Who we are and what we do?
Krasileva lab an inter-disciplinary group of people with a common interest in genomics and plant-microbe interactions. Our vision is to combine the latest technologies (such as sequencing, synthetic biology, genome editing) with fundamental research to improve our food security.
In natural ecosystems, plants generate sufficient variation in their immune receptors to recognize diverse and rapidly evolving pathogens. However, in crops, this diversity is often lost, while the pathogens still evolve rapidly – resulting in disease epidemics and pandemics. Environmental factors and changing climate also affect biodiversity and host-pathogen interactions.
Below are ongoing projects in the Krasileva lab that address genomic, evolutionary and molecular basis of plant immunity as well as evolution of virulence components in plant pathogens:
Evolution of plant immune receptors and signaling pathways
Plants rely on intracellular immune receptors called Nucleotide binding Leucine rich Repeat (NLR) proteins for pathogen recognition. The NLRs monitor and detect the presence of pathogen derived molecules. We look at three main types of natural variations in the NLRs in plants: 1) variation in copy number, 2) allelic variation, 3) structural variation. The NLR protein family expansions and contractions and the evolution of downstream signaling pathways are currently investigated by a graduate student Erin Baggs.
Previously, we characterized a new mechanism of generating new diversity in NLRs – gene fusions to other plant proteins that serve as ‘baits’ for the pathogen. Such NLRs with integrated domains (NLR-IDs) highlight plant proteins target by the pathogens and help to identify new sources of disease resistance.
We have rationally selected, cloned and tested natural NLR-IDs from wild relatives of wheat against pathogen-derived molecules. We have selected NLR-IDs where the integrated part is a mimic of previously described effector target. A postdoc Dr Elisha Thynne created a library of effectors derived from wheat yellow rust pathogen and screened over 30 IDs using batch yeast two hybrid combined with next generation sequencing. He identified novel effectors interacting with NLR-IDs, which represent new sources of disease resistance. We are currently following up these genes in plant assays.
Engineering plant immune receptors
We are now transferring our knowledge of NLR evolution into novel strategies of engineering plant immune receptors. We propose a rational design of synthetic plant immune receptors by gene fusion process. We already demonstrated that the ability to form such gene fusions is a naturally occurring mechanism in all flowering plants. We aim to deploy this principle to generate synthetic plant immune receptors with new ‘baits’ against pathogen molecules. A postdoc, Dr Janina Tamborski already adopted wheat cell-based assay for activation of the immune response which will allow us to transiently test synthetic NLRs directly in wheat.
Genome evolution in response to stress
A fundamental question in genome evolution is how genomes respond to stress. One of these responses is the shedding of extrachromosomal circular DNAs (eccDNAs) which have been implicated in cancer, aging, herbicide stress, and nutrient stress and are known to be ubiquitous in eukaryotes. EccDNAs can contain genes and can dramatically increase their copy number. However, while these eccDNAs have been observed in yeast, their role in the genome evolution of filamentous fungi, and especially plant pathogens, remains virtually unexplored. Fungal plant pathogens have two-speed genomes, with slowly evolving regions carrying housekeeping genes and rapidly evolving regions carrying effector genes that cause disease and genes that help the pathogens respond to environmental cues. However, the mechanisms of this rapid evolution remain poorly understood. Since the rapidly evolving regions of these genomes are rich in repeats and transposons and eccDNAs are thought to originate from similar regions, it follows that eccDNAs may be intimately linked to the rapid evolution of these pathogens under stress. EccDNAs were recently isolated from the rice blast fungus Magnaporthe oryzae and their role in response to stress by the pathogen is currently under investigation by second year microbiology student Pierre Joubert.
We are also interested in genome evolution under stress in plants (especially, NLRs!). For our thoughts on this topic, see Ksenia's recent review on The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes.
Mutational genomics to enhance disease resistance
We have previously identified 34 mutant wheat lines with enhanced adult plant resistance against a devastating wheat pathogen called wheat yellow (stripe) rust. The mutant collection is maintained in the lab by Andrew Deatker. Our goal is to identify mutations linked to resistance and clone genes with causative mutations. We are deploying exome capture and bulk segregant analysis of mutations in F2 population to map genetic interval co-segregating with resistance.
Our overarching research aims
- Uncover the natural history of plant-microbe interactions through comparative genomics.
- Understand the effects of domestication and adaptation to new environments on plant and fungal genomes.
- Engineer plant immunity using genome editing, mutagenesis and synthetic biology.