Employment History

• October 2007-present - Professor of Plant Pathology, Division of Plant Sciences, College of Life Sciences, University of Dundee (at SCRI).
• 2002-2007 - Molecular Plant Pathologist (Band 4), SCRI.
• 1999-2002 - Molecular Plant Pathologist (Band 5), SCRI.
• 1995-1999 - Molecular Plant Pathologist (Band 6), SCRI.

Research Interests

To be a successful pathogen, microbes need to suppress or otherwise manipulate host defences. For this, they secrete proteins and other chemicals that can interact with the host cell. In some cases, these virulence determinants are translocated inside host cells where they re-programme defences and metabolism to the pathogen’s benefit. My group focuses on two pathogens of potato, the oomycete late blight pathogen, Phytophthora infestans, and the bacterial blackleg and soft-rot pathogen, Pectobacterium atrosepticum (Pba).

We are using pathogen genomics to identify likely virulence determinants in these pathogens. We are particularly interested in proteins that are translocated inside the host cell and in the mechanisms by which they are delivered. We want to know when they are needed and where they are localised during infection (cell biology). We want to know the mode of action of such virulence determinants: what are their host targets and what roles do those targets play in plant defence? With the genomes of the hosts potato and tomato, the pathogens Pba and P. infestans all being sequenced, this is an exciting time to be undertaking comparative and functional genomics of plant-pathogen interactions.

Key Collaborators

• Dave Berger (University of Pretoria, South Africa).
• Jim Beynon (Warwick-HRI, UK).
• Orlando Borras-Hidalgo,(CIGB, Habana, Cuba).
• Teresa Coutinho (University of Pretoria, South Africa)
• Chris Hodgson (Moredun Research Institute, UK).
• Francine Govers (Wageningen University, Netherlands).
• Sophien Kamoun (Ohio State University, USA/Sainsbury Laboratory, JIC, UK).
• Gary Loake (University of Edinburgh, UK).
• Ari Sadanandom (University of Glasgow, UK).
• George Salmond (University of Cambridge, UK).
• Edwin van der Vossen (Wageningen University, Netherlands).
• Vivianne Vleeshouwers (Wageningen University, Netherlands).
• Pieter van West (University of Aberdeen, UK).

Recent Publications

2007

• Whisson, S.C., Boevink, P.C., Moleleki, L. , Avrova,  A.O., Morales, J.G., Gilroy, E.M., Armstrong,  M.R.,  Grouffaud, S., van West, P., Chapman, S., Hein, I., Toth, I.K., Pritchard, L. and Birch, P.R.J. 2007. A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450, 115-118. (doi:10.1038/nature06203)
• Gilroy, E.M., Hein, I., van der Hoorn, R., Boevink, P.C., Venter, E., McLellan, H., Kaffarnik, F., Pritchard, L., Hrubikova, K., Shaw, J., Holeva, M., Loake, G.J., Lacomme, C., Birch, P.R.J. 2007. Involvement of Cathepsin B in the Plant Disease Resistance Hypersensitive Response. Plant Journal 52, 1-13.
• van den Berg, N., Berger, D., Hein, I., Birch, P.R.J., Wingfield, M., Viljoen, A. 2007. Tolerance in banana to Fusarium wilt is associated with early up-regulation of cell wall-strengthening genes in the roots. Molecular Plant Pathology 8, 333-341.
• Avrova, A.O., Whisson, S.C., Pritchard, L., Venter, E., de Luca, S., Hein, I., Birch, P.R.J. 2007. A novel, non-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans. Microbiology 153, 747-759.
• Ravirala, R.S., Barabote, R.D., Wheeler, D.M., Reverchon, S., Tatum, O., Malouf, J., Liu, H., Pritchard, L., Hedley, P., Birch, P.R.J., Toth, I.K., Payton, P., San Francisco, M.J.D. 2007. Efflux pump gene expression in Erwinia chrysanthemi is induced by exposure to phenolic acids. Molecular Plant-Microbe Interactions 20, 313-320.

2006

• Bos, J.I., Kanneganti, T., Young, C., Cakir, C., Armstrong, M.R., Birch, P.R.J., Kamoun, S. 2006. The C-terminal half of Phytophthora infestans RXLR effector AVR3a is sufficient for triggering R3a-mediated hypersensitivity and suppressing INF1-induced cell death. Plant Journal 48, 165-176.
• Toth, I.K., Pritchard, L., Birch, P.R.J. 2006. Comparative genomics reveals what makes an enterobacterial plant pathogen. Annual Review of Phytopathology 44, 305-336.
• Balakrishnan, V., Babujee, L., Liu, H., Hedley, P., Fujikawa, T., Birch, P., Toth, I., Tsuyumu, S. 2006. Erwinia chrysanthemi 3937 PhoQ sensor kinase regulates several virulence determinants. Journal of Bacteriology 188, 3088-3098.
• Pritchard, L., White, J., Birch, P.R.J., Toth, I.K. 2006. GenomeDiagram: a python package for the visualisation of large-scale genomic data. Bioinformatics 22, 616-617.
• Birch, P.R.J., Rehmany, A.P., Pritchard, L., Kamoun, S., Beynon, J.L. 2006. Trafficking Arms: Oomycete Effectors Enter Host Plant Cells. Trends in Microbiology 14, 8-11.
• Toth, I.K., Moleleki, M., Pritchard, L., Liu, H., Humphris, S., Hyman, L., Axelsen, G.W., Brurberg, M.B., Ravensdale, M., Gilroy, E. and Birch, P.R.J. 2006. “Erwiniae: Genomics and the Secret Life of a Plant Pathogen” in Bailey, M.J. et al. (Eds). Microbial Ecology of Aerial Plant Surfaces, CABI Publishing. ISBN: 978-1-84593-061-5.

2005

• Toth, I.K., Birch, P.R.J. 2005. Rotting Softly and Stealthily. Current Opinion in Plant Biology 8, 424-429.
• Rehmany, A.P., Gordon, A., Rose, L.E., Allen, R.L., Armstrong, M.R., Whisson, S.C., Kamoun, S., Birch, P.R.J., Beynon, J.L. 2005. Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 genes from two Arabidopsis lines. The Plant Cell 17, 1839-1850.
• Armstrong, M.R., Whisson, S.C., Pritchard, L., Bos, J.I.B., Venter, E., Avrova A.O., Rehmany, A.P., Böhme, U., Brooks, K., Cherevach, I., Hamlin, N., White, B., Fraser, A., Lord, A., Quail, M., Churcher, C., Hall, N., Berriman, M., Huang, S., Kamoun, S., Beynon, J.L., Birch, P.R.J. 2005. An Ancestral Oomycete Locus Contains Late Blight Avirulence Gene Avr3a, Encoding a Protein that is Recognised in the Host Cytoplasm. Proceedings of the National Academy of Sciences USA 102, 7766-7771.
• Grenville-Briggs, L., Avrova, A.O., Bruce, C.R., Williams, A., Whisson, S.C., Birch, P.R.J., van West, P. 2005. Elevated amino acid biosynthesis in Phytophthora infestans during appressorium formation and potato infection. Fungal Genetics and Biology 42, 244-256.
• Liu, Z., Bos, J., Armstrong, M., Whisson, S.C., da Cunha, L., Torto, T., Win, J., Avrova, A.O., Wright, F., Birch, P.R.J., Kamoun, S. 2005. Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans. Molecular Biology and Evolution 22, 659-672.
• Randall, T.A., Dwyer, R.A., Huitema, E., Beyer, K., Cvitanich, C., Kelkar, H., Ah Fong, A., Gates, K., Roberts, S., Yatzkan, E., Gaffney, T., Law, M., Testa, A., Torto, T., Zhang, M., Zheng, L., Binder, A., Birch,  P.R.J., Gisi, U., Govers, F., Gow, N., Mauch, F., van West, P., Waugh, M., Yu, J., Boller, T., Kamoun, S., Lam, S.T., Judelson, H.S. 2005. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Molecular Plant-Microbe Interactions 18, 229-243.
• Pemberton, C.L., Whitehead, N.A., Sebaihia, M., Bell, K.S., Hyman, L.J., Harris, S.J., Matlin, A.J., Robson, N.D., Birch, P.R.J., Carr, Toth, I.K. and Salmond, G.P.C. 2005. Novel quorum sensing-controlled genes in Erwinia carotovora subspecies carotovora: Identification of a fungal elicitor homologue in a soft-rotting bacterium. Molecular Plant-Microbe Interactions 18, 343-353.
• Corbett, M., Virtue, S., Bell, K.S., Birch, P.R.J., Hyman, L.J., Lilley, K., Toth, I.K. and Salmond, G.P.C. 2005. Identification of a new quorum sensing-controlled virulence factor in Erwinia carotovora subspecies atroseptica secreted via the Type II targeting pathway. Molecular Plant-Microbe Interactions 18, 334-342.

2004

• van den Berg, N., Campbell, B.G., Hein, I., Birch, P.R.J., Berger, D.K. 2004. High throughput screening of SSH cDNA libraries using DNA microarray analysis. BioTechniques 37, 818-822.
• Bell, K.S., Sebaihia, M., Pritchard, L., Holden, M., Hyman, L.J., Holeva, M.C., Thomson, N.R., Bentley, S.D., Churcher, L.J.C., Mungall, K., Atkin, R., Bason, N., Brooks, K., Chillingworth, T., Clark, K., Doggett, J., Fraser, A., Hance, Z., Hauser, H., Jagels, K., Moule, S., Norbertczak, H., Ormond, D., Price, C., Quail, M.A., Sanders, M., Walker, D., Whitehead, S., Salmond, G.P.C., Birch, P.R.J., Parkhill, J., Toth, I.K. 2004. The genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica SCRI1043 and functional genomic identification of novel virulence factors. Proceedings of the National Academy of Sciences USA 101, 11105-10.
• Holeva, M.C., Bell, K.S., Hyman, L.J., Avrova, A.O., Whisson, S.C., Birch, P.R.J. and Toth, I.K. 2004. Use of a Pooled Transposon Mutation Grid to Demonstrate Roles in Disease Development for Erwinia carotovora subsp. atroseptica Putative Type III Secreted Effector (DspE/A) and Helper (HrpN) Proteins. Molecular Plant-Microbe Interactions 17, 943-950.
• Faivre-Rampant, O., Gilroy, E., Hrubikova, K., Hein, I., Millam, S., Loake, G., Birch, P.R.J., Taylor, M., Lacomme, C. 2004. Potato virus X-induced gene silencing in leaves and tubers of potato. Plant Physiology 134, 1308-1316.
• Hein, I., Campbell, E., Woodhead, M., Young, V., Hedley, P., Morris, W., Ramsey, L., Stockhaus, J., Lyon, G.D., Newton, A.C., Birch, P.R.J. 2004. Characterisation of early transcriptional changes involving multiple signalling pathways in the Mla13 barley interaction with Powdery Mildew (Blumeria graminis f.sp. hordei). Planta 218, 803-813.
• Avrova, A.O., Taleb, N., Rokka, V.M., Heilbronn, J., Hein, I., Gilroy, E., Cardle, L., Stewart, H., Loake, G., Jauferally-Fakim, Y., Birch, P.R.J. 2004. Potato Oxysterol Binding Protein and Cathepsin B are Rapidly Up-regulated in Independent Defence Pathways that Distinguish R Gene-mediated and Field Resistances to Phytophthora infestans. Molecular Plant Pathology 5, 45-56.
• Tani, H., Chen, X., Nurmberg, P., Grant, J.J., SantaMaria, M., Chini, A., Gilroy, E., Birch, P.R.J. and Loake, G.J. 2004. Activation tagging in plants: a tool for gene discovery. Functional and Integrative Genomics 4, 258-266.
• Birch, P.R.J., Cooke, D.E.L. 2004. Mechanisms of infection – oomycetes. In: Encyclopedia of Plant and Crop Science (Ed. R.M. Goodman). Marcel Dekker Inc, pp697-700.

Posters

(View all posters)

Attachment	Size
Expression profiles of RXLR motif-containing sequences during Phytophthora infestans-potato interactions	1.4 MB
Erwinia Overcomes Potato Resistance by Attacking Its Defences	103.14 KB
Identification Of Novel Erwinia Genes Involved In Disease	133.37 KB
Post-Genomic Analysis of Erwinia Carotovora Virulence Responses in In Vitro and In Planta Environments	119.48 KB
A step closer to blackleg control: Genomics opens our eyes to the true nature of Erwinia and its interaction with plants	212.62 KB
The Role of Protease Cathepsin B during non-host HR	203.17 KB
The Role of Protease Cathepsin B during non-host HR	147.75 KB
Viral-induced gene silencing (VIGS) vector development for functional studies in crop plants	154.46 KB
Viral-induced gene silencing (VIGS) vector development for functional studies in Solanaceae	192.55 KB
VIGS for functionally analysing novel defence genes in potato	170.77 KB
An Ancestral Oomycete Locus Contains Late BlightAvirulence Gene Avr3a	183.93 KB
Yeast 2 Hybrid Screening to Identify Plant Targets of Oomycete Effector Protein AVR3a	245.47 KB
Transient gene silencing - a step forward in identifying novel pathogenicity factors in the late blight pathogen Phytophthora infestans	326.51 KB
Identification of novel pathogenicity factors in the late blight pathogen Phytophthora infestans	325.8 KB
Role of Erwinia carotovora subsp. atroseptica harpins in the manipulation of host defences	115.22 KB
Role of Pectobacterium atrosepticum (Pba) effectors in the manipulation of host defences	414.71 KB
Screening wild potato accessions for resistance to the virulent allele of the Phytophthora infestans effector avr3a EM	307.83 KB
Genomics approaches uncover an alternative life-style of the plant pathogen Pectobacterium atrosepticum	210.23 KB
A whole genome transcriptomics approach to determine the quorum sensing regulon of Pectobacterium atrosepticum during infection	176.37 KB
Comparative Genomic Analysis of Erwinia carotovora subsp atroseptica: Evidence For Extensive Horizontal Gene Transfer with Plant Associated Bacteria	613.23 KB
Quorum sensing regulates novel phytotoxin production in the plant pathogen Pectobacterium atrosepticum	278.9 KB
Phytotoxins produced by Pectobacterium atrosepticum impact multiple defense hormone pathways in potato	479.11 KB
Quorum sensing and pectin catabolism regulate phytotoxin production in Pectobacterium atrosepticum	344.03 KB
Prediction of transcription factor binding sites in bacterial genomes: case study with Pectobacterium atrosepticum	405.75 KB
Development of a Computational Pipeline For Automated Prediction of Bacterial Transcription Factor Binding Sites	1.39 MB
Functional characterization of the RxLR-EER translocation signal for delivery of oomycete effector proteins into host plant cells	162.54 KB
Comparative and functional genomics identifies major differences between genomic islands in soft rotting enterobacterial plant pathogens	414.25 KB
Translocation of effector proteins from the oomycete Phytophthora infestans into plant cells	780.57 KB
Evolutionarily distinct RXLR effectors from distantly related oomycetes target the plant exocyst	1000.56 KB
Is KIPI30 the main virulence target of the Phytophthora infestans effector protein Avr3a?	175.3 KB
Exploiting the Phytophthora infestans genome to determine targets for sustainable potato protection	597.58 KB