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Rescooped by Shaikhul Islam from Plants and Microbes
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Frontiers: Effector proteins of rust fungi (2014)

Frontiers: Effector proteins of rust fungi (2014) | Molecular Biology and Life Science | Scoop.it

Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1 and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.


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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport

Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport | Molecular Biology and Life Science | Scoop.it
Potassium (K+) is one of the most abundant elements of soil composition but its very low availability limits plant growth and productivity of ecosystems. Because this cation participates in many biological processes, its constitutive uptake from soil solution is crucial for the plant cell machinery. Thus, the understanding of strategies responsible of K+ nutrition is a major issue in plant science. Mycorrhizal associations occurring between roots and hyphae of underground fungi improve hydro-mineral nutrition of the majority of terrestrial plants. The contribution of this mutualistic symbiosis to the enhancement of plant K+ nutrition is not well understood and poorly studied so far. This mini-review examines the current knowledge about the impact of both arbuscular mycorrhizal and ectomycorrhizal symbioses on the transfer of K+ from the soil to the plants. A model summarizing plant and fungal transport systems identified and hypothetically involved in K+ transport is proposed. In addition, some data related to benefits for plants provided by the improvement of K+ nutrition thanks to mycorrhizal symbioses are presented.

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Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis

Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis | Molecular Biology and Life Science | Scoop.it

Most land plant species live in symbiosis with arbuscular mycorrhizal (AM) fungi. These fungi differentiate essential functional structures called arbuscules in root cortical cells from which mineral nutrients are released to the plant. We investigated the role of miR393, a microRNA that targets several auxin receptors, in AM root colonization. Expression of the precursors of the miR393 was down-regulated during mycorrhization in three different plant species: Solanum lycopersicum (Solanaceae), Medicago truncatula (Fabaceae) and Oryza sativa (Poaceae). Treatment of S. lycopersicum, M. truncatula and O. sativa roots with concentration of synthetic auxin analogs that did not affect root development, stimulated mycorrhization, particularly arbuscule formation. DR5-GUS, a reporter for auxin response, was preferentially expressed in root cells containing arbuscules. Finally, overexpression of miR393 in root tissues resulted in downregulation of auxin receptor genes (TIR1, AFB) and in under-developed arbuscules in all three plant species. These results support the conclusion that miR393 is a negative regulator of arbuscule formation by hampering auxin perception in arbuscule-containing cells.


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Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport

Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport | Molecular Biology and Life Science | Scoop.it
Potassium (K+) is one of the most abundant elements of soil composition but its very low availability limits plant growth and productivity of ecosystems. Because this cation participates in many biological processes, its constitutive uptake from soil solution is crucial for the plant cell machinery. Thus, the understanding of strategies responsible of K+ nutrition is a major issue in plant science. Mycorrhizal associations occurring between roots and hyphae of underground fungi improve hydro-mineral nutrition of the majority of terrestrial plants. The contribution of this mutualistic symbiosis to the enhancement of plant K+ nutrition is not well understood and poorly studied so far. This mini-review examines the current knowledge about the impact of both arbuscular mycorrhizal and ectomycorrhizal symbioses on the transfer of K+ from the soil to the plants. A model summarizing plant and fungal transport systems identified and hypothetically involved in K+ transport is proposed. In addition, some data related to benefits for plants provided by the improvement of K+ nutrition thanks to mycorrhizal symbioses are presented.

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Rescooped by Shaikhul Islam from Plants and Microbes
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Frontiers: Effector proteins of rust fungi (2014)

Frontiers: Effector proteins of rust fungi (2014) | Molecular Biology and Life Science | Scoop.it

Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1 and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.


Via Kamoun Lab @ TSL
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Rescooped by Shaikhul Islam from Plants and Microbes
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F1000Prime Recommended Article: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

F1000Prime Recommended Article: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Molecular Biology and Life Science | Scoop.it

This paper is an excellent demonstration of the power of phylogenomics for the discovery of genes involved in traits of interest. 


The authors report a larger scale genome comparison between symbiotic (arbuscular mycorrhiza forming) and non-symbiotic plant groups. They identify gene loss in plant species that go back to a minimum of four independent loss-of-symbiosis events; one in the Brassicales, one in the Caryophyllales (Amaranthaceae), one in the Laminales (Orobanchaceae) and one in the Fabales (Lupinus). 

They performed an impressive phylogenomic analysis and identified a list of 300 Medicago genes that are present in most of the analyzed species but absent in all non-symbiotic Brassicaceae. Upon filtering the list further, by including paraphyletic non-symbiotic species, they arrived at a list of around 100 genes that were consistently absent in the non-mycorrhizal species. Lupinus as a plant that lost arbuscular mycorrhiza but maintained root nodule symbiosis was very informative because common symbiosis genes should be maintained in this genus. 

The results are consistent with an evolutionary scenario in which each of the independent loss-of-symbiosis events, for which the loss of a single gene function was sufficient, was followed by a subsequent larger scale gene erosion that consistently removed the same orthologous genes in the four different clades. 

This very interesting and largely unexpected observation reveals two opposing evolutionary forces that decide over the prevalence of this 'symbiosis-associated' gene set. On the one hand, the existing symbiosis leads to a successful maintenance of symbiosis genes. On the other hand, a yet unidentified force resulted in a consistent pattern of larger scale gene loss after each independent loss-of-symbiosis event. The forces behind this erosion must have acted either very quickly, before each of the non-symbiotic clades diversified from their respective common ancestor, or they independently led to consistent gene loss patterns after speciation. 

Because symbiosis-related genes are overrepresented in the eroded gene set, it is likely that a large proportion, if not all of them, are of specific functional relevance in arbuscular mycorrhization (AM). Therefore this study is of major importance not only from an evolutionary perspective, but also because it demonstrates a novel strategy to identify candidate genes involved in AM symbiosis.

 

By Martin Parniske, F1000 Plant Biology, Biocenter University of Munich (LMU), Martinsried, Germany.

 

Disclosures - Martin Parniske has published a joint paper with the corresponding author in 2012.
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Rescooped by Shaikhul Islam from Downy mildew pathogens
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454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif

454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif | Molecular Biology and Life Science | Scoop.it

Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensisgenomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. Using bioinformatics approaches, we identified 32 putative RXLR effector proteins. Interestingly, we also identified 29 secreted peptides with high similarity to RXLR effectors at the N-terminal translocation domain, yet containing an R-to-Q substitution in the first residue of the translocation motif. Among these, a family of QXLR-containing proteins, designated as PcQNE, was confirmed to have a functional signal peptide and was further characterized as being localized in the plant nucleus. Internalization of secreted PcQNE into plant cells requires the QXLR-EER motif. This family has a large number of near-identical copies within the P. cubensis genome, is under diversifying selection at the C-terminal domain, and is upregulated during infection of plants, all of which are common characteristics of characterized oomycete effectors. Taken together, the data suggest that PcQNE are bona fide effector proteins with a QXLR translocation motif, and QXLR effectors are prevalent in P. cubensis. Furthermore, the massive duplication ofPcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity.


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Rescooped by Shaikhul Islam from Plants and Microbes
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New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014)

New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014) | Molecular Biology and Life Science | Scoop.it

Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.


Via Kamoun Lab @ TSL
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Marie Zen Attitude's curator insight, July 26, 5:21 AM

Un petit lien spécial pour Emeric ;)

 

Rescooped by Shaikhul Islam from Plant-Microbe Symbioses
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Microorganism and filamentous fungi drive evolution of plant synapses

In the course of plant evolution, there is an obvious trend toward an increased complexity of plant bodies, as well as an increased sophistication of plant behavior and communication. Phenotypic plasticity of plants is based on the polar auxin transport machinery that is directly linked with plant sensory systems impinging on plant behavior and adaptive responses. Similar to the emergence and evolution of eukaryotic cells, evolution of land plants was also shaped and driven by infective and symbiotic microorganisms. These microorganisms are the driving force behind the evolution of plant synapses and other neuronal aspects of higher plants; this is especially pronounced in the root apices. Plant synapses allow synaptic cell-cell communication and coordination in plants, as well as sensory-motor integration in root apices searching for water and mineral nutrition. These neuronal aspects of higher plants are closely linked with their unique ability to adapt to environmental changes.

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Rescooped by Shaikhul Islam from Transport in plants and fungi
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The role of mycorrhizal associations in plant potassium nutrition

Potassium (K+) is one of the most abundant elements of soil composition but its very low availability limits plant growth and productivity of ecosystems. Because this cation participates in many biological processes, its constitutive uptake from soil solution is crucial for the plant cell machinery. Thus, the understanding of strategies responsible of K+ nutrition is a major issue in plant science. Mycorrhizal associations occurring between roots and hyphae of underground fungi improve hydro-mineral nutrition of the majority of terrestrial plants. The contribution of this mutualistic symbiosis to the enhancement of plant K+ nutrition is not well understood and poorly studied so far. This mini-review examines the current knowledge about the impact of both arbuscular mycorrhizal and ectomycorrhizal symbioses on the transfer of K+ from the soil to the plants. A model summarizing plant and fungal transport systems identified and hypothetically involved in K+ transport is proposed. In addition, some data related to benefits for plants provided by the improvement of K+ nutrition thanks to mycorrhizal symbioses are presented.


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Jean-Michel Ané's curator insight, June 26, 7:54 AM

Good job Kevin!

Rescooped by Shaikhul Islam from MycorWeb Plant-Microbe Interactions
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XVI International Congress on Molecular Plant-Microbe Interactions, Rhodes, Greece, 6-10 July 2014

XVI International Congress on Molecular Plant-Microbe Interactions, Rhodes, Greece, 6-10 July 2014 | Molecular Biology and Life Science | Scoop.it

Via Kamoun Lab @ TSL, Jean-Michel Ané, Francis Martin
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Jean-Michel Ané's curator insight, May 28, 5:52 AM

I can't wait for this conference!

Christophe Jacquet's comment, May 28, 7:15 AM
See you there!
Mary Williams's curator insight, May 29, 1:30 AM

Looks like a super conference, great poster too!


Rescooped by Shaikhul Islam from Plant-Microbe Symbioses
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Spatially robust estimates of biological nitrogen (N) fixation imply substantial human alteration of the tropical N cycle

Spatially robust estimates of biological nitrogen (N) fixation imply substantial human alteration of the tropical N cycle | Molecular Biology and Life Science | Scoop.it

Biological nitrogen fixation (BNF) is the largest natural source of exogenous nitrogen (N) to unmanaged ecosystems and also the primary baseline against which anthropogenic changes to the N cycle are measured. Rates of BNF in tropical rainforest are thought to be among the highest on Earth, but they are notoriously difficult to quantify and are based on little empirical data. We adapted a sampling strategy from community ecology to generate spatial estimates of symbiotic and free-living BNF in secondary and primary forest sites that span a typical range of tropical forest legume abundance. Although total BNF was higher in secondary than primary forest, overall rates were roughly five times lower than previous estimates for the tropical forest biome. We found strong correlations between symbiotic BNF and legume abundance, but we also show that spatially free-living BNF often exceeds symbiotic inputs. Our results suggest that BNF in tropical forest has been overestimated, and our data are consistent with a recent top-down estimate of global BNF that implied but did not measure low tropical BNF rates. Finally, comparing tropical BNF within the historical area of tropical rainforest with current anthropogenic N inputs indicates that humans have already at least doubled reactive N inputs to the tropical forest biome, a far greater change than previously thought. Because N inputs are increasing faster in the tropics than anywhere on Earth, both the proportion and the effects of human N enrichment are likely to grow in the future.


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Rescooped by Shaikhul Islam from Plant-Microbe Symbioses
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Phosphate solubilization potential and modeling of stress tolerance of rhizobacteria from rice paddy soil in northern Iran

The purposes of this study were to evaluate the phosphate solubilization activity of bacteria isolated from the rhizosphere of rice paddy soil in northern Iran, and to study the effect of temperature, NaCl and pH on the growth of these isolates by modeling. Three of the most effective strains from a total of 300 isolates were identified and a phylogenetic analysis was carried out by 16S rDNA sequencing. The isolates were identified as Pantoea ananatis (M36), Rahnella aquatilis (M100) andEnterobacter sp. (M183). These isolates showed multiple plant growth-promoting attributes such as phosphate solubilization activity and indole-3-acetic acid (IAA) production. The M36, M100 and M183 isolates were able to solubilize 172, 263 and 254 µg ml−1 of Ca3(PO4)2 after 5 days of growth at 28 °C and pH 7.5, and to produce 8.0, 2.0 and 3.0 μg ml−1 of IAA when supplemented with l-tryptophan (1 mg ml−1) for 72 h, at 28 °C and pH 7.0, respectively. The solubilization of insoluble phosphate was associated with a drop in the pH of the culture medium and there was an inverse relationship between pH and solubilized P (r = −0.98, P < 0.0952). There were no significant differences among isolates in terms of acidity tolerance based on their confidence limits as assessed by segmented model analysis and all isolates were able to grow at pH 4.3–11 (with optimum at 7.0–7.5). Based on a sigmoidal trend of a three-parameter logistic model, the salt concentration required for 50 % inhibition was 8.15, 6.30 and 8.23 % NaCl for M36, M100 and M183 isolates, respectively. Moreover, the minimum and maximum growth temperatures estimated by the segmented model were 5.0 and 42.75 °C for M36, 12.76 and 40.32 °C for M100, and 10.63 and 43.66 °C for M183. The three selected isolates could be deployed as inoculants to promote plant growth in an agricultural environment.


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Rescooped by Shaikhul Islam from Plants and Microbes
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New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014)

New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014) | Molecular Biology and Life Science | Scoop.it

Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.


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Marie Zen Attitude's curator insight, July 26, 5:21 AM

Un petit lien spécial pour Emeric ;)

 

Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Streptomyces-Induced Resistance Against Oak Powdery Mildew Involves Host Plant Responses in Defense, Photosynthesis, and Secondary Metabolism Pathways

Streptomyces-Induced Resistance Against Oak Powdery Mildew Involves Host Plant Responses in Defense, Photosynthesis, and Secondary Metabolism Pathways | Molecular Biology and Life Science | Scoop.it

Rhizobacteria are known to induce defense responses in plants without causing disease symptoms, resulting in increased resistance to plant pathogens. This study investigated how Streptomyces sp. strain AcH 505 suppressed oak powdery mildew infection in pedunculate oak, by analyzing RNA-Seq data from singly- and co-inoculated oaks. We found that this Streptomyces strain elicited a systemic defense response in oak that was, in part, enhanced upon pathogen challenge. In addition to induction of the jasmonic acid/ethylene–dependent pathway, the RNA-Seq data suggests the participation of the salicylic acid–dependent pathway. Transcripts related to tryptophan, phenylalanine, and phenylpropanoid biosynthesis were enriched and phenylalanine ammonia lyase activity increased, indicating that priming by Streptomyces spp. in pedunculate oak shares some determinants with the Pseudomonas-Arabidopsis system. Photosynthesis-related transcripts were depleted in response to powdery mildew infection, but AcH 505 alleviated this inhibition, which suggested there is a fitness benefit for primed plants upon pathogen challenge. This study offers novel insights into the mechanisms of priming by actinobacteria and highlights their capacity to activate plant defense responses in the absence of pathogen challenge.


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A comparison study of Agrobacterium-mediated transformation methods for root-specific promoter analysis in soybean - Springer

A comparison study of Agrobacterium-mediated transformation methods for root-specific promoter analysis in soybean - Springer | Molecular Biology and Life Science | Scoop.it

Key message

Both in vitro and in vivo hairy root transformation systems could not replace whole plant transformation for promoter analysis of root-specific and low-P induced genes in soybean.

Abstract

An efficient genetic transformation system is crucial for promoter analysis in plants. Agrobacterium-mediated transformation is the most popular method to produce transgenic hairy roots or plants. In the present study, first, we compared the two different Agrobacterium rhizogenes-mediated hairy root transformation methods using either constitutive CaMV35S or the promoters of root-preferential genes, GmEXPB2 and GmPAP21, in soybean, and found the efficiency of in vitro hairy root transformation was significantly higher than that of in vivo transformation. We compared Agrobacterium rhizogenes-mediated hairy root and Agrobacterium tumefaciens-mediated whole plant transformation systems. The results showed that low-phosphorous (P) inducible GmEXPB2 and GmPAP21 promoters could not induce the increased expression of the GUS reporter gene under low P stress in both in vivo and in vitro transgenic hairy roots. Conversely, GUS activity of GmPAP21 promoter was significantly higher at low P than high P in whole plant transformation. Therefore, both in vitro and in vivo hairy root transformation systems could not replace whole plant transformation for promoter analysis of root-specific and low-P induced genes in soybean.


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Rescooped by Shaikhul Islam from Plant-microbe interactions (on the plant's side)
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Pattern Triggered Immunity (PTI) in Tobacco: Isolation of Activated Genes Suggests Role of the Phenylpropanoid Pathway in Inhibition of Bacterial Pathogens

Pattern Triggered Immunity (PTI) in Tobacco: Isolation of Activated Genes Suggests Role of the Phenylpropanoid Pathway in Inhibition of Bacterial Pathogens | Molecular Biology and Life Science | Scoop.it

Background

 

Pattern Triggered Immunity (PTI) or Basal Resistance (BR) is a potent, symptomless form of plant resistance. Upon inoculation of a plant with non-pathogens or pathogenicity-mutant bacteria, the induced PTI will prevent bacterial proliferation. Developed PTI is also able to protect the plant from disease or HR (Hypersensitive Response) after a challenging infection with pathogenic bacteria. Our aim was to reveal those PTI-related genes of tobacco (Nicotiana tabacum) that could possibly play a role in the protection of the plant from disease.

Methodology/Principal Findings

 

Leaves were infiltrated with Pseudomonas syringae pv. syringae hrcC- mutant bacteria to induce PTI, and samples were taken 6 and 48 hours later. Subtraction Suppressive Hybridization (SSH) resulted in 156 PTI-activated genes. A cDNA microarray was generated from the SSH clone library. Analysis of hybridization data showed that in the early (6 hpi) phase of PTI, among others, genes of peroxidases, signalling elements, heat shock proteins and secondary metabolites were upregulated, while at the late phase (48 hpi) the group of proteolysis genes was newly activated. Microarray data were verified by real time RT-PCR analysis. Almost all members of the phenyl-propanoid pathway (PPP) possibly leading to lignin biosynthesis were activated. Specific inhibition of cinnamic-acid-4-hydroxylase (C4H), rate limiting enzyme of the PPP, decreased the strength of PTI - as shown by the HR-inhibition and electrolyte leakage tests. Quantification of cinnamate and p-coumarate by thin-layer chromatography (TLC)-densitometry supported specific changes in the levels of these metabolites upon elicitation of PTI.

Conclusions/Significance

 

We believe to provide first report on PTI-related changes in the levels of these PPP metabolites. Results implicated an actual role of the upregulation of the phenylpropanoid pathway in the inhibition of bacterial pathogenic activity during PTI.


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PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Molecular Biology and Life Science | Scoop.it

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


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PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Molecular Biology and Life Science | Scoop.it

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


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Rescooped by Shaikhul Islam from Downy mildew pathogens
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The cucurbit downy mildew pathogen Pseudoperonospora cubensis

The cucurbit downy mildew pathogen Pseudoperonospora cubensis | Molecular Biology and Life Science | Scoop.it

Pseudoperonospora cubensis[(Berkeley & M. A. Curtis) Rostovzev], the causal agent of cucurbit downy mildew, is responsible for devastating losses worldwide of cucumber, cantaloupe, pumpkin, watermelon and squash. Although downy mildew has been a major issue in Europe since the mid-1980s, in the USA, downy mildew on cucumber has been successfully controlled for many years through host resistance. However, since the 2004 growing season, host resistance has been effective no longer and, as a result, the control of downy mildew on cucurbits now requires an intensive fungicide programme. Chemical control is not always feasible because of the high costs associated with fungicides and their application. Moreover, the presence of pathogen populations resistant to commonly used fungicides limits the long-term viability of chemical control. This review summarizes the current knowledge of taxonomy, disease development, virulence, pathogenicity and control of Ps. cubensis. In addition, topics for future research that aim to develop both short- and long-term control measures of cucurbit downy mildew are discussed.


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Abundance and Diversity of Soybean Nodulating Rhizobia in Black Soil are Impacted by Land Use and Crop Managements

To investigate the effects of land use and crop managements on the soybean rhizobia communities, 280 nodule isolates were trapped from 7 fields with different land use and culturing histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) distributed widely in all treatments, while Bradyrhizobium sp. II was only found in GL treatment. Cultivation with soybean increased the rhizobial abundance and diversity, except for the soybean-monoculture (S-S) treatment. In monoculture systems, soybean favored Bradyrhizobium sp. I, while maize and wheat favoredBradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes, but did not change the species composition. The content of organic carbon (OC), available phosphorus (AP) and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I, II and B. japonicum, and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land use and crop managements could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and plants of legumes or non-legumes, which offered novel information for the biogeography of rhizobia.


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Rescooped by Shaikhul Islam from Rhizobium Research
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Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field | Molecular Biology and Life Science | Scoop.it

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

  Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K (2014). PLoS One. Jun 23;9(6):e100709.


Via IvanOresnik
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Interactions between the jasmonic and salicylic acid pathway modulate the plant metabolome and affect herbivores of different feeding types

Interactions between the jasmonic and salicylic acid pathway modulate the plant metabolome and affect herbivores of different feeding types | Molecular Biology and Life Science | Scoop.it

The phytohormones jasmonic acid (JA) and salicylic acid (SA) mediate induced plant defences and the corresponding pathways interact in a complex manner as has been shown on the transcript and proteine level. Downstream, metabolic changes are important for plant–herbivore interactions. This study investigated metabolic changes in leaf tissue and phloem exudates of Plantago lanceolataafter single and combined JA and SA applications as well as consequences on chewing-biting (Heliothis virescens) and piercing-sucking (Myzus persicae) herbivores. Targeted metabolite profiling and untargeted metabolic fingerprinting uncovered different categories of plant metabolites, which were influenced in a specific manner, indicating points of divergence, convergence, positive crosstalk and pronounced mutual antagonism between the signaling pathways. Phytohormone-specific decreases of primary metabolite pool sizes in the phloem exudates may indicate shifts in sink–source relations, resource allocation, nutrient uptake or photosynthesis. Survival of both herbivore species was significantly reduced by JA and SA treatments. However, the combined application of JA and SA attenuated the negative effects at least against H. virescens suggesting that mutual antagonism between the JA and SA pathway may be responsible. Pathway interactions provide a great regulatory potential for the plant that allows triggering of appropriate defences when attacked by different antagonist species.


Via Francis Martin
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The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes | Molecular Biology and Life Science | Scoop.it

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, andPhytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.


Via Francis Martin
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Biswapriya Biswavas Misra's curator insight, June 4, 7:57 PM

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, andPhytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.

Rescooped by Shaikhul Islam from Plant-Microbe Symbioses
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Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants | Molecular Biology and Life Science | Scoop.it

Microbial communities in plant roots provide critical links between above and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities we designed a trap-plant bioassay experiment. Replicate Populus, Quercus, and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of 4 loci (i.e. 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.

  


Via Stéphane Hacquard, Francis Martin, Jean-Michel Ané
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