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Ian Toth

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Recent publications

Staff picture: Ian Toth
Controlling Weeds, Pests and Diseases Research Theme Leader
+44 (0)844 928 5428 (*)

The James Hutton Institute
Dundee DD2 5DA
Scotland UK

  • Coordinator of Work Package 6.4 (Plant Health) and Theme 6 representative (for The James Hutton Institute Dundee) of the Scottish Government funded Programmes of Science

Current research interests 

  • Molecular bases of pathogenesis in the enterobacterial potato pathogens Pectobacterium atrosepticum (Pba - formerly Erwinia carotovora subsp. atroseptica) and Dickeya species, and the eucalyptus pathogen Pantoea ananatis using functional and comparative genomics and systems biology approaches.
  • Ecology of Pba and Dickeya species in the environment when not causing disease, including the role of alternative plant hosts (including weeds).
  • The interaction between human enteric pathogens and plants and the role of these plants in the spread of disease.

Past research 

Within the family Enterobacteriaceae, a wide range of bacteria cause disease on humans, animals and plants. Human and animal pathogens include E. coli and Salmonella species, while plant pathogens include species of PectobacteriumDickeya and Pantoea. The main areas of our research are investigating the pathogenesis and ecology of the potato pathogens Pectobacterium atrosepticum (Pba)and Dickeya species (including D. dianthicola and the yet to be officially named 'D. solani').  Similar aspects of Pantoea ananatis, a pathogen of several crops including onion, maize and eucalyptus, are also being investigated as part of a collaboration with the University of Pretoria in South Africa.  Our research on these pathogens ties in closely with the work of Nicola Holden, who is investigating the interactions between human pathogens and plants and the role of such plants in the spread of disease to humans (Holden et al. 2009). 

The soft rot pathogens Pba and Dickeya spp., which cause blackleg diseases in the field and soft rots in storage, are a major threat to potato production in Europe and elsewhere. It is particularly important to reduce or prevent the incidences of such diseases in GB as a whole and in Scottish seed production in particular. During my time at the Institute I have investigated the epidemiology of Pba and, in partnership with Paul Birch and Leighton Pritchard, have also initiated the research area of plant pathogen genomics.

In 2002, we received funding from the Scottish Government to sequence the genome of Pba, which we did in collaboration with the Sanger Institute in Cambridge (Bell et al. PNAS 2004). We have since used the genome sequence to develop comparative genomics tools such as GenomeDiagram (Pritchard et al. 2006), and have used these tools to investigate pathogenesis and other aspects of life on plants. This last aspect is now part of a second new research area called environmental pathology. We have also identified genes within the enterobacterial animal pathogens that may play roles in their survival on plants (Toth et al. 2006). Functional genomics tools have been developed including whole-genome microarrays for Pba, Dickeya dadantii and Erwinia amylovora to identify pathogenicity and life-style determinants novel to these pathogens. We have used the arrays to investigate areas such as quorum sensing (Liu et al. 2008), regulation of Type III secretion (Shihui Yang et al. 2010) and the distribution of genomic islands between closely related species (Pritchard et al. 2009).  

A partnership with Biomathematics and Statistics Scotland (BioSS) has allowed us to take a systems approach to unraveling regulatory networks involved in the infection process (Lin et al. 2010). 

More recent work, in collaboration with Prof. Teresa Coutinho at the University of Pretoria in South Africa, has been on pathogenesis and colonisation by Pantoea ananatis. As part of this work we obtained and published the P. ananatis genome sequence, which became the first bacterial phytopathogen to be sequenced in Africa (De Maayer et al. .2010).  

Our particular interests include:

  • Identification of determinants involved particularly in a biotrophic phase of infection. This includes the role of Type III effectors and phytotoxins in the manipulation of plant defences.
  • The determination of regulatory networks involved both in pathogenesis and defence during the pathogen-host interaction.
  • Screening for resistance in potato against Pba and Dickeya spp.  
  • Comparative genomics studies between these closely related pathogens to determine major differences in pathogenicity and their ability to survive on plants.
  • The identification and role of factors involved in the life of these pathogens away from the diseased plant, and how colonisation of other plant species impacts on crop contamination and disease.

Key Collaborators

  • George Salmond (University of Cambridge, UK)
  • Tracy Palmer (University of Dundee, UK)
  • Dirk Husmeier (BioSS, UK)
  • George Sundin (Michigan State University, USA)
  • Ching-Hong Yang (University of Wisconsin Milwaukee, USA)
  • Pablo Rodriguez Palenzuela (Polytechnical University of Madrid, Spain)
  • Teresa Coutinho (University of Pretoria, South Africa) 
  • May-Bente Brurberg (Bioforsk, Aas, Norway)
  • Andrew Pitman (Institute for Plant & Food Research, New Zealand)

Related Publication


  • Joanna K. Fyans, Dawn Bignell, Rosemary Loria, Ian Toth and Tracy Palmer. 2012. The ESX/Type VII secretion system modulates development of the plant pathogen Streptomyces scabies. Mol. Plant Pathol. In Press.
  • Marion F. Cubitt, Pete E. Hedley, Neil Williamson, Jenny A. Morris, Emma Campbell, Ian K. Toth and George P.C. Salmond. 2012. A metabolic regulator modulates virulence and quorum sensing signal production in Pectobacterium atrosepticum. Mol. Plant-Microbe Interact. In Press.
  • L. Pritchard, S. Humphris, G. S. Saddler, N. M. Parkinson, Valérie Bertrand, J. G. Elphinstone and I. K. Toth. 2012. Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathol. In Press.
  • Rita Monson, Tom Burr, Tim Carlton, Hui Liu, Peter Hedley, Ian Toth and George P.C. Salmond. 2012.  Dentification of genes within the VirR regulon of Pectobacterium atrosepticum and characterization of their roles in quorum sensing dependent virulence. Env. Microbiol. In Press.
  • Amy Charkowski, Carlos Blanco,Guy Condemine, Dominique Expert, Thierry Franza,Christopher Hayes,Nicole Hugouvieux-Cotte-Pattat, Emilia López Solanilla,David Low, Lucy Moleleki, Minna Pirhonen,Andrew Pitman, Nicole Perna,Sylvie Reverchon, Pablo Rodriguez Palenzuela, Michael San Francisco, Ian Toth, Shinji Tsuyumu, Jacquie van der Walls, Jan van der Wolf, Frédérique Van Gijsegem, Ching-Hong Yang and Iris Yedidia. 2012. The Role of Secretion Systems and Small Molecules in Soft-Rot Enterobacteriaceae Pathogenicity. Annu. Rev. Phytophathol. In Press.
  • John Mansfield, Stephane Genin, Shimpei Magori, Vitaly Citovsky, Malinee Sriariyanum, Pamela Ronald, Max Dow, Valérie Verdier, Steven V. Beer, Marcos A. Machado, Ian Toth, George Salmond and Gary D. Foster 2012. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol. Plant Pathol. In Press.
  • Paul R. J. Birch, Glenn Bryan, Brian Fenton, Eleanor M. Gilroy, Ingo Hein, John T. Jones, Ankush Prashar, Mark A. Taylor, Lesley Torrance and Ian K. Toth. 2012. Crops that feed the world. Potato: are the trends of increased 5 global production sustainable? Food Security
  • Leighton Pritchard, Nicola J. Holden, Martina Bielaszewska, Helge Karch and Ian K. Toth 2012. Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coliO104:H4 Outbreak Strains. PloS One. In Press.
  • Bhanupratap R. Vanga, Ruth C. Butler, Ian K. Toth, Clive W. Ronson and Andrew R. Pitman. 2012. Inactivation of PbTopo IIIβ causes hyper-excision of the Pathogenicity 1 Island HAI2 resulting in reduced virulence of Pectobacterium atrosepticum. Mol. Microbiol. In Press.
  • Adrian C. Newton, Lesley Torrance, Nicola Holden, Ian K. Toth, David E. L. Cooke, Vivian Blok and Eleanor Gilroy. 2012. Climate change and defence against pathogens in plants. Advances in Applied Microbiology, 81, 89-132.
  • R Ryan McNally, Ian K Toth, Peter JA Cock, Leighton Pritchard, Pete E Hedley, Jenny Morris, Youfu Zhoa and George Sundin. 2012. Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors. Mol. Plant Pathol. 13, 160-173. 
  • Daniel Pérez-Mendoza, Sarah J. Coulthurst, Sonia Humphris, Emma Campbell, Martin Welch, Ian K. Toth and George P.C. Salmond. 2011. A multi-repeat adhesin of the phytopathogen, Pectobacterium atrosepticum, is secreted by a Type I pathway and is subject to complex regulation involving a non-canonical diguanylate cyclise. Mol Micro. In Press.
  • Dongping Wang, Mingsheng Qi, Bernarda Calla, Schuyler S. Korban, Steven J. Clough, Peter J. A. Cock, George W. Sundin, Ian Toth, and Youfu Zhao 2011. Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. Mol.Plant Microbe Interact. 25, 6-17.
  • Isabel Rio-Alvarez, Jose J. Rodríguez-Herva, Raquel Cuartas-Lanza, Ian Toth, Leighton Pritchard, Pablo Rodríguez-Palenzuela and Emilia López-Solanilla. 2011. Genome-wide analysis of the response of Dickeya dadantii 3937 to plant antimicrobial peptides. Mol. Plant-Microbe Interact. 25, 523-533.
  • Glasner, J.D., Yang, C.H., Reverchon, S., Hugouvieux-Cotte-Pattat, N., Condemine, G., Bohin, J.P., Van Gijsegem, F., Yang, S., Franza, T., Expert, D., Plunkett, G. 3rd, San Francisco, M.J., Charkowski, A.O., Py, B., Bell, K., Rauscher, L., Rodriguez-Palenzuela ,P., Toussaint, A., Holeva, M.C., He, S.Y., Douet, V., Boccara, M., Blanco, C., Toth, I., Anderson, B.D., Biehl, B.S., Mau, B., Flynn, S.M., Barras, F., Lindeberg, M., Birch, P., Tsuyumu, S., Shi, X., Hibbing, M., Yap, M.N., Carpentier, M., Dassa, E., Umehara, M., Kim, J.F., Rusch, M., Soni, P., Mayhew, G.F., Fouts, D.E., Gill, S.R., Blattner, F.R., Keen, N.T., Perna, N.T. 2011. Genome sequence of the plant pathogenic bacterium Dickeya dadantii 3937. Journal of Bacteriology 2011 193, 2076-77.
  • Toth I. K., van der Wolf J.M., Saddler G., Pirhonen M., Lojkowska E., Helias V., Tsror L. and Elphinstone J.E. 2011. Dickeya species: An emerging problem for potato production in Europe. Plant Pathol. 60, 385-99.
  • Lin, K., Husmeier, D., Dondelinger, F., Mayer, C.D., Liu, H., Prichard, L., Salmond, G.P., Toth, I.K., Birch, P.R. 2010. Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum. Methods in Molecular Biology 673, 253-81.
  • Yang, S., Peng, Q., Zhang, Q., Zou, L., Li, Y., Robert, C., Pritchard, L., Liu, H., Hovey, R., Wang, Q., Birch, P.R.J., Toth, I.K. and Yang, C-H. 2010. Genome wide profiling of HrpL-regulated genes in the necrotrophic plant pathogen Dickeya dadantii 3937. PLoS One 5, e13472.
  • Joshi, M., Mann, S.G., Antelmann, H., Widdick, D., Fyans, J.K., Chandra, G., Hutchings, M., Toth, I., Hecker, M., Loria, R. and Palmer, T. 2010. The Tat pathway exports multiple virulence proteins in the plant pathogen Streptomyces scabies. Molecular Microbiology 77, 252-71.
  • De Maayer, P., Venter, S.N., Toth, I.K., Birch, P.R.J. and Coutinho, T.A. 2010. The genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback. Journal of Bacteriology 192, 2936-2937.
  • Antunez-Lamas M., Cabrera E., López-Solanilla E., Solano R., González-Melendi P., Chico J-M., Toth I. K., Birch P. R. J., Prichard L., Liu H., Rodríguez Palenzuela P. 2009. Bacterial chemo-attraction towards jasmonate plays a role in the penetration of Dickeya dadantii through wounded tissues. Molecular Microbiology 74, 662-671.
  • Blower T.R., Fineran P.C., Johnson M.J., Toth I.K., Humphreys D.P. and Salmond G.P.C. 2009. Mutagenesis and functional characterisation of the RNA and protein components of the toxIN abortive infection / toxin-antitoxin locus of Erwinia. Journal of Bacteriology 191, 6029-6039.
  • Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice Francois, Jacques Schrenzel, Peter E. Hedley, Paul R. J. Birch, Ian K. Toth 2009. Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens. PLoS Computational Biology 5, e1000473.
  • Holden N., Pritchard L. and Toth I. K. 2009. Colonisation outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microb. Rev. 33, 689-703.
  • Liu H., Coulthurst S. J., Pritchard L., Hedley P. E., Ravensdale M., Humphris S., Burr T., Takle G., Brurberg M-B, Birch P. R. J., Salmond G. P. C., Toth I. K. 2008. Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathogens 4, e1000093.
  • Coulthurst S. J, Lilley K. S., Hedley P., Liu H., Toth I. K. and Salmond G. P. C. 2008. DsbA plays a critical and multi-faceted role in the production of secreted virulence factors by the phytopathogen, Erwinia carotovora subsp. atroseptica. Journal of Biological Chemistry 283, 23739-23753.

PDF file: Ian Toth full publication list (109 KB)

Scientific posters/conferences

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 Onward into battle: Dickeya (Erwinia chrysanthemi) gets the upper hand 1.17 MB
File Environmental Change - Impacts on pests and Diseases 725.69 KB
File Characterisation of Effector Proteins Secreted By Erwinia carotovora subsp. atroseptica and Their Role on Host Resistance 103.14 KB
File Characterisation of Effector Proteins Secreted By Erwinia carotovora subsp. atroseptica and Their Role on Host Resistance 262.03 KB
File Post-Genomic Analysis of Erwinia Carotovora Virulence Responses in In Vitro and In Planta Environments 119.48 KB
File Identification Of Novel Erwinia Genes Involved In Disease 133.37 KB
File A whole genome transcriptomics approach to determine the quorum sensing regulon of Pectobacterium atrosepticum during infection 176.37 KB
File Role of Erwinia carotovora subsp. atroseptica harpins in the manipulation of host defences 115.22 KB
File Role of Pectobacterium atrosepticum (Pba) effectors in the manipulation of host defences 414.71 KB
File Genomics approaches uncover an alternative life-style of the plant pathogen Pectobacterium atrosepticum 210.23 KB
File Comparative Genomic Analysis of Erwinia carotovora subsp atroseptica: Evidence For Extensive Horizontal Gene Transfer with Plant Associated Bacteria 613.23 KB
File Comparative and functional genomics identifies major differences between genomic islands in soft rotting enterobacterial plant pathogens 414.25 KB
File Methods to investigate interactions between human pathogenic enterobacteria and plant hosts 235.09 KB
File Prediction of transcription factor binding sites in bacterial genomes: case study with Pectobacterium atrosepticum 405.75 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 Quorum sensing regulates novel phytotoxin production in the plant pathogen Pectobacterium atrosepticum 278.9 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.