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Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

"The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs."

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of Plants & Bacteria (and sometimes other fellows too)
A selection of publications concerning the diverse relationship between plants and microorganisms, with some special attention to plant-pathogenic bacteria.
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Profiling the extended phenotype of plant pathogens

Profiling the extended phenotype of plant pathogens | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host–pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an ‘extended phenotype’ that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control.

What determines whether a pathogen grows within a plant?

What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host?

How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?

Via Christophe Jacquet
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Negative Autogenous Control of the Master Type III Secretion System Regulator HrpL in Pseudomonas syringae

Negative Autogenous Control of the Master Type III Secretion System Regulator HrpL in Pseudomonas syringae | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Authors: Christopher Waite, Jörg Schumacher, Milija Jovanovic, Mark Bennett and Martin Buck.

Abstract:
The type III secretion system (T3SS) is a principal virulence determinant of the model bacterial plant pathogen Pseudomonas syringae. T3SS effector proteins inhibit plant defense signaling pathways in susceptible hosts and elicit evolved immunity in resistant plants. The extracytoplasmic function sigma factor HrpL coordinates the expression of most T3SS genes. Transcription of hrpL is dependent on sigma-54 and the codependent enhancer binding proteins HrpR and HrpS for hrpL promoter activation. hrpL is oriented adjacently to and divergently from the HrpL-dependent gene hrpJ, sharing an intergenic upstream regulatory region. We show that association of the RNA polymerase (RNAP)-HrpL complex with the hrpJ promoter element imposes negative autogenous control on hrpL transcription in P. syringae pv. tomato DC3000. The hrpL promoter was upregulated in a ΔhrpL mutant and was repressed by plasmid-borne hrpL. In a minimal Escherichia coli background, the activity of HrpL was sufficient to achieve repression of reconstituted hrpL transcription. This repression was relieved if both the HrpL DNA-binding function and the hrp-box sequence of the hrpJ promoter were compromised, implying dependence upon the hrpJ promoter. DNA-bound RNAP-HrpL entirely occluded the HrpRS and partially occluded the integration host factor (IHF) recognition elements of the hrpL promoter in vitro, implicating inhibition of DNA binding by these factors as a cause of negative autogenous control. A modest increase in the HrpL concentration caused hypersecretion of the HrpA1 pilus protein but intracellular accumulation of later T3SS substrates. We argue that negative feedback on HrpL activity fine-tunes expression of the T3SS regulon to minimize the elicitation of plant defenses.
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Behind the lines–actions of bacterial type III effector proteins in plant cells

Behind the lines–actions of bacterial type III effector proteins in plant cells | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Author: Daniela Büttner Journal: FEMS Microbiology Reviews Abstract: Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
Freddy Monteiro's insight:
An updated review from a widely recognized researchers in plant pathogens effector biology. In the current delivery Buttner includes Xanthomonas, P. syringae and R. solanacearum effectors with known plant target molecules.
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Symbiotic Fungi Control Plant Root Cortex Development through the Novel GRAS Transcription Factor MIG1

Symbiotic Fungi Control Plant Root Cortex Development through the Novel GRAS Transcription Factor MIG1 | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
In an approaching scenario of soil nutrient depletion, root association with soil microorganisms can be key for plant health and sustainability [ 1–3 ]. Symbiotic arbuscular mycorrhizal (AM) fungi are major players in helping plants growing under nutrient starvation conditions. They provide plants with minerals like phosphate and, furthermore, act as modulators of plant growth altering the root developmental program [ 4, 5 ]. However, the precise mechanisms involved in this latter process are not well understood. Here, we show that AM fungi are able to modulate root cortex development in Medicago truncatula by activating a novel GRAS-domain transcription factor, MIG1, that determines the size of cortical root cells. MIG1 expression peaks in arbuscule-containing cells, suggesting a role in cell remodeling during fungal accommodation. Roots ectopically expressing MIG1 become thicker due to an increase in the number and width of cortical cells. This phenotype is fully counteracted by gibberellin (GA) and phenocopied with a GA biosynthesis inhibitor or by expression of a dominant DELLA (Δ18DELLA1) protein. MIG1 downregulation leads to malformed arbuscules, a phenotype rescued by Δ18DELLA1, suggesting that MIG1 intersects with the GA signaling to control cell morphogenesis through DELLA1. DELLA1 was shown to be a central node controlling arbuscule branching [ 6–8 ]. Now we provide evidence that, together with MIG1, DELLA1 is responsible for radial cortical cell expansion during arbuscule development. Our data point toward DELLA proteins being not only longitudinal root growth repressors [ 9 ] but also positive regulators of cortical radial cell expansion, extending the knowledge of how DELLAs control root growth.

Via Francis Martin
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Decoding a new sentence in the plant-mycorrhiza transkingdom dialogue
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Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000 | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Authors
Laura A. Lewisa, Krzysztof Polanski, Marta de Torres-Zabala, Siddharth Jayaraman, Laura Bowden, Jonathan Moore, Christopher A. Penfold, Dafyd J. Jenkins, Claire Hill, Laura Baxter, Satish Kulasekaran, William Truman, George Littlejohn, Justyna Prusinska, Andrew Mead, Jens Steinbrenner, Richard Hickman, David Rand, David L. Wild, Sascha Ott, Vicky Buchanan-Wollaston, Nick Smirnoff, Jim Beynon, Katherine Denby and Murray Grant

Abstract
Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and that orchestrated by effectors. A high-resolution time course of genome-wide expression changes following challenge with Pseudomonas syringae pv tomato DC3000 and the nonpathogenic mutant strain DC3000hrpA- allowed us to establish causal links between the activities of pathogen effectors and suppression of MTI and infer with high confidence a range of processes specifically targeted by effectors. Analysis of this information-rich data set with a range of computational tools provided insights into the earliest transcriptional events triggered by effector delivery, regulatory mechanisms recruited, and biological processes targeted. We show that the majority of genes contributing to disease or defense are induced within 6 h postinfection, significantly before pathogen multiplication. Suppression of chloroplast-associated genes is a rapid MAMP-triggered defense response, and suppression of genes involved in chromatin assembly and induction of ubiquitin-related genes coincide with pathogen-induced abscisic acid accumulation. Specific combinations of promoter motifs are engaged in fine-tuning the MTI response and active transcriptional suppression at specific promoter configurations by P. syringae.
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Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Abstract:

Evolutionary innovations that enable organisms to colonize new ecological niches are rare compared to gradual evolutionary changes in existing traits. We discovered that key mutations in the gltA gene, which encodes citrate synthase (CS), occurred both before and after Escherichia coli gained the ability to grow aerobically on citrate (Cit+ phenotype) during the Lenski long-term evolution experiment. The first gltA mutation, which increases CS activity by disrupting NADH-inhibition of this enzyme, is beneficial for growth on the acetate and contributed to preserving the rudimentary Cit+ trait from extinction when it first evolved. However, after Cit+ was refined by further mutations, this potentiating gltA mutation became deleterious to fitness. A second wave of beneficial gltA mutations then evolved that reduced CS activity to below the ancestral level. Thus, dynamic reorganization of central metabolism made colonizing this new nutrient niche contingent on both co-opting and overcoming a history of prior adaptation.

 

 

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The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Abstract:

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.

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Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria (PLoS Pathogens)

Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria (PLoS Pathogens) | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Summary:

Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (kcat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.

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Treasure Your Exceptions: Unusual Domains in Immune Receptors Reveal Host Virulence Targets: Cell

Treasure Your Exceptions: Unusual Domains in Immune Receptors Reveal Host Virulence Targets: Cell | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Summary:

A mechanistic understanding of how plant pathogens modulate their hosts is critical for rationally engineered disease resistance in agricultural systems. Two new studies show that genomically paired plant immune receptors have incorporated decoy domains that structurally mimic pathogen virulence targets to monitor attempted host immunosuppression.

Freddy Monteiro's insight:

This is a short introduction to the back-to-back pieces:

 

1. A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors www.cell.com/cell/abstract/S0092-8674(15)00441-9

 

2. A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity http://www.cell.com/cell/abstract/S0092-8674%2815%2900442-0

 

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A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors: Cell

A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors: Cell | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Summary:

Defense against pathogens in multicellular eukaryotes depends on intracellular immune receptors, yet surveillance by these receptors is poorly understood. Several plant nucleotide-binding, leucine-rich repeat (NB-LRR) immune receptors carry fusions with other protein domains. The Arabidopsis RRS1-R NB-LRR protein carries a C-terminal WRKY DNA binding domain and forms a receptor complex with RPS4, another NB-LRR protein. This complex detects the bacterial effectors AvrRps4 or PopP2 and then activates defense. Both bacterial proteins interact with the RRS1 WRKY domain, and PopP2 acetylates lysines to block DNA binding. PopP2 and AvrRps4 interact with other WRKY domain-containing proteins, suggesting these effectors interfere with WRKY transcription factor-dependent defense, and RPS4/RRS1 has integrated a “decoy” domain that enables detection of effectors that target WRKY proteins. We propose that NB-LRR receptor pairs, one member of which carries an additional protein domain, enable perception of pathogen effectors whose function is to target that domain.

Freddy Monteiro's insight:

See also the back-to-back paper:

A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity http://www.cell.com/cell/abstract/S0092-8674%2815%2900442-0

 

See also the preview:

Treasure Your Exceptions: Unusual Domains in Immune Receptors Reveal Host Virulence Targets http://www.cell.com/cell/abstract/S0092-8674%2815%2900566-8

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Intersubgeneric hybridization between Glycine max and G. tomentella: production of F1, amphidiploid, BC1, BC2, BC3, and fertile soybean plants

Intersubgeneric hybridization between Glycine max and G. tomentella: production of F1, amphidiploid, BC1, BC2, BC3, and fertile soybean plants | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Abstract:

This paper describes methods for unlocking genetic treasure from wild perennial Glycine species of Australia for soybean improvement. The genetic resources of the ca. 26 species of the genus Glycine subgenus Glycine have not been exploited to broaden the genetic base of soybean (Glycine max; 2n = 40). The objectives of this study were to develop methods for producing F1, amphidiploid, BC1, BC2, BC3, and fertile soybean plants from crosses of soybean and the genus Glycine subgenus Glycine species, in order to utilize the subgenus Glycine germplasm in soybean breeding. Soybean cultivars were hybridized with six accessions of 78-chromosome G. tomentella as well as one accession each of 40-chromosome G. tomentella, G. argyrea and G. latifolia. They were chosen because they exhibit resistance to soybean rust. We were successful in producing fertile soybean from soybean cv. 'Dwight' and 78-chromosome G. tomentella accession PI 441001, while other hybrids were discontinued either at F1 or amphidiploid stage. The F1 seeds aborted prior to reaching maturity, so developing seeds from 19 to 21 day old pods were cultured aseptically in various media formulations. Seed maturation and multiple embryo generation media were developed. F1 plants with shoots and roots (2n = 59) were transplanted to pots in greenhouse. Amphidiploid (2n = 118) plants were backcrossed to 'Dwight'. BC1 (2n = 79) plants were propagated through in vitro and 43 mature BC2F1 seeds were harvested. Fifteen surviving BC2F1 plants were morphologically distinct, sterile, and had chromosome numbers ranging 2n = 56-59. Chromosome numbers of the BC3F1 plants ranged 2n = 40-49. Derived fertile soybeans were first planted in the field in 2008 and are being evaluated for yield, resistance to pathogens and pests and tolerance to salt through material transfer agreement.

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TWITTER ARCHIVE #NLR2015 - ALL DAYS! NLR BIOLOGY IN PLANTS AND ANIMALS; WORKSHOP AT SCHLOSS RINGBERG; May 2015


Via Kamoun Lab @ TSL
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MPMI: Candidate Effector Proteins of the Rust Pathogen Melampsora Larici-Populina Target Diverse Plant Cell Compartments (2015)

MPMI: Candidate Effector Proteins of the Rust Pathogen Melampsora Larici-Populina Target Diverse Plant Cell Compartments (2015) | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalogue of secreted proteins, some of which have been considered candidate effectors. Unravelling how these proteins function in host cells is key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localisation and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria and discrete cellular bodies. We also used coimmunoprecipitation and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and the TOPLESS-Related Protein 4 from poplar by in planta coimmunoprecipitation. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.


Via The Sainsbury Lab, Kamoun Lab @ TSL
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The Sainsbury Lab's curator insight, February 5, 2015 7:23 AM

Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalogue of secreted proteins, some of which have been considered candidate effectors. Unravelling how these proteins function in host cells is key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localisation and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria and discrete cellular bodies. We also used coimmunoprecipitation and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and the TOPLESS-Related Protein 4 from poplar by in planta coimmunoprecipitation. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.

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Ralstonia solanacearum differentially colonizes roots of resistant and susceptible tomato plants

Ralstonia solanacearum differentially colonizes roots of resistant and susceptible tomato plants | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Authors: Caldwell D, Kim BS, Iyer-Pascuzzi AS

Abstract:
Ralstonia solanacearum is the causal agent of bacterial wilt and infects over 200 plant species in 50 families. The soil-borne bacterium is lethal to many Solanaceous species, including tomatoes. Although resistant plants can carry high pathogen loads (between 105 and 108 CFU/g fresh weight), the disease is best controlled by the use of resistant cultivars, particularly resistant rootstocks. How these plants have latent infections yet maintain resistance is not clear. R. solanacearum first infects the plant through the root system, and thus early root colonization events may be key to understanding resistance. We hypothesized that the distribution and timing of bacterial invasion differed in roots of resistant and susceptible tomato cultivars. Here we use a combination of scanning electron microscopy and light microscopy to investigate R. solanacearum colonization in roots of soil-grown resistant and susceptible tomato cultivars at multiple timepoints after inoculation. Our results show that colonization of the root vascular cylinder is delayed in the resistant cultivar Hawaii7996 (H7996), and that once bacteria enter the root vascular tissues, colonization in the vasculature is spatially restricted. Our data suggest that resistance is due in part to the ability of the resistant cultivar to restrict bacterial root colonization in space and time.
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Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.

Via Christophe Jacquet
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Pseudomonas syringae Differentiates into Phenotypically Distinct Subpopulations During Colonization of a Plant Host

Pseudomonas syringae Differentiates into Phenotypically Distinct Subpopulations During Colonization of a Plant Host | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Authors: José S. Rufián, María-Antonia Sánchez-Romero, Diego López-Márquez, Alberto P. Macho, John W. Mansfield, Dawn L. Arnold, Javier Ruiz-Albert, Josep Casadesús and Carmen R. Beuzón.
Journal: Environmental Microbiology

Summary: 
Bacterial microcolonies with heterogeneous sizes are formed during colonization of Phaseolus vulgaris by Pseudomonas syringae. Heterogeneous expression of structural and regulatory components of the P. syringae type III secretion system (T3SS), essential for colonization of the host apoplast and disease development, is likewise detected within the plant apoplast. T3SS expression is bistable in the homogeneous environment of nutrient-limited T3SS-inducing medium, suggesting that subpopulation formation is not a response to different environmental cues. T3SS bistability is reversible, indicating a non-genetic origin, and the T3SSHIGH and T3SSLOW subpopulations show differences in virulence. T3SS bistability requires the transcriptional activator HrpL, the double negative regulatory loop established by HrpV and HrpG, and may be enhanced through a positive feedback loop involving HrpA, the main component of the T3SS pilus. To our knowledge, this is the first example of phenotypic heterogeneity in the expression of virulence determinants during colonization of a non-mammalian host. 
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Take note of this phenomenon. Findings described here will be validated in other plant pathogens.
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Sources of resistance and susceptibility to Septoria tritici blotch of wheat

Sources of resistance and susceptibility to Septoria tritici blotch of wheat | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Authors: Lia Arraiano and James Brown
Journal: Molecular Plant Pathology

Abstract:
An association genetics analysis was conducted to investigate the genetics of resistance to Septoria tritici blotch, caused by the fungus Zymoseptoria tritici (alternatively Mycosphaerella graminicola), in cultivars and breeding lines of wheat (Triticum aestivum) used in the UK between 1860 and 2000. The population was tested with Diversity Array Technology (DArT) and simple-sequence repeat (SSR or microsatellite) markers. The lines formed a single population with no evidence for subdivision, because there were several common ancestors of large parts of the pedigree. Quantitative trait loci (QTLs) controlling Septoria resistance were postulated on 11 chromosomes, but 38% of variation was not explained by the identified QTLs. Calculation of best linear unbiased predictions (BLUPs) identified lineages of spring and winter wheat carrying different alleles for resistance and susceptibility. Abundant variation in Septoria resistance may be exploited by crossing well-adapted cultivars in different lineages to achieve transgressive segregation and thus breed for potentially durable quantitative resistance, whereas phenotypic selection for polygenic quantitative resistance should be effective in breeding cultivars with increased resistance. The most potent allele reducing susceptibility to Septoria, on chromosome arm 6AL, was associated with reduced leaf size. Genes which increase susceptibility to Septoria may have been introduced inadvertently into UK wheat breeding programmes from cultivars used to increase yield, rust resistance and eyespot resistance between the 1950s and 1980s. This indicates the need to consider trade-offs in plant breeding when numerous traits are important and to be cautious about the use of non-adapted germplasm.
Freddy Monteiro's insight:
Reconstructing the breeding events leading to high yield wheat and lost of septoria resist. in modern cultivars
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An assessment of US microbiome research

An assessment of US microbiome research | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it
Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using ’omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.

Via Jean-Michel Ané
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Breeding for resistances to Ralstonia solanacearum

Ralstonia solanacearum is one of the most devastating bacterial plant pathogens due to its large host range, worldwide geographic distribution and persistence in fields. This soilborne pathogen is the causal agent of bacterial wilt and it can infect major agricultural crops thereby reducing significantly their yield. To favour infection, the bacterium delivers, through the type three secretion system, effectors that manipulate plant immunity. In this review, the relative efficiency of control strategies and existing resistances to R. solanacearum will be presented. Then, we will describe the genetic and molecular insights gained from the study of bacterial wilt in model plants. Finally, we will explore how the knowledge gathered from unravelling avirulence and virulence mechanisms of R. solanacearum effectors could help to develop more durable resistances in crop plants toward this destructive pathogen.
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Reviewed in 2013: Exploring the costs of horizontal gene transfer (Trends in Ecology & Evolution)

Reviewed in 2013: Exploring the costs of horizontal gene transfer (Trends in Ecology & Evolution) | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Summary:

Horizontal gene transfer (HGT) is one of the most important evolutionary forces within microbial populations. Although evidence for beneficial fitness effects of HGT is overwhelming, recently acquired regions often function inefficiently within new genomic backgrounds so that each transfer event has the potential to disrupt existing regulatory and physiological networks. Identifying and exploring costs is essential for guiding general discussions about the interplay between selection and HGT, as well as generating hypotheses to explain how HGT affects evolutionary potential through, for example, changing adaptive trajectories. Focusing on costs of HGT as foundations for future studies will enhance exploration at the interface between acquired regions and recipient genomes, including the process of amelioration, and enable experimental evaluation of the role of HGT in structuring genetic diversity across populations.

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A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity: Cell

A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity: Cell | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Summary:

Microbial pathogens infect host cells by delivering virulence factors (effectors) that interfere with defenses. In plants, intracellular nucleotide-binding/leucine-rich repeat receptors (NLRs) detect specific effector interference and trigger immunity by an unknown mechanism. The Arabidopsis-interacting NLR pair, RRS1-R with RPS4, confers resistance to different pathogens, including Ralstonia solanacearum bacteria expressing the acetyltransferase effector PopP2. We show that PopP2 directly acetylates a key lysine within an additional C-terminal WRKY transcription factor domain of RRS1-R that binds DNA. This disrupts RRS1-R DNA association and activates RPS4-dependent immunity. PopP2 uses the same lysine acetylation strategy to target multiple defense-promoting WRKY transcription factors, causing loss of WRKY-DNA binding and transactivating functions needed for defense gene expression and disease resistance. Thus, RRS1-R integrates an effector target with an NLR complex at the DNA to switch a potent bacterial virulence activity into defense gene activation.

Freddy Monteiro's insight:

See also the back-to-back paper:

A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. www.cell.com/cell/abstract/S0092-8674(15)00441-9

 

See also the preview:

Treasure Your Exceptions: Unusual Domains in Immune Receptors Reveal Host Virulence Targets. http://www.cell.com/cell/abstract/S0092-8674%2815%2900566-8

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Rescooped by Freddy Monteiro from Plant-Microbe Interaction
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Targeted DNA degradation using a CRISPR device stably carried in the host genome

Targeted DNA degradation using a CRISPR device stably carried in the host genome | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Abstract:
Once an engineered organism completes its task, it is useful to degrade the associated DNA to reduce environmental release and protect intellectual property. Here we present a genetically encoded device (DNAi) that responds to a transcriptional input and degrades user-defined DNA. This enables engineered regions to be obscured when the cell enters a new environment. DNAi is based on type-IE CRISPR biochemistry and a synthetic CRISPR array defines the DNA target(s). When the input is on, plasmid DNA is degraded 108-fold. When the genome is targeted, this causes cell death, reducing viable cells by a factor of 108. Further, the CRISPR nuclease can direct degradation to specific genomic regions (for example, engineered or inserted DNA), which could be used to complicate recovery and sequencing efforts. DNAi can be stably carried in an engineered organism, with no impact on cell growth, plasmid stability or DNAi inducibility even after passaging for >2 months.


Via IPM Lab, Guogen Yang
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Planting molecular functions in an ecological context with Arabidopsis thaliana

Planting molecular functions in an ecological context with Arabidopsis thaliana | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Recommended by a bright graduate student who recently joined the Dangl lab.

 

Author: Ute Krämer

Journal: eLIFE

Date: March 2015

Title: Planting molecular functions in an ecological context with Arabidopsis thaliana.

Abstract:

The vascular plant Arabidopsis thaliana is a central genetic model and universal reference organism in plant and crop science. The successful integration of different fields of research in the study of A. thaliana has made a large contribution to our molecular understanding of key concepts in biology. The availability and active development of experimental tools and resources, in combination with the accessibility of a wealth of cumulatively acquired knowledge about this plant, support the most advanced systems biology approaches among all land plants. Research in molecular ecology and evolution has also brought the natural history of A. thaliana into the limelight. This article showcases our current knowledge of the natural history of A. thaliana from the perspective of the most closely related plant species, providing an evolutionary framework for interpreting novel findings and for developing new hypotheses based on our knowledge of this plant. - See more at: http://elifesciences.org/content/4/e06100#sthash.i5tIzAvI.dpuf

 

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Rescooped by Freddy Monteiro from Insights into Soil Ecology
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Phylogenetic structure and host abundance drive disease pressure in communities

Phylogenetic structure and host abundance drive disease pressure in communities | of Plants & Bacteria (and sometimes other fellows too) | Scoop.it

Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally1, 2. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a ‘rare-species advantage’3, 4, 5. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species6, 7. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced8, 9. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.


Via Pedobiologia: Journal of Soil Ecology
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