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Norwich, United Kingdom

Clarke C.R.,Virginia Polytechnic Institute and State University | Cai R.,Virginia Polytechnic Institute and State University | Studholme D.J.,Sainsbury Laboratory | Guttman D.S.,University of Toronto | Vinatzer B.A.,Virginia Polytechnic Institute and State University
Molecular Plant-Microbe Interactions | Year: 2010

Pseudomonas syringae is best known as a plant pathogen that causes disease by translocating immune-suppressing effector proteins into plant cells through a type III secretion system (T3SS). However, P. syringae strains belonging to a newly described phylogenetic subgroup (group 2c) are missing the canonical P. syringae hrp/hrc cluster coding for a T3SS, flanking effector loci, and any close orthologue of known P. syringae effectors. Nonetheless, P. syringae group 2c strains are common leaf colonizers and grow on some tested plant species to population densities higher than those obtained by other P. syringae strains on nonhost species. Moreover, group 2c strains have genes necessary for the production of Phytotoxins, have an ice nucleation gene, and, most interestingly, contain a novel hrp/hrc cluster, which is only distantly related to the canonical P. syringae hrp/hrc cluster. This hrp/hrc cluster appears to encode a functional T3SS although the genes hrpK and hrpS, present in the classical P. syringae hrp/hrc cluster, are missing. The genome sequence of a representative group 2c strain also revealed distant orthologues of the P. syringae effector genes avrEl and hopMl and the P. aeruginosa effector genes exoU and exoY. A putative life cycle for group 2c P. syringae is discussed. © 2010 The American Phytopathological Society. Source


News Article
Site: http://www.nature.com/nature/current_issue/

Update: On 26 April, a team led by microbial population geneticist Daniel Croll, who is at the Swiss Federal Institute of Technology in Zurich, reported on github.com that the Bangladeshi wheat-blast strain is closely related to those collected in Brazilian wheat fields and on nearby weeds. His team’s analysis, which uses the data on the website Open Wheat Blast, reveals that the sample is not closely related to known rice-blast-causing strains of M. oryzae. Croll’s team concludes that wheat blast was probably introduced to Bangladesh from Brazil, and warns that other Asian countries that import Brazilian wheat, including Thailand, the Philippines and Vietnam, should be on the lookout for the disease. Fields are ablaze in Bangladesh, as farmers struggle to contain Asia’s first outbreak of a fungal disease that periodically devastates crops in South America. Plant pathologists warn that wheat blast could spread to other parts of south and southeast Asia, and are hurrying to trace its origins. “It’s important to know what the strain is,” says Sophien Kamoun, a biologist at the Sainsbury Laboratory in Norwich, UK, who has created a website, Open Wheat Blast (go.nature.com/bkczwf), to encourage researchers to share data. Efforts are also under way to find wheat genes that confer resistance to the disease. First detected in February and confirmed with genome sequencing by Kamoun’s lab this month, the wheat-blast outbreak has already caused the loss of more than 15,000 hectares of crops in Bangladesh. “It’s really an explosive, devastating disease,” says plant pathologist Barbara Valent of Kansas State University in Manhattan, Kansas. “It’s really critical that it be controlled in Bangladesh.” After rice, wheat is the second most cultivated grain in Bangladesh, which has a population of 156 million people. More broadly, inhabitants of south Asia grow 135 million tonnes of wheat each year. Wheat blast is caused by the fungus Magnaporthe oryzae. Since 1985, when scientists discovered it in Brazil’s Paraná state, the disease has raced across South America. The fungus is better known as a pathogen of rice. But unlike in rice, where M. oryzae attacks the leaves, the fungus strikes the heads of wheat, which are difficult for fungicides to reach. A 2009 outbreak in wheat cost Brazil one-third of that year’s crop. “There are regions in South America where they don’t grow wheat because of the disease,” Valent says. Wheat blast was spotted in Kentucky in 2011, but vigorous surveillance helped to stop it spreading in the United States. In South America, the disease tends to take hold in hot and humid spells. Such conditions are present in Bangladesh, and the disease could migrate across south and southeast Asia, say plant pathologists. In particular, it could spread over the Indo-Gangetic Plain through Bangladesh, northern India and eastern Pakistan, warn scientists at the Bangladesh Agricultural Research Institute (BARI) in Nashipur. Bangladeshi officials are burning government-owned wheat fields to contain the fungus, and telling farmers not to sow seeds from infected plots. The BARI hopes to identify wheat varieties that are more tolerant of the fungus and agricultural practices that can keep it at bay, such as crop rotation and seed treatment. It is unknown how wheat blast got to Bangladesh. One possibility is that a wheat-infecting strain was brought in from South America, says Nick Talbot, a plant pathologist at the University of Exeter, UK. Another is that an M. oryzae strain that infects south Asian grasses somehow jumped to wheat, perhaps triggered by an environmental shift: that is what happened in Kentucky, when a rye-grass strain infected wheat. To tackle the question, this month Kamoun’s lab sequenced a fungus sample from Bangladesh. The strain seems to be related to those that infect wheat in South America, says Kamoun, but data from other wheat-infecting strains and strains that plague other grasses are needed to pinpoint the outbreak’s origins conclusively. The Open Wheat Blast website might help. Kamoun has uploaded the Bangladeshi data, and Talbot has deposited M. oryzae sequences from wheat in Brazil. Talbot hopes that widely accessible genome data could help to combat the outbreak. Researchers could use them to screen seeds for infection or identify wild grasses that can transmit the fungus to wheat fields. Rapid data sharing is becoming more common in health emergencies, such as the outbreak of Zika virus in the Americas. Kamoun and Talbot say that their field should follow suit. “The plant-pathology community has a responsibility to allow data to be used to combat diseases that are happening now, and not worry too much about whether they may or may not get a Nature paper out of it,” says Talbot. Last month, Valent’s team reported the first gene variant known to confer wheat-blast resistance (C. D. Cruz et al. Crop Sci. http://doi.org/bfk7; 2016), and field trials of crops that bear the resistance gene variant have begun in South America. But plant pathologists say that finding one variant is not enough: wheat strains must be bred with multiple genes for resistance, to stop M. oryzae quickly overcoming their defences. The work could help in the Asian crisis, says Talbot. “What I would hope for out of this sorry situation,” he says, “is that there will be a bigger international effort to identify resistance genes.”


News Article
Site: http://www.nature.com/nature/current_issue/

Plant geneticist Stefan Jansson is champing at the bit to start field trials on crops tweaked with powerful gene-editing technologies. He plans to begin by using edits to study how the cress plant Arabidopsis protects its photosynthetic machinery from damage in excessively bright light. But the future of his work depends on the European Commission’s answer to a legal conundrum. Should it regulate a gene-edited plant that has no foreign DNA as a genetically modified (GM) organism? Jansson, who works at Umeå University in Sweden, says that he will drop his experiments if the plants are classed as GM, because Europe’s onerous regulations would make his work too expensive and slow. He and many others are anxiously awaiting the commission’s decision, which will dictate how they approach experiments using the latest gene-editing techniques, including the popular CRISPR–Cas9 method. The commission has repeatedly stalled on delivering its verdict, which will apply to edited animals and microorganisms as well as plants. It now says that it will make its legal analysis public by the end of March. Swedish authorities, meanwhile, have told Jansson that unless the commission specifies otherwise, they will not require his cress to be subject to GM regulations. The legal limbo is having a big impact on research, says René Smulders of the plant-breeding division at Wageningen University and Research Centre in the Netherlands. He says that this year, he was rejected for a European Union grant — on changing the composition of a plant’s oils by editing a gene — because referees were concerned about the legal uncertainty. “Some scientists hesitate to start using the new methods in case they end up being regulated and their research projects hit a dead end,” he says. At issue is the interpretation of a 2001 European Commission directive on releasing GM organisms into the environment, which covers field trials and cultivation. It defines GM organisms as having alterations that cannot occur naturally, which were made by genetic engineering. What is unclear is how this relates to experiments, such as Jansson’s, in which researchers introduce foreign DNA to direct a precise edit in a plant’s own genetic material but then use selective breeding to remove the foreign gene. The final plant has a few tweaked nucleotides, but cannot be distinguished from a wild plant that might have acquired the same mutation naturally — so it cannot be traced in the environ­ment as EU regulations require. Many EU member states — including Sweden — have conducted their own analyses of the directive, and argue that it should not apply to edited plants that do not contain foreign DNA. But some non-governmental organizations (NGOs) hostile to genetic manipulation have produced analyses that conclude the directive should apply because genetic engineering is involved. Academic scientists and seed and crop companies fear that plants made with the latest gene-editing techniques may share the fate of conventional GM plants in Europe. Strict regulations, cumbersome bureaucracy and activism against GM organisms have meant that scientists in some countries, such as Germany, do not even attempt field trials. The regulations have increased the costs of bringing a GM crop to market, and many European nations do not allow such crops to be cultivated at all. That is frustrating for plant scientists who want their work to be useful to the world, says Jonathan Jones, a plant researcher at the Sainsbury Laboratory in Norwich, UK. “We hoped that the new plant-breeding techniques would offer ways of achieving the same outcome without the onerous regulations — and fear that might not turn out to be the case,” he says. Many countries outside Europe do not face the same uncertainty, because they regulate GM organisms according to the nature of the product, not how it was made. In the United States, gene-edited crops containing no foreign genetic material are assessed on a case-by-case basis. In 2004, the biotechnology company Cibus, based in San Diego, California, was told that the US Department of Agriculture would not need to regulate its herbicide-resistant oilseed rape, made with an earlier form of gene-editing. Its crop is now cultivated in the United States. (The White House did, however, begin a review of all US biotechnology regulation in July.) Since 2011, Cibus has asked six countries — Finland, Germany, Ireland, Spain, Sweden and the United Kingdom — whether they would consider its crop to come under the scope of the EU directive. Without guidelines from the commission, each conducted its own analysis and said that it would not. Cibus has now done field trials in the United Kingdom and Sweden, but it put its activities on hold after the commission sent a letter to all EU member states on 15 June, asking them to wait for its legal interpretation. Whatever the commission decides, it is likely that either a member state, an NGO or a company will sue — meaning that the European Court of Justice may make the final, binding decision on the matter. Many plant scientists do basic research, so their gene-edited plants never need to leave the greenhouse. But Jansson must plant his cress outside to test its photosynthetic abilities in natural conditions. With his country’s approval, he plans to plant the crop in the spring. “Lawyers talk and talk — I think it is important for Europe to have a test case,” he says.


Farid A.,University of Natural Resources and Life Sciences, Vienna | Gro Malinovsky F.,Sainsbury Laboratory | Veit C.,University of Natural Resources and Life Sciences, Vienna | Schoberer J.,University of Natural Resources and Life Sciences, Vienna | And 2 more authors.
Plant Physiology | Year: 2013

Asparagine-linked glycosylation of proteins is an essential cotranslational and posttranslational protein modification in plants. The central step in this process is the transfer of a preassembled oligosaccharide to nascent proteins in the endoplasmic reticulum by the oligosaccharyltransferase (OST) complex. Despite the importance of the catalyzed reaction, the composition and the function of individual OST subunits are still ill defined in plants. Here, we report the function of the highly conserved OST subunit OST3/6. We have identified a mutant in the OST3/6 gene that causes overall underglycosylation of proteins and affects the biogenesis of the receptor kinase EF-TU RECEPTOR involved in innate immunity and the endo-b-1,4-glucanase KORRIGAN1 required for cellulose biosynthesis. Notably, the ost3/6 mutation does not affect mutant variants of the receptor kinase BRASSINOSTEROID-INSENSITIVE1. OST3/6 deficiency results in activation of the unfolded protein response and causes hypersensitivity to salt/osmotic stress and to the glycosylation inhibitor tunicamycin. Consistent with its role in protein glycosylation, OST3/6 resides in the endoplasmic reticulum and interacts with other subunits of the OST complex. Together, our findings reveal the importance of Arabidopsis (Arabidopsis thaliana) OST3/6 for the efficient glycosylation of specific glycoproteins involved in different physiological processes and shed light on the composition and function of the plant OST complex. © 2013 American Society of Plant Biologists. All Rights Reserved. Source


Searle I.R.,University of Cambridge | Searle I.R.,Sainsbury Laboratory | Pontes O.,Washington University in St. Louis | Melnyk C.W.,University of Cambridge | And 5 more authors.
Genes and Development | Year: 2010

JMJ14 is a histone H3 Lys4 (H3K4) trimethyl demethylase that affects mobile RNA silencing in an Arabidopsis transgene system. It also influences CHH DNA methylation, abundance of endogenous transposon transcripts, and flowering time. JMJ14 acts at a point in RNA silencing pathways that is downstream from RNA-dependent RNA polymerase 2 (RDR2) and Argonaute 4 (AGO4). Our results illustrate a link between RNA silencing and demethylation of histone H3 trimethylysine. We propose that JMJ14 acts downstream from the Argonaute effector complex to demethylate histone H3K4 at the target of RNA silencing. © 2010 by Cold Spring Harbor Laboratory Press. Source

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