The good, the bad and their fortuitous differences
Genetic differences between two very similar fungi, one that led to Quorn™, the proprietary meat substitute, and another that ranks among the world's most damaging crop pathogens, have exposed the significant features that dictate the pair's very different lifestyles.
While the manufacturer of Quorn™ cultivates strains of Fusarium venenatum via fermentation into a mycoprotein dough for human consumption, farmers try to fight off Fusarium graminearum as this pervasive fungal pathogen invades multiple crops and threatens global food security.
Researchers have now pinpointed several significant differences between the fungal pair that seem to turn F. graminearum nasty, features that promise targets for controlling disease. The findings, by a team from Rothamsted Research, are reported today in the journal, BMC Genomics.
The team discovered, for instance, that F. venenatum does not contain some clusters of genes that produce subsidiary compounds, or secondary metabolites, which are produced by F. graminearum during successful wheat infection.
"Using improved computer software, we have enhanced gene predictions and secondary metabolite gene cluster predictions in both species to a level not found in most other filamentous fungal species," says Robert King, the team's lead bioinformatician at Rothamsted.
Emphasising the importance of the findings, King notes: "All this improved data is immediately available in the public domain via ENSEMBL [a genome database]. In the medium term, it should be possible to achieve a resilient control strategy for this globally important, cereal-infecting pathogen."
The team also confirmed differences in mating strategies, notably that the pathogenic fungus can mate with itself, which influences gene transfer between generations and genome repair mechanisms, whereas the Quorn™ fungus would need to find a mate.
And they found that key areas in chromosomes, the centromeric regions, are 25% smaller in the benign fungus, for reasons unknown but that offer "an excellent starting point for follow-up investigations", notes Kim Hammond-Kosack, a molecular plant pathologist at Rothamsted and leader of the research team.
"This is an important and fascinating piece of work that shows the many differences between F. venenatum and the plant pathogen F. graminearum at a number of different levels," says Rob Johnson, Science Manager and Fermentation Specialist at Quorn Foods.
"Despite the close relationship revealed by the sequencing," continues Johnson, "the differences in lifestyle are written deep into the genomes of these fungi, with the saprophytic F. venenatum showing a range of genes devoted to breakdown of organic matter, whereas the F. graminearum contains unique genes for secondary metabolites and more devoted to its pathogenic nature."
Johnson adds: "The confirmation of the non-pathogenic nature of the species used to make Quorn™ and understanding of the genetics revealed by these data will make this paper one that Quorn™ will return to many times as we improve our process and grow our business."
In separate research, also funded at Rothamsted by the Biotechnology and Biological Sciences Research Council, the team has been unravelling the pan-genome of F. graminearum, a reference genome that includes the genetic make-up of the pathogen and also those of its various strains.
"We can now immediately identify which of the newly predicted secondary metabolite gene clusters and small secreted protein effector sequences are found in all pathogenic strains of F. graminearum," says Hammond-Kosack.
"These sequences then become the targets for a far narrower set of follow-up gene function studies in F. graminearum by reverse genetic experimentation to pinpoint the genes essential for the disease-causing abilities of this pathogen."
Hammond-Kosack concludes: "Starting from the fundamental new knowledge gained from these studies, a sustainable discover and disease control pipeline has begun to be created."
NOTES TO EDITORS
King et al., 2018, BMC Genomics: Inter-genome comparison of the Quorn™ fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum
Rothamsted Research contacts:
Kim Hammond-Kosack, Molecular Plant Pathologist
Tel: +44 (0) 1582 938 240
E-mail: [email protected]
Robert King, Bioinformatician
Tel: +44 (0) 1582 938 335
E-mail: [email protected]
Susan Watts, Head of Communications
Tel: +44 (0) 1582 938 109
Mob: +44 (0) 7964 832 719
E-mail: [email protected]
About Rothamsted Research
Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking discoveries, from crop treatment to crop protection, from statistical interpretation to soils management. Our founders, in 1843, were the pioneers of modern agriculture, and we are known for our imaginative science and our collaborative influence on fresh thinking and farming practices.
Through independent science and innovation, we make significant contributions to improving agri-food systems in the UK and internationally. In terms of the institute's economic contribution, the cumulative impact of our work in the UK was calculated to exceed £3000 million a year in 2015 (Rothamsted Research and the Value of Excellence: A synthesis of the available evidence, by Séan Rickard). Our strength lies in our systems approach, which combines science and strategic research, interdisciplinary teams and partnerships.
Rothamsted is also home to three unique resources. These National Capabilities are open to researchers from all over the world: The Long-Term Experiments, Rothamsted Insect Survey and the North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT). For more information, visit https://www.rothamsted.ac.uk/; Twitter @Rothamsted
The Biotechnology and Biological Sciences Research Council is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid from the UK government.
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by government, BBSRC invested £469 million in world-class bioscience in 2016-17. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
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The Lawes Agricultural Trust, established in 1889 by Sir John Bennet Lawes, supports Rothamsted Research's national and international agricultural science through the provision of land, facilities and funding. LAT, a charitable trust, owns the estates at Harpenden and Broom's Barn, including many of the buildings used by Rothamsted Research. LAT provides an annual research grant to the Director, accommodation for nearly 200 people, and support for fellowships for young scientists from developing countries. LAT also makes capital grants to help modernise facilities at Rothamsted, or invests in new buildings.
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