Computational Identification and Functional Characterisation of Candidate DNA Binding Effectors in <i>Phytophthora</i>

Phytophthora secretes a large repertoire of molecules (effectors) during infection to modulate host processes and enable infection. Microarray analysis on tomato-P. capsici timecourse experiments has revealed dramatic transcriptional changes as a consequence of infection, suggesting a role for pathogen effectors in transcriptional reprogramming throughout its disease cycle.<br/>We hypothesise that Phytophthora genomes encode effectors that translocate into host nuclei during infection, where they bind DNA and modify gene expression. Computational methods for predicting DNA-binding proteins can provide a high-throughput means of candidate selection. However, current prediction algorithms are limited in plants and pathogens. <br/>Here we have created a plant specific prediction model, which we have employed to predict DNA-binding proteins in the tomato (Solanum lycopersicum) genome. By validating these predictions we have demonstrated that this model is suitable for high-throughput prediction of DNA-binding proteins and will be a useful tool in genome annotation efforts. <br/>Applying our prediction model to effectors from P. capsici and P. infestans, we have identified a set of candidates which have been prioritised for experimental characterisation. From these candidates we have identified chromatin-associated effectors which localise to the nucleus and enhance P. capsici virulence. Taken together these results suggest DNA-binding may be an important feature for pathogen effectors. <br/>Finally we have assessed the use of three techniques to validate direct DNA-binding and identify target DNA sequences, for which we show preliminary results and outline planned use. Candidate DNA-binding effectors will be prioritised for use with these techniques. <br/>We conclude that this study has provided the means to identify candidate DNA-binding effectors which can be adopted by others wishing to study pathogen DNA-binding effectors. This will help further our understanding of not only pathogen effectors but also of plant DNA-associated processes during infection.<br/>

Name dc:type.qualificationname

Doctor of Philosophy

Level dc:type.qualificationlevel

Doctoral Thesis

Grantor dc:publisher.institution

University of Dundee

Year dc:date.issued

2015

Author dc:creator

• Motion, Graham B.

Advisor dc:contributor.advisor

• Huitema, Edgar

Language dc:language

eng

Identifier URI

https://discovery.dundee.ac.uk/files/7855327/Ch2_Supplementary_File_2.pl
https://discovery.dundee.ac.uk/files/7855328/Ch2_Supplementary_File_3.model
https://discovery.dundee.ac.uk/files/7855330/Ch2_Supplementary_File_5.xlsx
https://discovery.dundee.ac.uk/files/7855332/Ch3_Supplementary_File_1.xlsx

Identifier

oai:discovery.dundee.ac.uk:studenttheses/ee068a34-ce88-4344-b30a-86bb59c7daba
https://discovery.dundee.ac.uk/en/studentTheses/ee068a34-ce88-4344-b30a-86bb59c7daba

OAI identifier oai:identifier

oai:discovery.dundee.ac.uk:studenttheses/ee068a34-ce88-4344-b30a-86bb59c7daba