae

The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto and AvrPtoB-Pto complexes revealed that Pto binds each effector through both a shared and a unique interface. Here we use natural variation in wild species of tomato to further investigate Pto recognition of these two effectors. One species, Solanum chmielewskii, was found to have many accessions that recognize only AvrPtoB. The Pto ortholog from one of these accessions was responsible for recognition of AvrPtoB and it differed from Solanum pimpinellifolium Pto by only 14 amino acids, including two in the AvrPto-specific interface, glutamate-49/glycine-51. Converting these two residues to those in Pto (histidine-49/valine-51) did not restore recognition of AvrPto. Subsequent experiments revealed that a single substitution of a histidine-to-aspartate at position 193 in Pto, which is not near the AvrPto-specific interface, was sufficient for conferring recognition of AvrPto in plant cells. The reciprocal substitution of aspartate-to-histidine-193 in Pto abolished AvrPto recognition, confirming the importance of this residue. Our results reveal new aspects about effector recognition by Pto and demonstrate the value of using natural variation to understand the interaction between resistance proteins and pathogen effectors.

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

Targeted DNA mutations generated by vectors with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology have proven useful for functional genomics studies. While most cloning strategies are simple to perform, they generally use multiple steps and can require several days to generate the ultimate constructs. The method presented here is based on DNA assembly and can produce fully functional CRISPR vectors in a single cloning reaction. Vector construction can also be pooled, further increasing the efficiency and utility of the process. A modification of the method is used to create CRISPR vectors with multiple gene targets. CRISPR vectors are then transformed into tomato hairy roots to generate transgenic materials with targeted DNA modifications. Hairy roots are a useful system for testing vector functionality as they are technically simple to generate and amenable to large-scale production. The methods presented here will have wide application as they can be used to generate a variety of CRISPR vectors and be used in a wide range of plant species.

Monitoring stress in captive and free-ranging African wild dogs (Lycaon pictus) using faecal glucocorticoid metabolites

An understanding of stress physiology is important for species management because high levels of stress can hamper reproduction and affect an individual's ability to cope with threats to their survival, such as disease and human-wildlife conflict. A commonly used indicator of stress, faecal concentrations of cortisol metabolites (FCM), can be used to assess the impact of social, biological and environmental factors. Measurements of FCM are particularly valuable for endangered species that are logistically challenging to study and where non-invasive techniques are preferred. As the second most endangered canid in Africa, the African wild dog (Lycaon pictus) has been the focus of considerable conservation research, yet there is still little understanding of factors associated with stress, in either captive or free-ranging populations. The present study therefore aimed to determine whether stress levels differ between captive and free-ranging populations, and to detect social, biological and environmental factors that are stressful in these populations. Faecal samples were collected from 20 captive and 62 free-ranging animals. Within free-ranging populations, the sexes differed significantly, but there was no effect of social status, age or breeding period for either sex. Captive females had higher FCM concentrations than free-ranging females. In captive populations, FCM concentrations differed among zoos and with reproductive status in females, but were not related to age class or group-housing structure. In conclusion, FCM is a useful indicator of stress and should be considered an integrative aspect of management, for both in situ and ex situ African wild dog populations.

Detecting N-myristoylation and S-acylation of host and pathogen proteins in plants using click chemistry

BACKGROUND

The plant plasma membrane is a key battleground in the war between plants and their pathogens. Plants detect the presence of pathogens at the plasma membrane using sensor proteins, many of which are targeted to this lipophilic locale by way of fatty acid modifications. Pathogens secrete effector proteins into the plant cell to suppress the plant's defense mechanisms. These effectors are able to access and interfere with the surveillance machinery at the plant plasma membrane by hijacking the host's fatty acylation apparatus. Despite the important involvement of protein fatty acylation in both plant immunity and pathogen virulence mechanisms, relatively little is known about the role of this modification during plant-pathogen interactions. This dearth in our understanding is due largely to the lack of methods to monitor protein fatty acid modifications in the plant cell.

RESULTS

We describe a rapid method to detect two major forms of fatty acylation, N-myristoylation and S-acylation, of candidate proteins using alkyne fatty acid analogs coupled with click chemistry. We applied our approach to confirm and decisively demonstrate that the archetypal pattern recognition receptor FLS2, the well-characterized pathogen effector AvrPto, and one of the best-studied intracellular resistance proteins, Pto, all undergo plant-mediated fatty acylation. In addition to providing a means to readily determine fatty acylation, particularly myristoylation, of candidate proteins, this method is amenable to a variety of expression systems. We demonstrate this using both Arabidopsis protoplasts and stable transgenic Arabidopsis plants and we leverage Agrobacterium-mediated transient expression in Nicotiana benthamiana leaves as a means for high-throughput evaluation of candidate proteins.

CONCLUSIONS

Protein fatty acylation is a targeting tactic employed by both plants and their pathogens. The metabolic labeling approach leveraging alkyne fatty acid analogs and click chemistry described here has the potential to provide mechanistic details of the molecular tactics used at the host plasma membrane in the battle between plants and pathogens.

Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York

The complete genome sequence of an isolate of tomato mottle mosaic virus (ToMMV) infecting tomatoes in New York was obtained using small RNA (sRNA) deep sequencing. ToMMV_NY-13 shared 99% sequence identity with isolates from Mexico and Florida. Broader distribution of this emerging virus is a cause for concern to the tomato industry.

Identification of a Candidate Gene in Solanum habrochaites for Resistance to a Race 1 Strain of Pseudomonas syringae pv. tomato

Bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst) is a persistent problem on tomato (Solanum lycopersicum L.). Resistance against race 0 Pst strains is conferred by the Pto protein, which recognizes either of two pathogen effectors: AvrPto or AvrPtoB. However, current tomato varieties do not have resistance to the increasingly common race 1 strains, which lack these effectors. We identified accessions of Solanum habrochaites S. Knapp & D. M. Spooner that are resistant to the race 1 strain T1. Genome sequence comparisons of T1 and two Pst strains that are virulent on these accessions suggested that known microbe-associated molecular patterns (MAMPs) or effectors are not involved in the resistance. We developed an F₂ population from a cross between one T1-resistant accession, LA2109, and a susceptible tomato cultivar to investigate the genetic basis of this resistance. Linkage analysis using whole-genome sequence of 58 F₂ plants identified quantitative trait loci (QTL), qRph1, in a 5.8-Mb region on chromosome 2, and qRph2, in a 52.4-Mb region on chromosome 8, which account for 24 and 26% of the phenotypic variability, respectively. High-resolution mapping of qRph1 confirmed it contributed to T1 resistance and delimited it to a 1060-kb region containing 139 genes, including three encoding receptor-like proteins (RLPs) and 17 encoding receptor-like protein kinases (RLKs). One RLK gene, Solyc02g072470, is a promising candidate for qRph1, as it is highly expressed in LA2109 and induced on treatment with MAMPs. qRph1 might be useful for enhancing resistance to race 1 strains and its future characterization could provide insights into the plant immune system.

Twenty-four-hour profiles of metabolic and stress hormones in sheep selected for a calm or nervous temperament

Even in the absence of stressors, temperament is associated with changes in the concentration of stress-responsive hormones and, possibly because of such changes, temperament can affect metabolism. We tested whether, in sheep bred for temperament for 14 generations, "nervous" females have greater concentrations of stress-responsive hormones in the absence of stressors than "calm" females, and whether these differences are associated with changes in the concentrations of metabolic hormones. In resting "calm" (n = 8) and "nervous" (n = 8) sheep, concentrations of cortisol, prolactin, leptin, and insulin were measured in blood plasma sampled via jugular catheter every 20 min for 24 h. The animals were individually penned, habituated to their housing and human handling over 7 wk, and fed before sampling began. Diurnal variation was evident for all hormones, but a 24-h cortisol pattern was detected in only 7 individuals. There was no effect of temperament on any aspect of concentrations of cortisol or prolactin, but "calm" animals had greater concentrations of insulin in the early afternoon than "nervous" animals (14.5 ± 1.1 vs 10.0 ± 1.6 μU/mL; P = 0.038), and a similar tendency was seen for leptin (P = 0.092). We conclude that selection for temperament affects the concentration of metabolic hormones in the absence of stressors, but this effect is independent of stress-responsive hormones.

Five Xanthomonas type III effectors suppress cell death induced by components of immunity-associated MAP kinase cascades

Mitogen-activated protein kinase (MAPK) cascades play a fundamental role in signaling of plant immunity and mediate elicitation of cell death. Xanthomonas spp. manipulate plant signaling by using a type III secretion system to deliver effector proteins into host cells. We examined the ability of 33 Xanthomonas effectors to inhibit cell death induced by overexpression of components of MAPK cascades in Nicotiana benthamiana plants. Five effectors inhibited cell death induced by overexpression of MAPKKKα and MEK2, but not of MAP3Kε. In addition, expression of AvrBs1 in yeast suppressed activation of the high osmolarity glycerol MAPK pathway, suggesting that the target of this effector is conserved in eukaryotic organisms. These results indicate that Xanthomonas employs several type III effectors to suppress immunity-associated cell death mediated by MAPK cascades.

Pseudomonas syringae pv. tomato DC3000 Type III Secretion Effector Polymutants Reveal an Interplay between HopAD1 and AvrPtoB

The bacterial pathogen Pseudomonas syringae pv. tomato DC3000 suppresses the two-tiered plant innate immune system by injecting a complex repertoire of type III secretion effector (T3E) proteins. Beyond redundancy and interplay, individual T3Es may interact with multiple immunity-associated proteins, rendering their analysis challenging. We constructed a Pst DC3000 polymutant lacking all 36 T3Es and restored individual T3Es or their mutants to explore the interplay among T3Es. The weakly expressed T3E HopAD1 was sufficient to elicit immunity-associated cell death in Nicotiana benthamiana. HopAD1-induced cell death was suppressed partially by native AvrPtoB and completely by AvrPtoBM3, which has mutations disrupting its E3 ubiquitin ligase domain and two known domains for interacting with immunity-associated kinases. AvrPtoBM3 also gained the ability to interact with the immunity-kinase MKK2, which is required for HopAD1-dependent cell death. Thus, AvrPtoB has alternative, competing mechanisms for suppressing effector-triggered plant immunity. This approach allows the deconvolution of individual T3E activities.

Relationships among Puberty, Muscle and Fat, and Liveweight Gain during Mating in Young Female Sheep

Greater depths of muscle are associated with better reproductive performance in ewe lambs, but, in adult ewes, reproductive performance also seems to vary with liveweight gain during the mating period. Therefore, in a large field study with Merino ewe lambs, we tested whether the relationships among eye muscle depth (EMD), fat depth (FAT) and reproductive performance depend on liveweight gain during the mating period. We selected lambs with a wide range in phenotypic values for depths of eye muscle (EMD) and fat (FAT) and assigned them to dietary treatments designed to achieve low (LOW, n = 244) or high (HIGH, n = 237) rates of liveweight gain during a 28-day mating period. The LOW treatment maintained live weight, whereas the HIGH treatment gained 179 ± 3.8 g/day (p < 0.001). From those ewe lambs that attained puberty, first oestrus was detected at live weight 37.8 ± 0.2 kg and age 232 days. The proportion of ewes that attained puberty increased with EMD (p < 0.01). Ewes from the HIGH treatment were more fertile (pregnant ewes per 100 ewes exposed to rams) and had a higher reproductive rate (foetuses in utero per 100 ewes exposed to rams; p < 0.001) than those from the LOW treatment. Fertility and reproductive rate were positively correlated with weight gain during mating as well as live weight at the start of mating, FAT and EMD (p < 0.05 to <0.001). We conclude that faster growth, due to either extra nutrition during mating or higher phenotypic potential for fat and muscle, will increase reproductive performance in ewe lambs mated at 8 months of age.

Functional genomics of tomato for the study of plant immunity

Tomato (Solanum lycopersicum), along with many other economically valuable species, belongs to the Solanaceae family. Understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. Such changes can implicate the affected gene as participating in plant defense. Testing the involvement of these candidate genes in defense has relied largely on posttranscriptional gene silencing, particularly virus-induced gene silencing. We discuss how functional genomics has played a key role in our current understanding of the defense response in tomato and related species and what are the challenges and opportunities for the future.

Greasy tactics in the plant-pathogen molecular arms race

The modification of proteins by the attachment of fatty acids is a targeting tactic involved in mechanisms of both plant immunity and bacterial pathogenesis. The plant plasma membrane (PM) is a key battleground in the war against disease-causing microbes. This membrane is armed with an array of sensor proteins that function as a surveillance system to detect invading pathogens. Several of these sensor proteins are directed to the plasma membrane through the covalent addition of fatty acids, a process termed fatty acylation. Phytopathogens secrete effector proteins into the plant cell to subvert these surveillance mechanisms, rendering the host susceptible to infection. The targeting of effectors to specific locales within plant cells, particularly the internal face of the host PM, is critical for their virulence function. Several bacterial effectors hijack the host fatty acylation machinery to be modified and directed to this contested locale. To find and fight these fatty acylated effectors the plant leverages lipid-modified intracellular sensors. This review provides examples featuring how fatty acylation is a battle tactic used by both combatants in the molecular arms race between plants and pathogens. Also highlighted is the exploitation of a specific form of host-mediated fatty acid modification, which appears to be exclusively employed by phytopathogenic effector proteins.

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato.

Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported.

Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.