Bio 1

Bio: The roots.

I grew up in Saint Petersburg, Russia; moved to the Bay Area with my family as a teenager, and received my undergraduate degree from University of California (UC), Berkeley. As an undergraduate, I worked for two and a half years with Steven Lindow, studying mechanisms of bacterial interference of quorum sensing in Pseudomonas syringae [1].  This research stimulated my interests in both microbiology and plant pathology. Thus, in 2005, as I received BS in Plant Genetics and Microbiology, I was eager to enter graduate school.

Between 2005 and 2010, I was working towards a PhD in Brian Staskawicz’s lab in the Department of Plant and Microbial Biology, at UC Berkeley. The goal of my graduate work was to broaden our understanding of the molecular mechanisms that define plant-pathogen interactions. Specifically, I was working with the RPP1 resistance protein from Arabidopsis thaliana and its cognate effector ATR1 from an obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis. I demonstrated that RPP1 physically associates in a protein complex with ATR1 in planta in a recognition-specific manner [2]. I also got interested in studying the immediate molecular events that occur downstream of effector recognition triggering R-gene activation [2]. Since both RPP1 and ATR1 are encoded by rapidly evolving gene loci, I aimed to obtain further insight into the co-evolution of these genes by characterizing the natural variation in RPP1-mediated response among different accessions of Arabidopsis [3]. Using bioinformatics analyses in collaboration with Sophien Kamoun’s group, we performed in silico prediction of additional effectors from H. arabidopsidis [4]. Several of these were recently validated in vivo [5]. In collaboration with Tom Alber’s group at Berkeley, we obtained a 3D structure of ATR1 protein by X-ray crystallography [6]. Besides gaining sheer excitement of seeing a molecule I’ve been working on in 3D, the structure provided an intriguing insight into the evolution of plant immunity. Recognition of ATR1 by two alleles of RPP1 was mediated through different protein surfaces, which suggested that the two receptors evolved independently to recognize ATR1. Serendipitously, structures of two other oomycete effectors were solved at the same time and comparing them revealed a common structural fold, almost indiscernible from primary sequence analyses [7]. If for some reason you get interested in glancing over my full dissertation [8], it is open access, the pdf is available from the Berkeley library. During my PhD, I also learned to code.

More bio: Did I mention coding + science got me a faculty job?

My interest in bioinformatics started from wonderful classes taught at Berkeley. Under the guidance of Kimmen Sjolander I expanded my bioinformatics skills and completed a designated emphasis in Genomics and Computational Biology as a part of my PhD.

Coding allowed me to dive into wheat genomics, one of the challenging and most rewarding areas of research I have seen. From mid 2011 to the end of 2014 I have been post-doctoral scholar with Jorge Dubcovsky at University of California Davis and a recipient of a post-doctoral AFRI-NIFA fellowship from the United States Department of Agriculture. I studied the tetraploid wheat species Triticum turgidum that provides us with semolina for pasta and couscous and serves as an important model for wheat research. Using next generation technology and optimized bioinformatics pipelines, I have sequenced, assembled, and annotated tetraploid wheat transcriptome [9], developed wheat exome capture and applied it to sequence over 1,000 mutant lines with help of fancy modern robotics and indispencable input from colleagues and collaborators. Both transcriptome and predicted proteome among other resources are available here without any restrictions.

In parallel, I started an exciting forward genetics screen for induced resistance/susceptibility to wheat pathogens (we got preliminary mutants). Defining the components of wheat immunity and broadening our knowledge of immunity in grasses.

Now, I have my own group at The Genome Analysis Centre and The Sainsbury Laboratory in Norwich, UK.

http://www.tgac.ac.uk/science-faculty/triticeae-genomics/

http://www.tsl.ac.uk/groups/krasileva-group/

E-mail: Ksenia.Krasileva@tgac.ac.uk
Twitter @kseniakrasileva
LinkedIn: http://www.linkedin.com/pub/ksenia-krasileva/46/142/b91

References:

1. Dulla GF, Krasileva KV, Lindow SE: Interference of quorum sensing in Pseudomonas syringae by bacterial epiphytes that limit iron availability. Environ Microbiol 2010, 12:1762-1774.

2. Krasileva KV, Dahlbeck D, Staskawicz BJ: Activation of an Arabidopsis resistance protein is specified by the in planta association of its leucine-rich repeat domain with the cognate oomycete effector. Plant Cell 2010, 22:2444-2458.

3. Krasileva KV, Zheng C, Leonelli L, Goritschnig S, Dahlbeck D, Staskawicz BJ: Global analysis of Arabidopsis/downy mildew interactions reveals prevalence of incomplete resistance and rapid evolution of pathogen recognition. PLoS One 2011, 6:e28765.

4. Win J, Morgan W, Bos J, Krasileva KV, Cano LM, Chaparro-Garcia A, Ammar R, Staskawicz BJ, Kamoun S: Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 2007, 19:2349-2369.

5. Goritschnig S, Krasileva KV, Dahlbeck D, Staskawicz BJ: Computational prediction and molecular characterization of an oomycete effector and the cognate Arabidopsis resistance gene. PLoS Genet 2012, 8:e1002502.

6. Chou S, Krasileva KV, Holton JM, Steinbrenner AD, Alber T, Staskawicz BJ: Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces. Proc Natl Acad Sci U S A 2011, 108:13323-13328.

7. Win J, Krasileva KV, Kamoun S, Shirasu K, Staskawicz BJ, Banfield MJ: Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species. PLoS Pathog 2012, 8:e1002400.

8. Krasileva KV: The Molecular Basis for Recognition of Oomycete Effectors in Arabidopsis. pp. 131. Berkeley, CA. 2011. PDF

9. Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Consortium I, Akhunov E, Uauy C, Dubcovsky J: Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol 2013, 14:R66.

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