Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds host plants, including economically important crops, such as rice, wheat, cassava, banana, mango, tomato, citrus, cabbage, pepper, bean and cotton. Diseases occurring in nature comprise black rot, leaf/fruit spot, canker, wilt, leaf blight and streak. These bacteria are present worldwide where some phytopathogenic strains are emergent or re-emergent and, consequently, dramatically impact agriculture, economy and food safety.
Xanthomonas bacteria provide excellent models for genomic studies and hundreds of Xanthomonas genome sequences have been obtained since 2002 and many other are underway (www.xanthomonas.org/genomes.html). Comparative genomics between and/or within bacterial species and/or pathovars will be of a great help to decipher commonalities and particularities that underly host range definition.
Most of the Xanthomonas possesses a type III secretion system (T3SS) that is required for injection of various effectors inside plant cells, thus contributing to pathogenicity. Transcription Activator-Like (tal) genes, encode bacterial transcription factors which are injected through the T3SS by many Xanthomonas to promote pathogenicity. Some Ralstonia, Bulkholderia and marine bacteria also express TAL-like proteins which function and mode of action is starting to be deciphered. TALs are addressed to the plant nucleus where they activate plant gene expression by direct binding to the corresponding promoter sequences. Targeted genes essentially act as susceptibility genes. A few years after the cracking of the code allowing the TAL/Host promoter sequence recognition, combined to the ever-growing availability of plant genomes, many efforts have been done to identify TAL targets. These data collected for many Xanthomonas/host pathosystems will assuredly help breeders to breed resistance resistant in important crops.
In this Research Topic we aim to collect manuscripts covering the current knowledge of Xanthomonas genomics and effectomics, with a special focus on TAL effector biology. Specifically, we encourage the submission of manuscripts (Original Research, Hypothesis & Theory, Methods, Reviews, Mini Reviews, Perspective and Opinion) covering the following topics: 1. Manuscripts reporting genome sequencing of Xanthomonas strains. 2. Manuscripts describing functional and comparative genomics in Xanthomonas species/pathovars. 3. Manuscripts describing functional studies on Xanthomonas type III effectors. 3. Manuscripts describing discovery, evolution, bio-informatics and functional genomics of TAL effectors and their targets in plant genomes, as well as for TAL-like in non-Xanthomonas bacteria. 4. Manuscripts describing applications of TAL effector research for resistance breeding in crops.
We anticipate that this Research Topic will be of importance for plant pathologists and breeders.
Recognition of extracellular peptides by plasma membrane‐localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE‐9. GRI is cleaved by METACASPASE‐9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane‐localized, atypical leucine‐rich repeat receptor‐like kinase POLLEN‐SPECIFIC RECEPTOR‐LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS‐dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.
Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plantArabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.
Plant nucleotide-binding leucine-rich repeat (NB-LRR) disease resistance (R) proteins recognize specific “avirulent” pathogen effectors and activate immune responses. NB-LRR proteins structurally and functionally resemble mammalian Nod-like receptors (NLRs). How NB-LRR and NLR proteins activate defense is poorly understood. The divergently transcribed Arabidopsis R genes, RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1), function together to confer recognition of PseudomonasAvrRps4 and Ralstonia PopP2. RRS1 is the only known recessive NB-LRR R gene and encodes a WRKY DNA binding domain, prompting suggestions that it acts downstream of RPS4 for transcriptional activation of defense genes. We define here the early RRS1-dependent transcriptional changes upon delivery of PopP2 via Pseudomonas type III secretion. The Arabidopsis slh1 (sensitive to low humidity 1) mutant encodes an RRS1 allele (RRS1SLH1) with a single amino acid (leucine) insertion in the WRKY DNA-binding domain. Its poor growth due to constitutive defense activation is rescued at higher temperature. Transcription profiling data indicate that RRS1SLH1-mediated defense activation overlaps substantially with AvrRps4- and PopP2-regulated responses. To better understand the genetic basis of RPS4/RRS1-dependent immunity, we performed a genetic screen to identify suppressor of slh1 immunity (sushi) mutants. We show that many sushi mutants carry mutations in RPS4, suggesting that RPS4 acts downstream or in a complex with RRS1. Interestingly, several mutations were identified in a domain C-terminal to the RPS4 LRR domain. Using an Agrobacterium-mediated transient assay system, we demonstrate that the P-loop motif of RPS4 but not of RRS1SLH1 is required for RRS1SLH1 function. We also recapitulate the dominant suppression of RRS1SLH1 defense activation by wild type RRS1 and show this suppression requires an intact RRS1 P-loop. These analyses of RRS1SLH1shed new light on mechanisms by which NB-LRR protein pairs activate defense signaling, or are held inactive in the absence of a pathogen effector.
Plant pathogens display impressive versatility in adapting to host immune systems. Pathogen effector proteins facilitate disease but can become avirulence (Avr) factors when the host acquires discrete recognition capabilities that trigger immunity. The mechanisms that lead to changes to pathogen Avr factors that enable escape from host immunity are diverse, and include epigenetic switches that allow for reuse or recycling of effectors. This perspective outlines possibilities of how epigenetic control of Avr effector gene expression may have arisen and persisted in plant pathogens, and how it presents special problems for diagnosis and detection of specific pathogen strains or pathotypes.
Rust diseases caused by fungi of the order Pucciniales afflict a wide range of plants, including cereals, legumes, ornamentals, and fruit trees, and pose a serious threat to cropping systems and global food security. The obligate parasitic lifestyle of these fungi and their complex life cycles, often involving alternate hosts for the sexual and asexual stages, also make this group of pathogens of great biological interest. One of the most remarkable adaptations of rust fungi is the specialized infection structure that underpins the sustained biotrophic association with hosts; the haustorium (Figure 1A and C). This organ forms after penetration of the wall of a live host cell, expanding on the inner side of the cell wall while invaginating the surrounding host plasma membrane (Figure 1C). Through haustoria, the pathogen derives nutrients from the host and secretes virulence proteins called effectors, which are believed to be the key players that manipulate the physiological and immune responses of host cells –. Analogous terminal feeding structures have independently evolved in other organisms such as the haustorium in powdery mildews (ascomycetes) and downy mildews (oomycetes, not true fungi), and the arbuscules in arbuscular mycorrhizae, suggesting that such architecture represents a successful adaptation of these organisms to interact with their respective host plants , .
Garnica DP, Nemri A, Upadhyaya NM, Rathjen JP, Dodds PN
While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.
Ralf Weßling, Petra Epple, Stefan Altmann,Yijian He, Li Yang, Stefan R. Henz, Nathan McDonald, Kristin Wiley, Kai Christian Bader, Christine Glaßer, M. Shahid Mukhtar, Sabine Haigis, Lila Ghamsari, Amber E. Stephens, Joseph R. Ecker, Marc Vidal, Jonathan D.G. Jones,Klaus F.X. Mayer, Emiel Ver Loren van Themaat, Detlef Weigel, Paul Schulze-Lefert, Jeffery L. Dangl, Ralph Panstruga, and Pascal Braun
The type III secretion system (T3SS) is a membrane-embedded nanomachine found in several Gram-negative bacteria. Upon contact between bacteria and host cells, the syringe-like T3SS transfers proteins termed effectors from the bacterial cytosol to the cytoplasm or the plasma membrane of a single target cell. This is a major difference from secretion systems that merely release molecules into the extracellular milieu, where they act on potentially distant target cells expressing the relevant surface receptors. The syringe architecture is conserved at the structural and functional level and supports injection into a great variety of hosts and tissues. However, the pool of effectors is species specific and determines the outcome of the interaction, via modulation of target-cell function.
Transcription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant–pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.
The YopJ-family of type III effector (T3E) proteins is one of the largest and widely distributed families of effector proteins whose members are highly diversified in virulence functions. In the present study, HopZ4, a member of the YopJ-family of T3Es from the cucumber pathogen Pseudomonas syringae pv. lachrymans is described. HopZ4 shares high sequence similarity with the Xanthomonas T3E XopJ and a functional analysis suggests a conserved virulence function between these two T3Es. As has previously shown for XopJ, HopZ4 interacts with the proteasomal subunit RPT6 in yeast and in planta to inhibit proteasome activity during infection. The inhibitory effect on the proteasome is dependent on localization of HopZ4 to the plasma membrane as well as on an intact catalytic triad of the effector protein. Furthermore, HopZ4 is able to complement loss of XopJ in Xanthomonas as it prevents precocious host cell death during a compatible interaction of Xanthomonas with pepper. The data presented here suggest that different bacterial species employ inhibition of the proteasome as a virulence strategy by making use of conserved T3Es from the YopJ-family of bacterial effector proteins.
Recently, emission of volatile organic compounds (VOCs) has emerged as a mode of communication between bacteria and plants. Although some bacterial VOCs that promote plant growth have been identified, their underlying mechanism of action is unknown. Here we demonstrate that indole, which was identified using a screen for Arabidopsis growth promotion by VOCs from soil-borne bacteria, is a potent plant-growth modulator. Its prominent role in increasing the plant secondary root network is mediated by interfering with the auxin-signalling machinery. Using auxin reporter lines and classic auxin physiological and transport assays we show that the indole signal invades the plant body, reaches zones of auxin activity and acts in a polar auxin transport-dependent bimodal mechanism to trigger differential cellular auxin responses. Our results suggest that indole, beyond its importance as a bacterial signal molecule, can serve as a remote messenger to manipulate plant growth and development.
Many phytopathogenic type III secretion effectors (T3Es) have been shown to target and suppress plant immune signaling, but perturbation of the plant immune system by T3Es can also elicit a plant response. XopX is a “core” Xanthomonas T3E that contributes to growth and symptom development during Xanthomonas euvesicatoria (Xe) infection of tomato, but its functional role is undefined. We tested the effect of XopX on several aspects of plant immune signaling. XopX promoted ethylene production and plant cell death (PCD) during Xe infection of susceptible tomato and in transient expression assays in Nicotiana benthamiana, which is consistent with its requirement for the development of Xe-induced disease symptoms. Additionally, although XopX suppressed flagellin-induced reactive oxygen species, it promoted the accumulation of pattern-triggered immunity (PTI) gene transcripts. Surprisingly, XopX co-expression with other PCD elicitors resulted in delayed PCD, suggesting antagonism between XopX-dependent PCD and other PCD pathways. However, we found no evidence that XopX contributed to the suppression of effector-triggered immunity during Xe-tomato interactions, suggesting that XopX’s primary virulence role is to modulate PTI. These results highlight the dual role of a core Xanthomonas T3E in simultaneously suppressing and activating plant defense responses.
Plants have evolved disease resistance (R) genes encoding for nucleotide-binding site (NB) and leucine-rich repeat (LRR) proteins with N-terminals represented by either Toll/Interleukin-1 receptor (TIR) or coiled-coil (CC) domains. Here, a genome-wide study of presence and diversification of CC-NB-LRR and TIR-NB-LRR encoding genes, and shorter domain combinations in 19 Arabidopsis thaliana accessions and Arabidopsis lyrata, Capsella rubella, Brassica rapa and Eutrema salsugineum are presented.ResultsOut of 528 R genes analyzed, 12 CC-NB-LRR and 17 TIR-NB-LRR genes were conserved among the 19 A. thaliana genotypes, while only two CC-NB-LRRs, including ZAR1, and three TIR-NB-LRRs were conserved when comparing the five species. The RESISTANCE TO LEPTOSPHAERIA MACULANS 1 (RLM1) locus confers resistance to the Brassica pathogen L. maculans the causal agent of blackleg disease and has undergone conservation and diversification events particularly in B. rapa. On the contrary, the RLM3 locus important in the immune response towards Botrytis cinerea and Alternaria spp. has recently evolved in the Arabidopsis genus.ConclusionOur genome-wide analysis of the R gene repertoire revealed a large sequence variation in the 23 cruciferous genomes. The data provides further insights into evolutionary processes impacting this important gene family.
Plants posses an intricate innate immune system that enables them to fight off most invading pathogens. Around the world, agriculture relies on robust disease resistance to ensure adequate food and feed production. Researchers and breeders are constantly generating new resistant crop varieties mostly employing the lengthy process of conventional breeding. Nonetheless, crop losses due to plant pathogens are estimated to be over 15% every year - the main cause of such losses is rapid evolution of new virulent races. In order to keep up with emerging pathogens, we need to gain a deeper and more systematic understanding of the immune system of our crops. During the past two decades, molecular understanding of plant innate immune signaling has been greatly expanded using dicotyledonous model systems such as Arabidopsis thaliana. Now, it is time to connect this volume of knowledge with the immune system of the crop species.
In this Research Topic we aim to collect manuscripts covering the current knowledge of the immune systems of major crop species. Specifically, we encourage the submission of manuscripts (Original Research, Hypothesis & Theory, Methods, Reviews, Mini Reviews, Perspective and Opinion) covering the following topics:
a. Manuscripts describing our current understanding of the plant immune system with a focus on crop species or comparative analyses between model systems and crops.
b. Manuscripts exploring how to best exploit our insight into genomes of plant pathogens and molecular understanding of effector function. c. Manuscripts debating (novel) strategies of how to generate more resistant crop varieties. These might include biotechnological, social and economical aspects of crop improvement.
We anticipate that this Research Topic will become an important resource for plant immunologists especially those interested in comparative studies of plant innate immune systems of model systems and crop species.
Benjamin Schwessinger UC Davis Davis, USA
Rebecca Bart Donald Danforth Plant Science Center St. Louis, USA
Gitta Coaker University of California, Davis Davis, USA
Ksenia V Krasileva University of California Davis Davis, USA
Plant immunity is often triggered by the specific recognition of pathogen effectors by intracellular nucleotide-binding, leucine-rich repeat (NLR) receptors. Plant NLRs contain an N-terminal signaling domain that is mostly represented by either a Toll-interleukin1 receptor (TIR) domain or a coiled coil (CC) domain. In many cases, single NLR proteins are sufficient for both effector recognition and signaling activation. However, many paired NLRs have now been identified where both proteins are required to confer resistance to pathogens. Recent detailed studies on the Arabidopsis thaliana TIR-NLR pair RRS1 and RPS4 and on the rice CC-NLR pair RGA4 and RGA5 have revealed for the first time how such protein pairs function together. In both cases, the paired partners interact physically to form a hetero-complex receptor in which each partner plays distinct roles in effector recognition or signaling activation, highlighting a conserved mode of action of NLR pairs across both monocotyledonous and dicotyledonous plants. We also discuss a new ‘integrated decoy’ effector recognition model to describe these receptor complexes that may be common to many other plant NLR pairs.
Xanthomonas axonopodis pathovar vasculorum strain NCPPB 900 was isolated from sugarcane on Reunion island in 1960. Consistent with its belonging to fatty acid type D, multi-locus sequence analysis confirmed that NCPPB 900 falls within the species X. axonopodis. This genome harbours sequences similar to plasmids pXCV183 from X. campestris pv. vesicatoria 85-10 and pPHB194 from Burkholderia pseudomallei. Its repertoire of predicted effectors includes homologues of XopAA, XopAD, XopAE, XopB, XopD, XopV, XopZ, XopC and XopI and transcriptional activator-like (TAL) effectors and it is predicted to encode a novel phosphonate natural product also encoded by the genome of the phylogenetically distant X. vasicola pv. vasculorum. Availability of this novel genome sequence may facilitate the study of interactions between xanthomonads and sugarcane, a host-pathogen system that appears to have evolved several times independently within the genus Xanthomonas and may also provide a source of target sequences for molecular detection and diagnostics.
Ca2+ is a ubiquitous second messenger for cellular signalling in various stresses and developmental processes. Here, we summarize current developments in the roles of Ca2+ during plant immunity responses. We discuss the early perception events preceding and necessary for triggering cellular Ca2+ fluxes, the potential Ca2+-permeable channels, the decoding of Ca2+ signals predominantly via Ca2+-dependent phosphorylation events and transcriptional reprogramming. To highlight the complexity of the cellular signal network, we briefly touch on the interplay between Ca2+-dependent signalling and selected major signalling mechanisms – with special emphasis on reactive oxygen species at local and systemic levels.
Banana is a major staple crop in East Africa produced mostly by smallholder subsistence farmers. More bananas are produced and consumed in East Africa than in any region of the world. Uganda is the world’s second foremost grower with a total annual production of about 10.5 million tons. The average daily per capita consumption in Uganda ranges from 0.61 to over 1.6 kg, one of the highest in the world. In this Correspondence, we report preliminary results from a confined field trial in Uganda of transgenic bananas resistant to the deadly banana Xanthomonas wilt disease.
Leena Tripathi, Jaindra Nath Tripathi, Andrew Kiggundu, Sam Korie, Frank Shotkoski & Wilberforce Kateera Tushemereirwe
The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated.
Odile Berge, Caroline L. Monteil, Claudia Bartoli, Charlotte Chandeysson, Caroline Guilbaud
Breeding agricultural crops for resistance against pathogens is essential to secure global food production. Despite efforts to control crop diseases, pathogens are estimated to account for losses of 15% of global food production. It is suggested that losses would be almost twice as much without disease control measures, such as crop resistance breeding . There are now opportunities to improve the effectiveness of breeding crops for resistance against damaging pathogens by exploiting new molecular and genetic insights to improve understanding of the defence system of crop plants against pathogens. In this opinion, we focus on the resistance of crops against foliar fungal pathogens that exploit the host apoplast for retrieval of nutrients. Some of these pathogens are globally widespread and of considerable economic importance. They include pathogens that penetrate the host leaf cuticle and then exploit a niche underneath it (e.g., Pyrenopeziza brassicae, oilseed rape light leaf spot; Venturia inaequalis, apple scab; and Rhynchosporium commune, barley leaf blotch, global losses of approximately US$3.5 billion per year). Others enter leaves through stomata, then grow between host mesophyll cells (e.g., Cladosporium fulvum, tomato leaf mould; Leptosphaeria maculans, oilseed rape phoma stem canker, global losses of approximately US$1 billion per year; and Zymoseptoria tritici, wheat septoria leaf blotch, with a global loss of approximately US$5 billion per year) (Table 1, Figure 1). These apoplastic pathogens are all ascomycetes and many of them are dothideomycetes .
We report here the draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369, the causal agent of bacterial blight of onion. The draft genome has a size of 5,425,942 bp and a G+C content of 64.4%.
L. Gagnevin, S. Bolot, J. L. Gordon, O. Pruvost, C. Vernière, I. Robène, M. Arlat, L. D. Noël, S. Carrère, M.-A. Jacques, R. Koebnik
The gene-for-gene concept has historically been applied to describe a specific resistance interaction wherein single genes from the host and the pathogen dictate the outcome. These interactions have been observed across the plant kingdom and all known plant microbial pathogens. In recent years, this concept has been extended to susceptibility phenotypes in the context of transcription activator like (TAL) effectors that target SWEET sugar transporters. However, as this interaction has only been observed in rice, it was not clear whether the gene-for-gene susceptibility was unique to that system. Here we show, through a combined systematic analysis of the TAL effector-complement of Xanthomonas axonopodis pv. manihotis (Xam), and RNA-Sequencing to identify targets in cassava, that TAL20Xam668 specifically induces the sugar transporter MeSWEET10a to promote virulence. Designer TAL effectors (dTALEs) complement TAL20Xam668 mutant phenotypes, demonstrating that MeSWEET10a is a susceptibility gene in cassava. Sucrose uptake-deficient Xam do not lose virulence, indicating that sucrose may be cleaved extracellularly and taken up as hexoses into Xam. Together, our data suggest that pathogen hijacking of plant nutrients is not unique to rice blight but also plays a role in bacterial blight of the dicot cassava.