Image of Pectobacterium

We are investigating diseases caused by enterobacterial plant pathogens.

At The James Hutton Institute we are investigating diseases caused by enterobacterial plant pathogens, with a focus on the potato pathogens Pectobacterium atrosepticum (Pba- formerly Erwinia carotovora subsp. atroseptica), and Dickeya species (formerly Erwinia chrysanthemi), including D. dianthicola and ‘D. solani’ (Toth et al 2010). Our main interest is to understand the interactions between these pathogens and their hosts and we are employing genomics tools to do this.


In 2004, we published the first genome sequence of an enterobacterial plant pathogen (that of Pba – Bell et al. 2004) and was part of an international team to annotate the genome of its close relative Dickeya dadantii (Perna et al. 2011). We have also developed powerful comparative genomics tools to compare and visualise large genome sequence data sets to help identify pathogen-specific virulence determinants, as well as the similarities and differences between enterobacterial plant pathogens and other bacterial plant, animal and human pathogens (Pritchard et al. 2005; Toth et al. 2006).

Image showing array data

Using comparative genomics, together with techniques such as transposon mutation grids (Holeva et al. 2004), we have uncovered the first evidence of phytotoxins (for example, coronafacic acid), a Type IV secretion system and other virulence determinants previously uncharacterized in this group of pathogens and demonstrated their roles in disease (Bell et al. 2004). We have developed the first genome-wide microarrays to Pba and Dda and are using them as part of a systems biology approach to unravel the complex regulatory cascades involved in pathogenesis (with a main emphasis on quorum sensing and Type III secretion), and to investigate the presence and distribution of genomic islands in these pathogens (Corbett et al. 2005; Coulthurst et al. 2008; Liu et al. 2008; Lin et al. 2010; Pemberton et al. 2005; Perez-Mendosa et al. 2011; Pritchard et al. 2009; Venkatesh et al. 2006; Wang et al. 2011; Yang et al. 2010). These are currently the only whole genome microarrays available for this group of pathogens and are thus a key resource for other groups worldwide.


The “effectors” coronafacic acid and Type III proteins (including DspA/E and HrpW) in Pba have been identified as playing a role in the suppression of plant host defenses (Holeva et al. 2004; Moleleki et al. submitted). Using this approach we have uncovered potato genes involved in resistance; shown that over-expression of one of these genes in a transgenic potato plant increases resistance to Pba; and discovered that this gene is naturally highly expressed in resistant cultivars used to breed for resistance to Pba (thus acting as a potential marker in the breeding process). This has led to screening of the Institute’s pre-breeding potato material to identify resistances that could be deployed to commercial varieties. We have used microarrays to investigate the regulation of the Type III secretion system and associated genes in D. dadantii and E. amylovora in collaboration with groups at University of Wisconsin-Milwaukee and Michigan State University, respectively (McNally et al. 2011; Yang et al. 2010).

Our genomics approaches have identified a number of genes within the Pba genome that suggest a potential host range away from potato. For example, a specific mechanism of attachment to the roots of brassica crop and weed species has been found, together with the ability to fix nitrogen on these roots. This work has important implications on the spread and survival of this and other plant pathogens in the environment (for example, its role in crop rotation and weed management) and is also relevant to the survival and spread of enterobacterial human pathogens on plants (Holden et al. 2009).


A more recent interest is the pathogenicity and epidemiology of the potato pathogens Dickeya dianthicola and D. solani, which are becoming an increasing threat to potato production in Europe. As part of this work we have sequenced 22 strains from this genus and are now undertaking comparative genome analyses to identify primers, probes and other sequences for diagnostics and strain typing, as well as to investigate pathogenicity. An important consideration in the research on Dickeya species will be to investigate the role of climate change on their spread and disease-causing abilities.

Current collaborators:

  • Teresa Coutinho, Lucy Moleleki and Fanus Venter, University of Pretoria, South Africa: “Pantoea ananatis on eucalyptus” (de Maajer et al. 2010).
  • George Sundin, Michigan State University, USA: “HrpL regulation in Erwinia amylovora” (McNally et al. 2011).
  • Youfu Zhao, University of Illinois, USA: “Rcs regulation in Erwinia amylorvora” (Wang et al. 2011)
  • George Salmond, University of Cambridge: “Quorum sensing in P. atrosepticum” (Liu et al. 2008); “Abortive infection in P. atrosepticum” (Blower et al. 2009); “DspA regulation in P. atrosepticum” (Coulthurst et al. 2008).
  • Sarah Coulthurst, University of Dundee: “Quorum sensing in P. atrosepticum” (Liu et al. 2008); “DspA regulation in P. atrosepticum” (Coulthurst et al. 2008).
  • Tracy Palmer, University of Dundee: “Tat secretion system in Streptomyces scabies” (Joshi et al. 2010).
  • Pablo Rodriguez Palenzuela, Universidad Politécnica de Madrid, Spain: “Chemo-attraction towards jasmonate in D. dadantii” (Antunez-Lamas et al. 2010).
  • Andy Pitman, The New Zealand Institute for Plant & Food Research Christchurch, New Zealand: “Hypo-excision of pathogenicity islands from P. atrosepticum”.
  • Daniel Pérez Mendoza, CSIC Granada, Spain: “diguanylate cyclise regulation of multi-repeat adhesion in P. atrosepticum” (Pérez Mendoza et al. 2011).
  • Nicole Perna and Jeremy Glasner, University of Wisconsin-Madison, USA: “Genome sequence of D. dadantii” (Perna et al. 2011).
  • Dirk Husmeier, Biomathematics and Statistics Scotland (BioSS), Edinburgh: “Reverse engineering of regulatory newtworks in P. atrosepticum” (Lin et al. 2010).
  • Ching-Hong Yang, University of Wisconsin-Milwaukee, USA: “HrpL regulation in D. dadantii” (Yang et al. 2010).
  • Jacques Schrenzel, University of Geneva, Switzerland: “Microarray comparative genomic hybridisation analysis of genomic islands in enterobacterial plant pathogens” (Pritchard et al. 2009).
  • May-Bente Brurberg, Bioforsk, Aas, Norway: “Quorum sensing in P. atrosepticum” (Liu et al. 2008).