Plants&Bacteria
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Plants&Bacteria
A selection of publications concerning the diverse relationship between plants and microorganisms, with some special atention to plant-pathogenic bacteria.
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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 | Plants&Bacteria | 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 | Plants&Bacteria | 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 | Plants&Bacteria | 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) | Plants&Bacteria | 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, 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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Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum

Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum | Plants&Bacteria | Scoop.it

 

 

Abstract:

Background
Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection.

Results
A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK,cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes.

Conclusion
This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum.

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Bugs Split to Attack and Gamble to Survive

Bugs Split to Attack and Gamble to Survive | Plants&Bacteria | Scoop.it

PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.

Freddy Monteiro's insight:

This "Sypnosis" article by Roland G. Roberts on PLoS Biology is simply beautiful. A must read before digesting Arnoldini M et al paper

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Alteration of gene expression profile in the roots of wild diploid Arachis duranensis inoculated with Ralstonia solanacearum

Alteration of gene expression profile in the roots of wild diploid Arachis duranensis inoculated with Ralstonia solanacearum | Plants&Bacteria | Scoop.it

Scooped from: Plant Pathology, 2014

Authors:     Y. N. Chen, X. P. Ren, X. J. Zhou, L. Huang, J. Q. Huang, L. Y. Yan, Y. Lei, Y Qi, W. H. Wei and H. F. Jiang

 

Abstract

Bacterial wilt caused by Ralstonia solanacearum is a serious disease of peanut (Arachis hypogaea) in China. However, the molecular basis of peanut resistance to R. solanacearum is poorly understood. Arachis duranensis, a wild diploid species of the genus Arachis, has been proven to be resistant to bacterial wilt, and thus holds valuable potential for understanding the mechanism of resistance to bacterial wilt and genetic improvement of peanut disease resistance. Here, suppression subtractive hybridization (SSH) and macroarray hybridization were employed to detect differentially expressed genes (DEGs) in the roots of A. duranensis after R. solanacearum inoculation. A total of 317 unique genes were obtained, 265 of which had homologues and functional annotations. KEGG analysis revealed that a large proportion of these unigenes are mainly involved in the biosynthesis of phytoalexins, particularly in the biosynthetic pathways of terpenoids and flavonoids. Subsequent real-time polymerase chain reaction (PCR) analysis showed that the terpenoid and flavonoid synthesis-related genes showed higher expression levels in a resistant genotype of A. duranensis than in a susceptible genotype, indicating that the terpenoids and flavonoids probably played a fundamental role in the resistance of A. duranensis to R. solanacearum. This study provides an overview of the gene expression profile in the roots of wild Arachis species in response to R. solanacearum infection. Moreover, the related candidate genes are also valuable for the further study of the molecular mechanisms of resistance to R. solanacearum.

Freddy Monteiro's insight:

Terpenoids and flavonoids MIGHT be responsible for resistance of Arachis duranensis to R. solanacearum.

There's room for more studies.

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Molecular Steps in the Immune Signaling Pathway Evoked by Plant Elicitor Peptides: Ca2+-Dependent Protein Kinases, Nitric Oxide, and Reactive Oxygen Species Are Downstream from the Early Ca2+ Signal

Molecular Steps in the Immune Signaling Pathway Evoked by Plant Elicitor Peptides: Ca2+-Dependent Protein Kinases, Nitric Oxide, and Reactive Oxygen Species Are Downstream from the Early Ca2+ Signal | Plants&Bacteria | Scoop.it

Scooped from: Plant Physiology, 2013.

Authors: Yi Ma, Yichen Zhao, Robin K. Walker and Gerald A. Berkowitz.

 

Abstract:

Endogenous plant elicitor peptides (Peps) can act to facilitate immune signaling and pathogen defense responses. Binding of these peptides to the Arabidopsis (Arabidopsis thaliana) plasma membrane-localized Pep receptors (PEPRs) leads to cytosolic Ca2+ elevation, an early event in a signaling cascade that activates immune responses. This immune response includes the amplification of signaling evoked by direct perception of pathogen-associated molecular patterns by plant cells under assault. Work included in this report further characterizes the Pep immune response and identifies new molecular steps in the signal transduction cascade. The PEPR coreceptor BRASSINOSTEROID-INSENSITIVE1 Associated Kinase1 contributes to generation of the Pep-activated Ca2+ signal and leads to increased defense gene expression and resistance to a virulent bacterial pathogen. Ca2+-dependent protein kinases (CPKs) decode the Ca2+ signal, also facilitating defense gene expression and enhanced resistance to the pathogen. Nitric oxide and reduced nicotinamide adenine dinucleotide phosphate oxidase-dependent reactive oxygen species generation (due to the function of Respiratory Burst Oxidase Homolog proteins D and F) are also involved downstream from the Ca2+ signal in the Pep immune defense signal transduction cascade, as is the case with BRASSINOSTEROID-INSENSITIVE1 Associated Kinase1 and CPK5, CPK6, and CPK11. These steps of the pathogen defense response are required for maximal Pep immune activation that limits growth of a virulent bacterial pathogen in the plant. We find a synergism between function of the PEPR and Flagellin Sensing2 receptors in terms of both nitric oxide and reactive oxygen species generation. Presented results are also consistent with the involvement of the secondary messenger cyclic GMP and a cyclic GMP-activated Ca2+-conducting channel in the Pep immune signaling pathway.

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Thermo-Regulation of Genes Mediating Motility and Plant Interactions in Pseudomonas syringae

Thermo-Regulation of Genes Mediating Motility and Plant Interactions in Pseudomonas syringae | Plants&Bacteria | Scoop.it

Scooped from: PLOS ONE, 2013

Authors:  Kevin L. Hockett, Adrien Y. Burch and Steven E. Lindow

 

Abstract:

Pseudomonas syringae is an important phyllosphere colonist that utilizes flagellum-mediated motility both as a means to explore leaf surfaces, as well as to invade into leaf interiors, where it survives as a pathogen. We found that multiple forms of flagellum-mediated motility are thermo-suppressed, including swarming and swimming motility. Suppression of swarming motility occurs between 28° and 30°C, which coincides with the optimal growth temperature of P. syringae. Both fliC (encoding flagellin) and syfA (encoding a non-ribosomal peptide synthetase involved in syringafactin biosynthesis) were suppressed with increasing temperature. RNA-seq revealed 1440 genes of the P. syringae genome are temperature sensitive in expression. Genes involved in polysaccharide synthesis and regulation, phage and IS elements, type VI secretion, chemosensing and chemotaxis, translation, flagellar synthesis and motility, and phytotoxin synthesis and transport were generally repressed at 30°C, while genes involved in transcriptional regulation, quaternary ammonium compound metabolism and transport, chaperone/heat shock proteins, and hypothetical genes were generally induced at 30°C. Deletion of flgM, a key regulator in the transition from class III to class IV gene expression, led to elevated and constitutive expression of fliC regardless of temperature, but did not affect thermo-regulation of syfA. This work highlights the importance of temperature in the biology of P. syringae, as many genes encoding traits important for plant-microbe interactions were thermo-regulated.

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Regulatory network of hrp gene expression in Xanthomonas oryzae pv. oryzae

Regulatory network of hrp gene expression in Xanthomonas oryzae pv. oryzae | Plants&Bacteria | Scoop.it

Scooped from: Journal of General Plant Pathology, 2014

Authors: Seiji Tsuge, Ayako Furutani, Yumi Ikawa

 

Abstract:

Like other plant-pathogenic bacteria, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight of rice, has hrp genes that are indispensable for its virulence. The hrp genes are involved in the construction of the type III secretion (T3S) apparatus, through which dozens of virulence-related proteins, called effectors, are directly secreted into plant cells to suppress and disturb plant immune systems and/or induce plant susceptibility genes. The expression of hrp genes is strictly regulated and induced only in plants and in certain nutrient-poor media. Two proteins, HrpG and HrpX, are known as key regulators for hrp gene expression. Great efforts by many researchers have revealed unexpectedly that, besides HrpG and HrpX, many regulators are involved in this regulation, some of which also regulate the expression of virulence-related genes other than hrp. Moreover, it has been found that HrpG and HrpX regulate not only hrp genes and effector genes but also genes unrelated to the T3S system. These findings suggest that the expression of the hrp gene is orchestrally regulated with other virulence-related genes by a complicated, sophisticated regulatory network in X. oryzaepv. oryzae.

Freddy Monteiro's insight:

there you are HrcC!

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Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the Type Three Secretion System

Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the Type Three Secretion System | Plants&Bacteria | Scoop.it
Authors: Milija Jovanovic*, Edward Lawton, Jörg Schumacher andMartin BuckAbstractPs. syringae pv tomato DC3000, a plant pathogenic gram negative bacterium, employs the Type III Secretion System (T3SS) to cause disease in tomato and Arabidopsis and to induce the hypersensitive response in non-host plants. The expression of T3SS is regulated by the HrpL extracytoplasmic sigma factor. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS and negative regulator HrpV. In this study we analysed the organization of HrpRS and HrpV regulatory proteins and interplay between them. We identified one key residue I26 in HrpS required for repression by HrpV. Substitution of I26 in HrpS abolishes its interaction with HrpV, impairs interactions between HrpS and HrpR and the self-association of HrpS. We show that HrpS self-associates and can associate simultaneously with HrpR and HrpV. We now propose that HrpS has a central role in the assembly of the regulatory HrpRSV complex. Deletion analysis of HrpR and HrpS proteins showed that C-terminal parts of HrpR and HrpS confer determinants indispensable for their self-assembly.
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PODCAST: How bacteria turn plants into zombies discussed in TWIM (This Week in Microbiology)

PODCAST: How bacteria turn plants into zombies discussed in TWIM (This Week in Microbiology) | Plants&Bacteria | Scoop.it

"Vincent Racaniello, Elio Schaechter, Michael Schmidt, and Michele Swanson review how a pathogen promotes plant attractiveness to insect vectors, and activation of sensory neurons that modulate pain and inflammation by bacterial infection". Source: http://feeds.feedburner.com/twim


"This Week in Microbiology (TWiM) is a podcast about unseen life on Earth hosted by Vincent Racaniello and friends. Following in the path of his successful shows 'This Week in Virology' (TWiV) and 'This Week in Parasitism' (TWiP), Racaniello and guests produce an informal yet informative conversation about microbes which is accessible to everyone, no matter what their science background". Source: http://www.microbeworld.org/podcasts/this-week-in-microbiology



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Original research article: http://www.nature.com/nature/journal/v508/n7495/full/508152c.html

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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 | Plants&Bacteria | 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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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 | Plants&Bacteria | 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 | Plants&Bacteria | 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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Phylogenetic structure and host abundance drive disease pressure in communities

Phylogenetic structure and host abundance drive disease pressure in communities | Plants&Bacteria | 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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Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite

Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite | Plants&Bacteria | Scoop.it

Authors: Mark McMullan,Anastasia Gardiner,Kate Bailey,Eric Kemen,Ben J Ward,Volkan Cevik,Alexandre Robert-Seilaniantz,Torsten Schultz-Larsen,Alexi Balmuth,Eric Holub,Cock van Oosterhout, Jonathan D G Jones

DOI: http://dx.doi.org/10.7554/eLife.04550

 

Abstract

How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ~1%. Despite this divergence, their genomes are mosaic-like, with ~25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.

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The Clavibacter michiganensis subsp. michiganensis–Tomato Interactome Reveals the Perception of Pathogen by the Host and Suggests Mechanisms of Infection

The Clavibacter michiganensis subsp. michiganensis–Tomato Interactome Reveals the Perception of Pathogen by the Host and Suggests Mechanisms of Infection | Plants&Bacteria | Scoop.it

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes wilt and canker disease of tomato (Solanum lycopersicum). Mechanisms of Cmm pathogenicity and tomato response to Cmm infection are not well understood. To explore the interaction between Cmm and tomato, multidimensional protein identification technology (MudPIT) and tandem mass spectrometry were used to analyze in vitro and in planta generated samples. The results show that during infection Cmm senses the plant environment, transmits signals, induces, and then secretes multiple hydrolytic enzymes, including serine proteases of the Pat-1, Ppa, and Sbt familes, the CelA, XysA, and NagA glycosyl hydrolases, and other cell wall-degrading enzymes. Tomato induction of pathogenesis-related (PR) proteins, LOX1, and other defense-related proteins during infection indicates that the plant senses the invading bacterium and mounts a basal defense response, although partial with some suppressed components including class III peroxidases and a secreted serine peptidase. The tomato ethylene-synthesizing enzyme ACC-oxidase was induced during infection with the wild-typeCmm but not during infection with an endophytic Cmm strain, identifying Cmm-triggered host synthesis of ethylene as an important factor in disease symptom development. The proteomic data were also used to improve Cmm genome annotation, and thousands of Cmm gene models were confirmed or expanded.

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High resolution time-resolved imaging of in vitro Arabidopsis rosette growth

High resolution time-resolved imaging of in vitro Arabidopsis rosette growth | Plants&Bacteria | Scoop.it

Scooped from: The Plant Journal, 2014

Authors:

 

Abstract:

Although the quantitative characterization of growth phenotypes is of key importance for the understanding of essential networks driving plant growth, the majority of growth-related genes is still being identified based on qualitative visual observations and/or single endpoint quantitative measurements. We developed an IGIS, an In vitro Growth Imaging System to perform time-resolved analysis of rosette growth. With this system, Arabidopsis plants are grown in Petri dishes mounted on a rotating disk and pictures from each plate are taken on an hourly basis. Automated image analysis was developed in order to extract several growth-related parameters, such as projected rosette area, rosette relative growth rate, compactness and stockiness, over time. To illustrate the use of the platform and the resulting data, we present the growth response of Col-0 plants subjected to three different mild stress conditions. Although at 19 DAS the reduction in rosette area was relatively similar, the time-lapse analysis demonstrated that plants react differently to salt, osmotic and oxidative stress. Rosette area was altered at different moments during development, but also leaf movement and shape parameters were affected differently. We also used the IGIS to analyze in detail the growth behavior of mutants showing enhanced leaf size. The analysis of several growth-related parameters overtime in these mutants revealed several particularities in growth behavior, underlining the high complexity of leaf growth coordination. These results demonstrate that time-resolved imaging of in vitro rosette growth generates a better understanding of growth phenotypes compared to endpoint measurements.

Freddy Monteiro's insight:

In vitro Growth Imaging System for Arabidopsis development

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Elucidation of a pH-folding switch in the Pseudomonas syringae effector protein AvrPto

Elucidation of a pH-folding switch in the Pseudomonas syringae effector protein AvrPto | Plants&Bacteria | Scoop.it

Scooped from: PNAS, 2009.

Authors: Jennifer E. Dawson, Jolita Šečkutė, Soumya De, Samuel A. Schueler, Aaron B. Oswald and Linda K. Nicholson.

 

Abstract:

Pathogenic bacteria have developed extraordinary strategies for invading host cells. The highly conserved type III secretion system (T3SS) provides a regulated conduit between the bacterial and host cytoplasm for delivery of a specific set of bacterial effector proteins that serve to disrupt host signaling and metabolism for the benefit of the bacterium. Remarkably, the inner diameter of the T3SS apparatus requires that effector proteins pass through in at least a partially unfolded form. AvrPto, an effector protein of the plant pathogen Pseudomonas syringae, adopts a helical bundle fold of low stability (ΔGF→U = 2 kcal/mol at pH 7, 26.6 °C) and offers a model system for chaperone-independent secretion. P. syringae effector proteins encounter a pH gradient as they translocate from the bacterial cytoplasm (mildly acidic) into the host cell (neutral). Here, we demonstrate that AvrPto possesses a pH-sensitive folding switch controlled by conserved residue H87 that operates precisely in the pH range expected between the bacterial and host cytoplasm environments. These results provide a mechanism for how a bacterial effector protein employs an intrinsic pH sensor to unfold for translocation via the T3SS and refold once in the host cytoplasm and provide fundamental insights for developing strategies for delivery of engineered therapeutic proteins to target tissues.


 

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Comparison of the Transcriptomes of Ginger (Zingiber officinale Rosc.) and Mango Ginger (Curcuma amada Roxb.) in Response to the Bacterial Wilt Infection

Comparison of the Transcriptomes of Ginger (Zingiber officinale Rosc.) and Mango Ginger (Curcuma amada Roxb.) in Response to the Bacterial Wilt Infection | Plants&Bacteria | Scoop.it

Scooped from: PLoS One, 2014.

Authors: Duraisamy Prasath, Raveendran Karthika, Naduva Thadath Habeeba, Erinjery Jose Suraby, Ottakandathil Babu Rosana, Avaroth Shaji, Santhosh Joseph Eapen, Uday Deshpande and Muthuswamy Anandaraj

 

Summary:

Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.

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A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis

A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis | Plants&Bacteria | Scoop.it

Scooped from: The Plant Cell 2014
Authors: Radka Slovak, Christian Göschl, Xiaoxue Su, Koji Shimotani, Takashi Shiina and Wolfgang Busch

 

Abstract:

 Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a high-resolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.

Freddy Monteiro's insight:

An impressive set-up that SIGNIFICATIVELY reduces the time of image (root length phenotypes) analysis.

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Comparative analysis of type III secreted effector genes reflects divergence of Acidovorax citrulli strains into three distinct lineages

Comparative analysis of type III secreted effector genes reflects divergence of Acidovorax citrulli strains into three distinct lineages | Plants&Bacteria | Scoop.it

Scooped from: Phytopathology 2014

Authors: Mr. Noam Eckshtain-Levi , Mrs. Tamar Munitz , Miss Marija Živanović , Mr. Sy Mamadou Traore , Mrs. Cathrin Spröer , Prof. Bingyu Zhao , Prof. Gregory Welbaum , Dr. Ron Ricardo Walcott PhD , Dr. Johannes Sikorski and Dr. Saul Burdman

 

Abstract:

Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a serious economic threat to watermelon (Citrullus lanatus) and melon (Cucumis melo) production worldwide. Based on genetic and biochemical traits, A. citrulli strains have been divided into two distinct groups: group I strains have been mainly isolated from various non-watermelon hosts, while group II strains have been generally isolated from and are highly virulent on watermelon. The pathogen depends on a functional type III secretion system (T3SS) for pathogenicity. Annotation of the genome of the group II strain, AAC00-1, revealed eleven genes encoding putative type III secreted (T3S) effectors. Due to the crucial role of type III secretion for A. citrulli pathogenicity, we hypothesized that group I and II strains differ in their T3S effector repertoire. Comparative analysis of the eleven effector genes from a collection of 22 A. citrulli strains confirmed this hypothesis. Moreover, this analysis led to the identification of a third A. citrulli group, which was supported by DNA:DNA hybridization, DNA fingerprinting, multilocus sequence analysis (MLSA) of conserved genes and virulence assays. The effector genes assessed in this study are homologous of effectors from other plant pathogenic bacteria, mainly belonging to Xanthomonas species and Ralstonia solanacearum. Analyses of the effective number of codons and GC content of effector genes relative to a representative set of housekeeping genes support that these effector genes were acquired by lateral gene transfer. Further investigation is required to identify new T3S effectors of A. citrulli and to determine their contribution to virulence and host preferential association.


Image source: http://departments.agri.huji.ac.il/plantpath/burdman/sb-aac.html

Image credit: Dr. Saul Burdman

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