CRISPR opens up new method of creating virus resistant plants

Researchers have found a new way to make plants virus-resistant by harnessing the ability of the gene-editing tool CRISPR to chop up invading viral DNA, according to a study in Genome Biology. CRISPR evolved in bacteria as a defense system against viral infection, and by partially inserting the CRISPR-Cas9 system into the genome of model plants in the laboratory the research team made plants that were resistant to a major crop viruses.


Dr. Adam Bogdanove, Professor, Plant Pathology and Plant-Microbe Biology Section, Cornell University (webpage):

Expertise: understanding mechanisms of bacterial plant pathogenesis and plant defense to develop better means of disease control.

“CRISPR-Cas9 has been used extensively in plants to edit the plant genome but never before to attack the foreign DNA of viruses. Attacking invading viruses was one of the potential uses of gene-editing tools that was talked about a lot early on, and because the natural function of CRISPR-Cas9 is a bacterial defense system against viruses it is conceptually satisfying that this paper shows this defense system could be ported to plants.

“Plants do have a natural immune system against viruses called RNA silencing. Silencing is effective against many viruses, but many others (including the virus targeted in this study) have evolved to deal with that immune response by suppressing the silencing. Against such viruses, many of which are economically important, using CRISPR-Cas9 in the way the authors describe is a potentially very powerful approach because it is unrelated to silencing and is so readily engineered.

“The way the authors achieved virus resistance was by engineering the plant genome to express the Cas9 half of the system, and by engineering a relatively harmless plant virus (different from the virus they were attempting to generate resistance to) to deliver the other half,  the CRISPR guide RNA, which is the part designed to recognize invading viral DNA. In the study, it is this engineered virus that enabled the whole CRISPR-Cas9 system to chew away at the targeted virus.

“This method of engineering a virus to deliver the guide RNA is not practical to apply in the field. Instead you would want the guide RNA to be expressed by a gene in the plant genome, and it is not certain whether you would see the same effect as the authors report. So these are promising and exciting initial results, but it remains to be seen whether plants stably expressing both the Cas9 protein and the CRISPR guide RNAs will show the same effect.

“The other reason for cautious optimism here is that the authors have shown that you can target a viral sequence that is shared by several different viruses and get resistance to each of those viruses. Viruses mutate readily so it is possible that the resistance will not be stable: if there is a subpopulation of the virus that persists there will be strong selection pressure on that subpopulation to evolve to become unrecognizable by the CRISPR-Cas9 that is targeting it. However, one advantage of the approach is that even if a virus evolves to overcome the particular CRISPR-Cas9 that has been deployed, by substituting another CRISPR guide RNA a second round of virus resistant plants could be developed.”


Dr. Chris Dardick, Molecular Biologist, Appalachian Fruit Research Laboratory, USDA Agricultural Research Service (webpage):

Expertise: Molecular interactions between plants and disease causing microbes; plant development; genomics; genetic engineering.

“The paper is potentially very exciting. What the authors have done is intriguing because it is a novel use of the CRISPR system in plants and there is potentially real promise for developing plants with resistance against viruses, particularly DNA viruses. With RNA viruses we have tools that have worked quite well, but with DNA viruses it hasn’t been quite so simple. New tools to combat DNA viruses would be beneficial  – every tool in the box helps.

“The viruses the researchers focused on are geminiviruses, a class of DNA viruses. These and other DNA viruses are usually insect transmitted and cause serious problems to crops all over the world, in particular tropical and subtropical areas regions in the third world. We don’t have good tools to combat them so there is a need for new technologies.

“It is still very early in the development process. What the authors describe is very much an experimental system to see if they could get it to work in the laboratory. How that would be deployed in a crop system in the field still has to be worked out. There is a lot of possibility for innovation but a lot of additional work to be done.”


Dr. Allen Miller, Professor, Plant Pathology Department, Iowa State University (webpage):

Expertise: molecular biology of plant viruses.

“This paper uses a more precise method to engineer a plant to target and resist specific plant viruses than has been used previously.  The method appears to be very rapid and easy. The authors point out that traditional plant breeding and genetic engineering methods have not led to useful resistance to this very important pathogen, tomato yellow leaf curl virus (TYLCV).  This technique could be adapted readily to many crops including tomato, which is the main host of TYLCV, and could easily be applied to many other DNA viruses of plants.  The Geminviridae family, which includes TYLCV, is the largest, most important family of plant viruses in tropical regions, causing many serious plant diseases worldwide such as African cassava mosaic virus.

“Because the plant must be genetically engineered to express the Cas9 protein, which is a protein of the bacterial immune system, it would still be considered GMO.  But it is hard to envision how this Cas9 protein would be a risk to humans or the environment.  Other bacterial genes such as the Bacillus thuringensis toxin (Bt) have been approved and used safely in millions of acres of crops worldwide.

“Another possible limitation is that the resistance may not be complete enough, still allowing significant virus infection.  Moreover, the CRISPR-Cas9 systems works by mutating the viral DNA, mostly inactivating it, but it’s possible that random mutations introduced during the DNA repair process could create a functional, resistance-breaking mutant of the virus. Not likely but conceivable.

“However, the advantage of the system described is that multiple viral targeting sequences can be introduced at the same time.  In fact, the authors showed that more complete resistance was achieved when two TYLCV genes were targeted simultaneously.  It would be hard to imagine a virus overcoming resistance if several sites on the target virus genome were targeted at once.”


Declared interests (see GENeS register of interests policy):

No interests declared.



CRISPR/Cas9-Mediated Viral Interference in Plants‘ by Mahfouz et al, published in Genome Biology on Tuesday 10 November, 2015.

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