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Nature Reviews Microbiol: Genome evolution in filamentous plant pathogens: why bigger can be better (2012)

Nature Reviews Microbiol: Genome evolution in filamentous plant pathogens: why bigger can be better (2012) | Publications | Scoop.it

Many species of fungi and oomycetes are plant pathogens of great economic importance. Over the past 7 years, the genomes of more than 30 of these filamentous plant pathogens have been sequenced, revealing remarkable diversity in genome size and architecture. Whereas the genomes of many parasites and bacterial symbionts have been reduced over time, the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansions. In these lineages, the genes encoding proteins involved in host interactions are frequently polymorphic and reside within repeat-rich regions of the genome. Here, we review the properties of these adaptable genome regions and the mechanisms underlying their plasticity, and we illustrate cases in which genome plasticity has contributed to the emergence of new virulence traits. We also discuss how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts.

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Horizon: Can CRISPR feed the world? (2017)

Horizon: Can CRISPR feed the world? (2017) | Publications | Scoop.it

Scientists want to edit the genes of potatoes and wheat.

 

As the world’s population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

 

By 2040, there will be 9 billion people in the world. ‘That’s like adding another China onto today’s global population,’ said Professor Sophien Kamoun of the Sainsbury Laboratory in Norwich, UK.

 

Prof. Kamoun is one of a growing number of food scientists trying to figure out how to feed the world. As an expert in plant pathogens such as Phytophthora infestans – the fungus-like microbe responsible for potato blight – he wants to make crops more resistant to disease.

 

Potato blight sparked the Irish famine in the 19th century, causing a million people to starve to death and another million migrants to flee. European farmers now keep the fungus in check by using pesticides. However, in regions without access to chemical sprays, it continues to wipe out enough potatoes to feed hundreds of millions of people every year.

 

‘Potato blight is still a problem,’ said Prof. Kamoun. ‘In Europe, we use 12 chemical sprays per season to manage the pathogen that causes blight, but other parts of the world cannot afford this.’

 

Plants try to fight off the pathogens that cause disease but these are continuously changing to evade detection by the plant’s immune system.

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Wired: Who Wants Disease-Resistant GM Tomatoes? Probably Not Europe (2017)

Wired: Who Wants Disease-Resistant GM Tomatoes? Probably Not Europe (2017) | Publications | Scoop.it

ENGINEERING A TOMATO resistant to a pernicious fungal disease doesn’t seem like it’d be the easiest part of a plant pathologist’s job. But compared to getting that tomato to market? It’s a snap.


At least, that’s how Sophien Kamoun sees it. Kamoun studies plant diseases at the Sainsbury Laboratory in England, and in March his team published a paper describing a tomato they’d tweaked. Using the gene-editing technique Crispr/Cas9, Kamoun’s group snipped out a piece of a gene called Mildew Resistant Locus O, or Mlo. That deletion makes the tomato resistant to powdery mildew, a serious agricultural problem that takes a lot of chemicals to control.


Kamoun’s “Tomelo” actually looks a lot like a naturally occurring tomato, a mutant with the same resistance. “At least in the tomato plants we have, there was no detectable difference between the mutant and the wild type,” Kamoun says. “Obviously we’d need to do more detailed field trials, but there was certainly nothing obvious.”


But for now, that’s where Kamoun’s work stops. European regulations make the tomato essentially illegal—he and others can do the science, but probably can’t get it to field trials, and certainly can’t get it to market. “There’s more clarity in the US. One could probably get approval. But in Europe, it’s a big question mark,” he says. “I’m very frustrated by this, I have to be honest. Scientifically this plant is no different from any mutant we’d get from traditional breeding or traditional mutagenesis. I really don’t understand what the problem is.”


If you’re wondering how agriculture is going to feed 10 billion people on a climatically chaotic, hotter, more disaster-prone planet, you might not understand the problem, either.

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Marcus Jansen's curator insight, May 3, 10:24 AM
Great work, this plant has potential to avoid pesticide applications. It is good for the Environment, let's hope that European regulation authorities understand this.
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Video: European Research Council@10: the impact on science and scientists (2017)

Scientists at the John Innes Centre and The Sainsbury Laboratory reflect on the success of the ERC over the last ten years and the impact that ERC grant

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Scientific Reports: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017)

Scientific Reports: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017) | Publications | Scoop.it

Genome editing has emerged as a technology with a potential to revolutionize plant breeding. In this study, we report on generating, in less than ten months, Tomelo, a non-transgenic tomato variety resistant to the powdery mildew fungal pathogen using the CRISPR/Cas9 technology. We used whole-genome sequencing to show that Tomelo does not carry any foreign DNA sequences but only carries a deletion that is indistinguishable from naturally occurring mutations. We also present evidence for CRISPR/Cas9 being a highly precise tool, as we did not detect off-target mutations in Tomelo. Using our pipeline, mutations can be readily introduced into elite or locally adapted tomato varieties in less than a year with relatively minimal effort and investment.

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bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017)

bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017) | Publications | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012, Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013, Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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Phil. Trans. R. Soc. B: Emerging oomycete threats to plants and animals (2016)

Phil. Trans. R. Soc. B: Emerging oomycete threats to plants and animals (2016) | Publications | Scoop.it

Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans , Phytophthora palmivora , Phytophthora ramorum , Plasmopara obducens , and the animal pathogens Aphanomyces invadans , Saprolegnia parasitica and Halioticida noduliformans . For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.

This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

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BBC News: Four good things that happened in 2016

BBC News: Four good things that happened in 2016 | Publications | Scoop.it

A lot has gone wrong this year. We don't mean Brexit or the election of Donald Trump, both of which split opinion in Britain and the US.

 

We mean the thousands of migrants who died in the Med, the war in Syria, Zika virus, terror attacks all over the world, the hottest temperatures ever recorded. And, as if all that wasn't bad enough, David Bowie died.

 

So from the BBC World Service Inquiry programme here are four things that went right in 2016 from the perspective of four people who helped make them happen.

 

Four stories united by just one thing: the ambition to achieve the seemingly impossible.

 

Gene editing

 

Professor Sophien Kamoun is a plant biologist from Tunisia. He has always been interested in plant diseases, particularly after seeing the devastating effects of pesticides in developing countries.

 

Every year, thousands die after using pesticides on diseased crops. What if you could create a type of plant that doesn't get diseases?

 

That's what Sophien Kamoun has been experimenting with in his lab at Norwich University, using a new technique invented in the US that came of age this year - gene editing. It allows scientists to modify the genes of living things like plants.

 

Professor Kamoun experimented with editing the genes of a tomato plant so that it would no longer be susceptible to a particular disease.

 

First they isolated the gene that makes the tomato vulnerable to that disease. Then they removed the gene from the genome of the tomato. "And it became resilient to the fungal disease," he says.

 

Gene editing is an incredibly powerful tool. There are real concerns about how such a technology could be used, but regulate it properly, and you could change the way we feed the world.

 

"Every year we lose enough food to feed hundreds of millions of people to pathogens and parasites," he says. "If we could make some of our crops more resilient, then that would be an unique achievement."

 

It is not only plant biologists who are experimenting with gene editing: doctors are using it to reverse the mutations that cause blindness, to stop cancer cells from multiplying and to make cells resistant to the virus that causes AIDS.

 

It is why some have called gene editing the invention of the century.

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BBC World Service - The Inquiry: What Went Right in 2016?

BBC World Service - The Inquiry: What Went Right in 2016? | Publications | Scoop.it

What Went Right in 2016?

 

A lot has gone wrong this year. We’re not talking about Brexit or the election of Donald Trump – both of which split opinion in Britain and the US – we’re talking about terror attacks, the brutal conflict in Syria, and the thousands of migrants who died trying to reach Europe.

 

Good things did happen. But the good news was mostly buried under the bad. So for this edition of The Inquiry – our final show of the year – we wanted to find about four things that went right in 2016. And we wanted to talk to the people who made those things happen. That’s it.

 

Four amazing stories united by one thing: the ambition of a small number of extraordinary people to achieve the seemingly impossible.

 

Presenter: Helena Merriman

 

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BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016)

BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016) | Publications | Scoop.it

Background. In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields.

Results. Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.

Conclusion. Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

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JBC: Structural basis of host Autophagy-related protein 8 (ATG8) binding by the Irish potato famine pathogen effector protein PexRD54 (2016)

JBC: Structural basis of host Autophagy-related protein 8 (ATG8) binding by the Irish potato famine pathogen effector protein PexRD54 (2016) | Publications | Scoop.it

Filamentous plant pathogens deliver effector proteins to host cells to promote infection. The Phytophthora infestans RXLR-type effector PexRD54 binds potato ATG8 via its ATG8-family interacting motif (AIM) and perturbs host selective autophagy. However, the structural basis of this interaction remains unknown. Here we define the crystal structure of PexRD54, which comprises a modular architecture including five tandem repeat domains, with the AIM sequence presented at the disordered C-terminus. To determine the interface between PexRD54 and ATG8, we solved the crystal structure of potato ATG8CL in complex with a peptide comprising the effectors AIM sequence, and established a model of the full-length PexRD54/ATG8CL complex using small angle X-ray scattering. Structure-informed deletion of the PexRD54 tandem domains reveals retention of ATG8CL binding in vitro and in planta. This study offers new insights into structure/function relationships of oomycete RXLR effectors and how these proteins engage with host cell targets to promote disease.

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Plantae: I'm Plant Pathologist Sophien Kamoun, And this is how I work (2016)

Plantae: I'm Plant Pathologist Sophien Kamoun, And this is how I work (2016) | Publications | Scoop.it

Location: Norwich, United Kingdom
Current job/title: Senior Group Leader
One word that describes how you work: Starbucks
Favorite thing you do at work: Tweet
Favorite plant: “benth” aka Nicotiana benthamiana 
One interesting project you have been working on: Open wheat blast http://wheatblast.net

I studied genetics at Pierre and Marie Curie University in Paris and UC Davis, before working at Wageningen University, The Ohio State University, and The Sainsbury Laboratory (TSL) where I served as Head from 2009-2014. At TSL, my group studies several aspects of plant-pathogen interactions, ranging from genome-level analyses to mechanistic research focused on individual proteins. Our projects are driven by some of the major questions in the field: How do plant pathogens evolve? How do they adapt and specialize on their hosts? How do plant pathogen effectors co-opt host processes? One aim is to narrow the gap between mechanistic and evolutionary research by testing specific hypotheses about how evolution has shaped molecular mechanisms of pathogenicity and immunity.
 
*What is your workspace setup like?
 
A standing desk surrounded by piles of papers and stuff, or a sofa in some coffee shop.
 
*What are some tools, apps, or websites that you use or visit every day? Do you have a favorite resource?
 
Twitter has become the primary source for all knowledge.
 
If a magical scientific genie appeared from an erlenmeyer flask in your lab, what would you ask for?
 
3D structures of protein complexes. Loads of them!
 
*What have been the biggest productivity tools you’ve been using either for a long time or recently adopted?
 
Typing or dictating notes on my phone and being able to do so at any time.
 
*What’s some of the best advice you’ve ever received? 
 
Never worry about things you cannot control.
 
*What’s the best thing you’ve ever learned? 
 
Doing some basic bioinformatics on my MacBook.
 
*Music, silence, white noise - what works for you?
 
Music! My zen playlist.
 
What do you do when the pipette is down and the computer is powered off?
 
Travel, food, and sports.
 
*What do you spend time thinking about that’s not your next proposal, publication, or project deadline?
 
I’m really excited about the travel plans for this summer.
 
Plant biology has long been a field of pioneering discoveries with broad impacts. What’s the next pioneering discovery in plant biology?
 
Synthetic immune receptors.
 
*If you’re OK sharing, what’s one way readers can get in touch or follow along with your work (email, blog, twitter, etc.)? 

Kamoun Lab Web Site http://www.kamounlab.net
Twitter @KamounLab http://twitter.com/kamounlab
Twitter DM.

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You Can Call Me Al (Parody by an Albugo)

An Albugo sings about its relationships with some unwilling (and o occasionally willing) partners. Lyrics by Sophien Kamoun, performed by Jon Baker, inspired by "You Can Call Me Al" by Paul Simon.

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bioRxiv: The potato NLR immune receptor R3a does not contain non-canonical integrated domains (2016)

bioRxiv: The potato NLR immune receptor R3a does not contain non-canonical integrated domains (2016) | Publications | Scoop.it

A recent study by Kroj et al. (New Phytologist, 2016) surveyed nucleotide binding-leucine rich repeat (NLR) proteins from plant genomes for the presence of extraneous integrated domains that may serve as decoys or sensors for pathogen effectors. They reported that a FAM75 domain of unknown function occurs near the C-terminus of the potato late blight NLR protein R3a. Here, we investigated in detail the domain architecture of the R3a protein, its potato paralog R3b, and their tomato ortholog I2. We conclude that the R3a, R3b, and I2 proteins do not carry additional domains besides the classic NLR modules, and that the FAM75 domain match is likely a false positive among computationally predicted NLR-integrated domains.

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BMC Biology: Can a biologist fix a smartphone?—Just hack it! (2017)

BMC Biology: Can a biologist fix a smartphone?—Just hack it! (2017) | Publications | Scoop.it

Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems.

 

This article was inspired by the influential and entertaining essay by Yuri Lazebnik who argued that there are fundamental flaws in how biologists approach problems [1]. Lazebnik proposed that the complexity of biological systems calls for a systems approach to the study of living systems using a radio as a colourful metaphor to illustrate his points [1]. He postulated that, conceptually, a radio functions similarly to a biological system by converting a signal from one form into another using a signal transduction pathway [1]. Here I argue that Lazebnik’s thesis is limited by two fundamental principles of biology. First, the clear-cut separation between the software code—the operating information for living systems as written in the genome sequence—and hardware, or the organism itself [2, 3]. Second, biological systems are not optimally designed but are shaped by historicity—the historical constraints that are integral to their evolution [4]. This limits the extent to which principles of design and engineering can be useful in understanding and manipulating the structures and functions of living organisms. In contrast, modern day biologists are starting to operate as software engineers to hack biological systems and write apps despite a somewhat superficial understanding of the underlying complexity of these systems.

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MPMI: Foundational and translational research opportunities to improve plant health (2017)

MPMI: Foundational and translational research opportunities to improve plant health (2017) | Publications | Scoop.it

This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture. Specific findings: ● Genetic improvement of crops is the most reliable, least expensive management strategy when suitable genetic variation is available. Nonetheless, some interventions have not proved durable due to the evolution and global dispersal of virulent pathogens and pests as well as herbicide-resistant weeds. ● Additional strategies are becoming essential as multiple fungicides, nematicides, and herbicides become ineffective due to the evolution of resistance and/or are phased out due to registration withdrawals. ● Strategies are needed that maximize the evolutionary hurdles for pathogens, pests, and weeds to overcome control measures. Interventions need to evolve as fast as the biotic challenges. Moreover, deployments of interventions must be driven by knowledge of the evolutionary capacity of the biotic challenge. ● Considerable knowledge exists but more research into the mechanisms of plant immunity and other forms of resistance is needed as the foundation for translational applications. ● Several new technologies are increasing foundational knowledge and providing numerous opportunities for generating crops with durable resistance to pests and diseases as well as control of weeds and reduction of the environmental impact of agriculture. ● There are multiple strategies for counteracting biotic challenges involving canonical and non-canonical disease resistance genes, genes encoding susceptibility factors, small RNAs, or immunomodulators. Simultaneous deployment of disease resistance strategies with different modes of action, as well as the judicious use of fungicides, will enhance durability of control measures. ● Pathogen effectors provide tools for discovering resistance genes and susceptibility factors as well as for dissecting/manipulating plant biology and breeding plants for durable disease resistance. ● There are several, as yet little exploited, opportunities for leveraging beneficial interactions among plants, microbes, insects and other organisms in the phytobiome to enhance plant health and productivity as well as breeding plants to promote beneficial phytobiome communities. ● Global monitoring of plant health is feasible and desirable in order to anticipate and counter threats. ● Climate change increases the need for continual global monitoring of pathogens, pests, and weeds and adjusting of control strategies. ● There are numerous current and future opportunities for knowledge exchange and partnerships between developed and developing countries to foster improved local and global food security. ● Both genetically modified (GM) and non-GM strategies are needed to maximize plant health and food security. ● Significant, sustained financial support is required if the beneficial impacts of foundational and translational research on global food security are to be realized. The needs, opportunities, approaches, and deliverables for addressing biotic challenges to plant health are detailed in Table 1. These can be broadly classified as assessing variation, characterizing it in detail at a variety of scales, and deploying beneficial interventions. Immediate investments in global monitoring of pathogens/pests and in situ and ex-situ determination of what natural variation exists in crop plants for countering challenges and threats should be a high priority. Detailed investigations of the molecular basis of the various types of plant resistance and of the basis of pathogen/pest virulence are critical for providing the foundation for novel intervention strategies; these will be facilitated by development of high resolution structural and functional analytical techniques. Optimization of protocols for delivery of reagents for allele replacement and gene insertions into diverse major and minor crop plants should be a high priority. Monitoring and deployment should be a global endeavor involving multinational partnerships and knowledge exchanges in order to ensure that interventions are locally relevant and globally durable.

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BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian...

BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian... | Publications | Scoop.it
Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection.Empty description

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The Sainsbury Lab's curator insight, March 22, 8:01 AM
Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection.
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Microbiology Molecular Biology Reviews: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017)

Microbiology Molecular Biology Reviews: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017) | Publications | Scoop.it

Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.

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bioRxiv: Host autophagosomes are diverted to a plant-pathogen interface (2017)

bioRxiv: Host autophagosomes are diverted to a plant-pathogen interface (2017) | Publications | Scoop.it

Filamentous plant pathogens and symbionts invade their host cells but remain enveloped by host-derived membranes. The mechanisms underlying the biogenesis and functions of these host-microbe interfaces are poorly understood. Recently, we showed that PexRD54, an effector from the Irish potato famine pathogen Phytophthora infestans, binds host protein ATG8CL to stimulate autophagosome formation and deplete the selective autophagy receptor Joka2 from ATG8CL complexes. Here, we show that during P. infestans infection, ATG8CL autophagosomes are diverted to the pathogen interface. Our findings are consistent with the view that the pathogen coopts host selective autophagy for its own benefit.

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Plant Methods: Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana (2016)

Plant Methods: Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana (2016) | Publications | Scoop.it

CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate. CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.

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Trends in Plant Science: ATG8 Expansion: A Driver of Selective Autophagy Diversification? (2016)

Trends in Plant Science: ATG8 Expansion: A Driver of Selective Autophagy Diversification? (2016) | Publications | Scoop.it

Selective autophagy is a conserved homeostatic pathway that involves engulfment of specific cargo molecules into specialized organelles called autophagosomes. The ubiquitin-like protein ATG8 is a central player of the autophagy network that decorates autophagosomes and binds to numerous cargo receptors. Although highly conserved across eukaryotes, ATG8 diversified from a single protein in algae to multiple isoforms in higher plants. We present a phylogenetic overview of 376 ATG8 proteins across the green plant lineage that revealed family-specific ATG8 clades. Because these clades differ in fixed amino acid polymorphisms, they provide a mechanistic framework to test whether distinct ATG8 clades are functionally specialized. We propose that ATG8 expansion may have contributed to the diversification of selective autophagy pathways in plants.

 

  • Selective autophagy is an ancient membrane-trafficking pathway that is essential for cellular homeostasis.
  • Selective autophagy involves engulfment of autophagic cargo within double-membrane vesicles called autophagosomes.
  • Autophagosomes are decorated by ATG8, a ubiquitin-like protein conserved across eukaryotes that is expanded in higher plants.
  • Selective cargo recruitment is mediated by autophagy receptors that interact with ATG8 via an ATG8 interaction motif (AIM). Specialization of autophagy receptors toward ATG8 variants contributes to selective autophagy.
  • Although selective autophagy plays important roles in development and stress tolerance, the molecular mechanisms underlying selectivity are currently elusive in plants.
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bioRxiv: NLR signaling network mediates immunity to diverse plant pathogens (2016)

bioRxiv: NLR signaling network mediates immunity to diverse plant pathogens (2016) | Publications | Scoop.it

Plant and animal nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins often function in pairs to mediate innate immunity to pathogens. However, the degree to which NLR proteins form signaling networks beyond genetically linked pairs is poorly understood. In this study, we discovered that a large NLR immune signaling network with a complex genetic architecture confers immunity to oomycetes, bacteria, viruses, nematodes, and insects. The network emerged over 100 million years ago from a linked NLR pair that diversified into up to one half of the NLR of asterid plants. We propose that this NLR network increases robustness of immune signaling to counteract rapidly evolving plant pathogens.

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New Phytologist: Nine things to know about elicitins (2016)

New Phytologist: Nine things to know about elicitins (2016) | Publications | Scoop.it

Elicitins are structurally conserved extracellular proteins in Phytophthora and Pythium oomycete pathogen species. They were first described in the late 1980s as abundant proteins in Phytophthora culture filtrates that have the capacity to elicit hypersensitive (HR) cell death and disease resistance in tobacco. Later, they became well-established as having features of microbe-associated molecular patterns (MAMPs) and to elicit defences in a variety of plant species. Research on elicitins culminated in the recent cloning of the elicitin response (ELR) cell surface receptor-like protein, from the wild potato Solanum microdontum, which mediates response to a broad range of elicitins. In this review, we provide an overview on elicitins and the plant responses they elicit. We summarize the state of the art by describing what we consider to be the nine most important features of elicitin biology.

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Cellular Microbiology: Arabidopsis late blight: Infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans (2016)

Cellular Microbiology: Arabidopsis late blight: Infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans (2016) | Publications | Scoop.it

The oomycete pathogen Phytophthora infestans causes potato late blight, and as a potato and tomato specialist pathogen, is seemingly poorly adapted to infect plants outside the Solanaceae. Here, we report the unexpected finding that Pinfestans can infect Arabidopsis thaliana when another oomycete pathogen, Albugo laibachii, has colonized the host plant. The behaviour and speed of Pinfestans infection in Arabidopsis pre-infected with Alaibachii resemble Pinfestans infection of susceptible potato plants. Transcriptional profiling of Pinfestans genes during infection revealed a significant overlap in the sets of secreted-protein genes that are induced in Pinfestans upon colonization of potato and susceptible Arabidopsis, suggesting major similarities in Pinfestans gene expression dynamics on the two plant species. Furthermore, we found haustoria of Alaibachii and Pinfestans within the same Arabidopsis cells. This Arabidopsis - Alaibachii - Pinfestans tripartite interaction opens up various possibilities to dissect the molecular mechanisms of Pinfestans infection and the processes occurring in co-infected Arabidopsis cells.

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bioRxiv: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016)

bioRxiv: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016) | Publications | Scoop.it

In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,741 hectares, about 16% of cultivated wheat area in Bangladesh, with yield losses reaching up to 100%. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. Population genomics analyses revealed that the outbreak was caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. We show that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

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Lynne Reuber's curator insight, June 20, 2016 10:53 AM
Molecular epidemiology for plant pathology
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Global Plant Council: Protecting plants, protecting people (2016)

Global Plant Council: Protecting plants, protecting people (2016) | Publications | Scoop.it

This week on the blog, Professor Sophien Kamoun describes his work on plant–pathogen interactions at The Sainsbury Lab, UK, and discusses the future of plant disease.

 

Could you begin by describing the focus of your research on plant pathogens?

 

We study several aspects of plant–pathogen interactions, ranging from genome-level analyses to mechanistic investigations focused on individual proteins. Our projects are driven by some of the major questions in the field: how do plant pathogens evolve? How do they adapt and specialize to their hosts? How do plant pathogen effectors co-opt host processes?

 

One personal aim is to narrow the gap between research on the mechanisms and evolution of these processes. We hope to demonstrate how mechanistic research benefits from a robust phylogenetic framework to test specific hypotheses about how evolution has shaped molecular mechanisms of pathogenicity and immunity.

 

Tree diseases such as sudden oak death, ash dieback and olive quick decline syndrome have been making the news a lot recently. Are diseases like these becoming more common, and if so, why?

 

It’s well documented that the scale and frequency of emerging plant diseases has increased. There are many factors to blame. Increased global trade is one. Climate change is another. There is no question that we need to increase our surveillance and diagnostics efforts. We’re nowhere near having coordinated responses to new disease outbreaks in plant pathology, especially when it comes to deploying the latest genomics methods. We really need to remedy this.

 

The wheat blast fungus recently hit Bangladesh. Could you briefly outline how it is being tackled by plant pathologists?

 

Wheat blast has just emerged this last February in Bangladesh – its first report in Asia. It could spread to neighboring countries and become a major threat to wheat production in South Asia. Thus, we had to act fast. We used an Open Science approach to mobilize collaborators in Bangladesh and the wider blast fungus community, and managed to identify the pathogen strain in just a few weeks. It turned out that the Bangladeshi outbreak was caused by a clone related to the South American lineage of the pathogen. Now that we know the enemy, we can proceed to put in place an informed response plan. It’s challenging but at least we know the nature of the pathogen – a first step in any response plan to a disease outbreak.

 

Which emerging diseases do you foresee having a large impact on food security in the future?

 

Obviously, any disease outbreak in the major food crops would be of immediate concern, but we shouldn’t neglect the smaller crops, which are so critical to agriculture in the developing world. This is one of the challenges of plant pathology: how to handle the numerous plants and their many pathogens.

 

As far as new problems, I view insect pests as being a particular challenge. Our basic understanding of insect–plant interactions is not as well developed as it is for microbial pathogens, and research has somewhat neglected the impact of plant immunity. The range of many insect pests is expanding because of climate change, and we are moving to ban many of the widely used insecticides. This is an area of research I would recommend for an early career scientist.

 

What advice would you give to a young researcher in this area?

 

Ask the right questions and look beyond the current trends. Think big. Be ambitious. Don’t shy away from embracing the latest technologies and methods. It’s important to work on real world systems. Thanks to technological advances, genomics, genome editing etc., the advantages of working on model systems are not as obvious as they were in the past.

 

How can we mitigate the risks to crops from plant diseases in the future?

 

My general take is to be suspicious of silver bullets. I like to say “Don’t bet against the pathogen”. I believe that for truly sustainable solutions, we need to continuously alter the control methods, for example by regularly releasing new resistant crop varieties. Only then we can keep up with rapidly evolving pathogens. One analogy would be the flu jab, which has a different formulation every year depending on the make-up of the flu virus population.

 

Is there anything else you’d like to add?

 

I read that public and private funding of plant science is less than one tenth of biomedical research. Not a great state of affairs when one considers that we will add another two billion people to the planet in the next 30 years. As one of my colleagues once said: “medicine might save you one day; but plants keep you alive everyday”.

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