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Rescooped by Jianguang Jia from Phytophthora biology
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Sudden Oak Death plagues local groves

Sudden Oak Death plagues local groves | phytophthora biology | Scoop.it

So far, the organism that causes sudden oak death (SOD) inhabits only about 15 percent of available oak forests, but the problem will likely get worse. People visiting infested areas should not remove leaves or branches, and should clean the dirt from their shoes before leaving, to prevent spreading the pathogen. Oak populations do not have much natural resistance to the disease, and once it arrives in a forest, no one knows how to eradicate it.


Via Niklaus Grunwald
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PLOS ONE: Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity

PLOS ONE: Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity | phytophthora biology | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

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PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum

PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum | phytophthora biology | Scoop.it

Phytophthora plant pathogens contain many hundreds of effectors potentially involved in infection of host plants. Comparative genomic analyses have shown that these effectors evolve rapidly and have been subject to recent expansions. We examined the recent sequence evolution of RXLR-class effector gene families in the sudden oak death pathogen, P. ramorum. We found that P. ramorum RXLR effectors have taken multiple evolutionary paths, including loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations. Sequencing of homologs from two subfamilies in P. ramorum’s closest known relatives revealed repeated gene duplication and divergence since speciation with P. lateralis. One family showed strong signatures of recombination while the other family has evolved primarily by point mutation. Comparison of a small number of the hundreds of RXLR-class effectors across three clonal lineages of P. ramorum shows striking divergence in alleles among lineages, suggesting the potential for functional differences between lineages. Our results suggest future avenues for examination of rapidly evolving effectors in P. ramorum, including investigation of the functional and coevolutionary significance of the patterns of sequence evolution that we observed.


Via Niklaus Grunwald
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Niklaus Grunwald's curator insight, November 8, 2013 4:07 PM

Our paper on evoution of RXLR effectors in the sudden oak death pathogen Phytophthora ramorum describing loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations and more.

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Phytophthora Database

Phytophthora Database | phytophthora biology | Scoop.it

Web-based database on Phytophthora species. Its aim is to provide  a global atlas of the diversity and distribution of Phytophthora species, and ultimately to consitute a global network of scientists and other stakeholders.

 

http://www.phytophthoradb.org/welcome.php?a=intro


Via Anne-Sophie Roy
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Detection of mRNA by reverse-transcription PCR as an indicator of viability in Phytophthora ramorum - Chimento - 2012 - Forest Pathology

Detection of mRNA by reverse-transcription PCR as an indicator of viability in Phytophthora ramorum - Chimento - 2012 - Forest Pathology | phytophthora biology | Scoop.it

In the last few decades, the use of molecular tools has greatly improved the efficiency of plant disease diagnosis. However, one of the major setbacks of most molecular diagnostic approaches is their inability to differentiate between dead and viable pathogens. We propose a new strategy for the detection of plant pathogens, based on the use of mRNA as a viability marker, on the basis that mRNA degradation in dead cells is significantly more rapid than that of DNA. A real-time reverse-transcription PCR (RT-PCR) assay targeting the mRNA of the subunit I of the cytochrome oxidase gene was designed for Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight. In controlled laboratory tests, the developed RT-PCR assay did not detect the target mRNA a week after the pathogen had been killed by rapid lyophilization, while DNA of the pathogen could still be detected 3 months after the pathogen had died. The RT-PCR assay was then compared with a traditional culturing approach using PARP selective medium and two nested real-time PCR techniques on symptomatic California bay laurel leaves. Samples were either collected in three different sites in July, or in the same site but in three different seasons. Overall, RT-PCR results showed less positive samples than DNA-based nested PCR techniques (p < 0.0001), but more than culturing (p = 0.017). Nested PCR-positive but RT-PCR-negative samples may not be viable. On the other hand, RT-PCR-positive but culture-negative samples may be viable but dormant. A comparative analysis of the results indicated that RT-PCR and culturing provide comparable results when climatic conditions are optimal for the pathogen, but RT-PCR may be the most accurate approach to determine pathogen viability when climatic conditions are less than optimal for the pathogen.

 

A. Chimento, S. O. Cacciola and M. Garbelotto 

FOREST PATHOLOGY
Volume 42, Issue 1, February 2012, Pages: 14–21
DOI: 10.1111/j.1439-0329.2011.00717.x


Via Stefano Ghignone
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Oomycetes: Attacking the mediator : Nature Reviews Microbiology : Nature Publishing Group

Oomycetes: Attacking the mediator : Nature Reviews Microbiology : Nature Publishing Group | phytophthora biology | Scoop.it

Plants use a range of mechanisms to respond to challenge by plant pathogens and, in turn, plant pathogens use a range of mechanisms to interfere with and evade these responses. Plant defence responses include those that are mediated by salicylic acid and jasmonic acid–ethylene but, so far, few phytopathogen effectors that interfere with these hormone-based systems have been identified. A study in PLoS Biology now shows that an effector from the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis attenuates the salicylic acid response, thus enhancing biotrophy.

 

Many oomycete effectors contain an amino-terminal RXLR (where X is any amino acid) motif that correlates with entry into host cells. Previous characterization of the RXLR effector repertoire of H. arabidopsidis identified a subset of effectors that localize to the plant cell nucleus and interact with components of the Mediator complex — a multisubunit transcriptional regulation complex that is present in all eukaryotes. In plants, Mediator has been shown to influence key processes, including plant development and, recently, plant immunity.

 

Caillaud and colleagues present an in-depth characterization of one of the H. arabidopsidis RXLR nuclear effectors, HaRxL44, which interacts with the MED19a subunit of the Mediator complex. Analysis of transgenic Arabidopsis thaliana lines showed that those in which MED19a was non-functional were more susceptible than the wild type to infection with H. arabidopsidsis. By contrast, transgenic lines in which MED19a was overproduced were more resistant to infection than the wild type. This indicates that MED19a is a positive regulator of A. thaliana immunity to H. arabidopsidsisinfection. Confocal microscopy to monitor the subcellular localization of MED19a-containing and HaRxL44-containing fusion proteins showed that both localize to the plant nucleolus and nucleoplasm. However, colocalization analysis showed that when HaRxL44 was present in the nucleoplasm MED19a could not be detected. Further investigations revealed that HaRxL44 degrades MED19a in a proteasome-dependent manner.

 

To pinpoint the mechanism by which HaRxL44-mediated MED19a degradation affects the immune response to H. arabidopsidsis infection, the authors used quantitative reverse transcription (qRT)-PCR analysis and gene expression profiling. They found that, in the presence of HaRxL44, marker genes that were consistent with jasmonic acid–ethylene signalling were upregulated, whereas marker genes that were consistent with salicylic acid signalling — which has a key role in the response to biotrophic pathogens — were downregulated. Finally, the authors investigated the cell-specific expression patterns of marker genes that are associated with the salicylic acid response and found that H. arabidopsidsis infection only suppresses the salicylic acid response in those cells that have been parasitized by oomycete haustoria.

 

These data show that the H. arabidopsidsis HaRxL44 effector targets MED19a to modulate the balance between jasmonic acid–ethylene and salicylic acid signalling, such that the salicylic acid response is attenuated and biotrophic infection is favoured. It will be interesting to follow future studies that characterize the functions of the other H. arabidopsidsis RXLR nuclear effectors.

 

References

 

Caillaud, M.-C. et al. A downy mildew effector attenuates salicylic acid-triggered immunity inArabidopsis by interacting with the host mediator complex. PLoS Biol. 11, e1001732 (2013)

PubMed 

 


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PLOS Pathogens: An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus (2013)

PLOS Pathogens: An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus (2013) | phytophthora biology | Scoop.it

The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation. However, little is known about the host targets of these effectors and how they are manipulated by the pathogen. This work describes the identification of two putative membrane-associated NAC transcription factors (TF) as the host targets of the RxLR effector PITG_03192 (Pi03192). The effector interacts with NAC Targeted by Phytophthora (NTP) 1 and NTP2 at the endoplasmic reticulum (ER) membrane, where these proteins are localised. Transcripts of NTP1 and NTP2 rapidly accumulate following treatment with culture filtrate (CF) from in vitro grown P. infestans, which acts as a mixture of Phytophthora PAMPs and elicitors, but significantly decrease during P. infestans infection, indicating that pathogen activity may prevent their up-regulation. Silencing of NTP1 or NTP2 in the model host plant Nicotiana benthamiana increases susceptibility to P. infestans, whereas silencing of Pi03192 in P. infestans reduces pathogenicity. Transient expression of Pi03192 in planta restores pathogenicity of the Pi03192-silenced line. Moreover, colonisation by the Pi03192-silenced line is significantly enhanced on N. benthamiana plants in which either NTP1 or NTP2 have been silenced. StNTP1 and StNTP2 proteins are released from the ER membrane following treatment with P. infestans CF and accumulate in the nucleus, after which they are rapidly turned over by the 26S proteasome. In contrast, treatment with the defined PAMP flg22 fails to up-regulate NTP1 and NTP2, or promote re-localisation of their protein products to the nucleus, indicating that these events follow perception of a component of CF that appears to be independent of the FLS2/flg22 pathway. Importantly, Pi03192 prevents CF-triggered re-localisation of StNTP1 and StNTP2 from the ER into the nucleus, revealing a novel effector mode-of-action to promote disease progression.


Via Kamoun Lab @ TSL, Niklaus Grunwald
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PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs | phytophthora biology | Scoop.it

In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.


Via Niklaus Grunwald
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Real-time PCR to detect Phytophthora kernoviae

Real-time PCR to detect Phytophthora kernoviae | phytophthora biology | Scoop.it

A new diagnostic method for Phytophthora kernoviae:

 

Hughes KJD, Tomlinson JA, Giltrap PM, Barton V, Hobden E, Boonham N, Lane CR (2011) Development of a real-time PCR assay for detection of Phytophthora kernoviae and comparison of this method with a conventional culturing technique. European Journal of Plant Pathology.

 

http://www.springerlink.com/content/al767565vh6r8745/

 

 This test is included in the draft EPPO diagnosic protocol for Phytophthora kernoviae currently under country consultation

 


Via Petter Françoise
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