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Paul Birch

Staff picture: Paul Birch
University of Dundee Division of Plant Sciences
Cell and Molecular Sciences
paul.birch@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

Employment history

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

Current 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 the oomycete late blight pathogen of potato, Phytophthora infestans.

We are particularly interested in ‘effector’ proteins that are translocated inside the host cell, in the mechanisms by which they are delivered and the means by which they are regulated in P. infestans. We want to know when they are needed and where they are localised during infection. 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, development or metabolism? We also want to identify those effectors that are recognised by resistance proteins in wild potato and non-host plants, and to elucidate the precise mechanisms underpinning recognition.

Key Collaborators

  • Jim Beynon (University of Warwick, UK).
  • Frederic Brunner (University of Tuebingen, Germany)
  • Teresa Coutinho, Dave Berger, Lucy Moleleki, Noelani van den Berg (University of Pretoria, South Africa).
  • Francine Govers (Wageningen University, Netherlands).
  • Howard Judelson (University of California, Riverside, USA).
  • Sophien Kamoun, Jonathan Jones (The Sainsbury Laboratory, JIC, UK).
  • Veronique Lefebvre (INRA, Avignon, France).
  • Juan Morales (National University of Colombia, Medellin, Colombia).
  • Ari Sadanandom (University of Durham, UK).
  • Tian Zhendong, Xie Conghua (Huazhong Agricultural University, Wuhan, China)
  • Vivianne Vleeshouwers (Wageningen University, Netherlands).
  • Pieter van West (University of Aberdeen, UK).

Bibliography

  • Feechan, A.; Turnbull, D.; Stevens, L.J.; Engelhardt, S.; Birch, P.R.J.; Hein, I.; Gilroy, E.M., (2015) The hypersensitive response in PAMP- and effector-triggered immune responses., In: Gunawardena, A. & McCabe, P. (eds.). Plant Programmed Cell Death. Springer, New York, Chapter 10, pp235-258.
  • Boevink, P.; McLellan, H.; Bukharova, T.; Engelhardt, S.; Birch P.R.J., (2014) In vivo protein-protein interaction studies with BiFC: conditions, cautions, and caveats., In: Birch, P.R.J., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, 2nd ed. Volume 1127, Chapter 6, 81-90.
  • Birch, P.; Jones, J.; Bos, J.I. (eds)., (2014) Plant-pathogen interactions: methods and protocols., Methods in Molecular Biology, Volume 1127. 2nd edition, Humana Press, New York, 306pp.
  • Birch, P.R.J.; Coates, M.; Beynon, J., (2012) Evolution of virulence in oomycete plant pathogens., In: Howlett, B., Heitman, J. & Sibley, D. (eds.). Evolution of Virulence in Eukaryotic Microbes. Wiley Press, pp387-403.
  • Boevink, P.; Birch, P.R.J.; Whisson, S.C., (2011) Imaging fluorescently tagged Phytophthora effector proteins inside infected plant tissue., In: McDowell, J.M. (ed.). Methods in Molecular Biology Plant Immunity: Methods and Protocols. Humana Press, Totowa, New Jersey, USA, Chapter 712, pp195-209.
  • Lin, K.; Husmeier, D.; Dondelinger, F.; Mayer, C.D.; Liu, H.; Pritchard, L.; Salmond, G.P.C.; Toth, I.K.; Birch, P.R.J., (2010) Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum., In: Fenyo, D. (ed.). Computational Biology. Springer, New York, Chapter 17, pp253-281.
  • Birch, P.R.J.; Avrova, A.O., (2009) Gene expression profiling., In: Lamour, K.H. & Kamoun, S. (eds.). Oomycete Genetics and Genomics: Diversity, Interactions and Research Tools. Wiley-Blackwell, Hoboken, New Jersey, USA, 477-492.
  • Toth, I.K.; Pritchard, L.; Birch, P.R.J.; Liu, H., (2008) Genomics of the enterobacterial plant pathogens., In: Jackson, R.W. (ed.). Plant Pathogenic Bacteria: Genomics and Molecular Biology. Caister Academic Press, Norfolk, 163-174.
  • Toth, I.K.; Moleleki, L.N.; Pritchard, L.; Liu, H.; Humphris, S.N.; Hyman, L.; Axelsen, G.W.; Brurberg, M.B.; Ravensdale, M.; Gilroy, E.M.; Birch, P.R.J., (2006) Erwiniae: genomics and the secret life of a plant pathogen., In: Bailey, M.J., Lilley, A.K., Timms-Wilson, T.M. & Spencer-Phillips, P.T.N. (eds.). Microbial Ecology of Aerial Plant Surfaces. CABI Publishing, Wallingford, pp191-201.
  • Birch, P.R.J.; Cooke, D.E.L., (2004) Mechanisms of infection - oomycetes., In: Goodman, R.G. (ed.). Encyclopedia of Plant and Crop Science. Marcel Dekker Inc., New York, pp697-700.
  • Birch, P.R.J.; Avrova, A.O.; Dellagi, A.; Lacomme, C.; Santa Cruz, S.; Lyon, G.D., (2000) To die and let live: programmed cell death in plants in response to pathogen attack., In: Molecular Plant Pathology (eds. M. Dickinson and J. Beynon). Annual Plant Reviews, Sheffield Academic Press, Sheffield, Volume 4, pp175-197.
  • Duncan, J.M.; Cooke, D.E.L.; Birch, P.R.J.; Toth, R.L., (1998) Molecular variability in sexually reproducing fungal plant pathogens., In: Bridge, P., Couteaudier, Y. & Clarkson, J. (eds.). Molecular Variability of Fungal Pathogens. CAB International, Wallinford, pp19-39.

  • Hein, I.; Birch, P.R.J.; Chapman, S.N.; Bryan, G.J., (2011) Pathogen effector driven search for more durable potato late blight resistance., Annual Report of the Scottish Crop Research Institute for 2010, pp38-40.
  • Avrova, A.O.; Birch, P.R.J.; Hein, I.; Jones, J.T.; Pritchard, L., (2010) Functional analysis of pathogen effectors: how to go from genomics to durable resistance., Annual Report of the Scottish Crop Research Institute for 2009, 39-41.
  • Whisson, S.C.; Boevink, P.; Pritchard, L.; Avrova, A.O.; Morales, J.; Birch, P.R.J., (2006) Effector protein translocation in the Phytophthora infestans - potato infection., Annual Report of the Scottish Crop Research Institute for 2006, pp24-25.
  • Toth, I.K.; Pritchard, L.; Holeva, M.C.; Hyman, L.J.; Bell, K.S.; Whisson, S.C.; Avrova, A.O.; Birch, P.R.J., (2004) New discoveries with Erwinia genomics., Annual Report of the Scottish Crop Research Institute for 2002/2003, p101.
  • Whisson, S.C.; Avrova, A.O.; Birch, P.R.J.; Adam, M.; Blok, V.C.; Jones, J.T., (2004) Functional genomic tools for the major eukaryotic pathogens of potato., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp127-128.
  • Whisson, S.C.; Avrova, A.O.; Armstrong, M.R.; Jones, J.T.; Venter, E.; Birch, P.R.J., (2004) Targeting late blight with gene discovery., Annual Report of the Scottish Crop Research Institute for 2002/2003, pp102-103.
  • Hrubikova, K.; Gilroy, E.M.; Faivre-Rampant, O.; Loake, G.; Birch, P.R.J.; Taylor, M.A.; Lacomme, C., (2003) Viral induced gene silencing in crop species., Annual Report of the Scottish Crop Research Institute for 2002/2003, pp98-99.
  • Toth, I.K.; Bell, K.S.; Holeva, M.C.; Bryan, G.J.; Avrova, A.O.; Hyman, L.; Birch, P.R.J., (2002) Erwinia genomics: A new era in the battle against potato disease., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp25-28.
  • Whisson, S.C.; Avrova, A.O.; Armstrong, M.R.; Campbell, E.; Birch, P.R.J., (2002) Late blight of potato: Pathogen genomics approaches to a continuing problem., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp29-32.
  • Blok, V.C.; Armstrong, M.R.; Banks, B.; Birch, P.R.J.; Bryan, G.J.; Castelli, L.; Jones, J.T.; Kumar, A.; Phillips, M.S.; Purvis, A.; Ramsay, G.; Waugh, R.; Wishart, J., (2002) Investigating gene expression in nematode-infected roots., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp122-124.
  • Whisson, S.C.; van der Lee, T.; Bryan, G.J.; Waugh, R.; Govers, F.; Birch, P.R.J., (2001) Phytophthora infestans genomics: positional cloning of avirulence genes., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp132-135.
  • De Jong, W.; Davidson, J.; Bryan, G.J.; Birch, P.R.J.; Waugh, R.; Marshall, D.F., (2000) Gene discovery in potato., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp105-107.
  • Cooke, D.E.L.; Maughan, V.; Birch, P.R.J.; Toth, R.; Gourlay, F.; Carnegie, S.; Duncan, J.M., (2000) The status of Scottish late blight populations., Annual Report of the Scottish Crop Research Institute for 1999/2000, 150-153.
  • Cooke, D.E.L.; Birch, A.N.E.; Birch, P.R.J.; Duncan, J.M.; Griffiths, D.W.; Lyon, G.D.; Trudgill, D.L.; Williamson, B.; Wilson, T.M.A.; Hillman, J.R., (1998) Are diseased and blemished foodstuffs good for you? The need for plant pathology., Annual Report of the Scottish Crop Research Institute for 1997/98, pp54-60.

Scientific posters/conferences

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

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.