Bacterial Pathogens Team
Research on bacterial pathogens at SCRI
At SCRI we have been studying the biology of Pectobacterium atrosepticum (Pba) for over 40 years and our work and expertise are internationally recognised. We undertake both applied and strategic research, interacting regularly with members of the potato industry, and providing solutions to longer-term disease control through potato resistance. More recently, through genomic and bioinformatics approaches, we have begun to explore a new area of research: investigating the establishment and survival of enteric human pathogens on plants.
Our research on bacterial pathogens can be grouped under five linked themes:
- Pectobacterium genomics
- bioinformatics
- Pectobacterium-potato interaction
- host resistance
- environmental pathology.
Pectobacterium genomics
Staff: Ian Toth, Hui Liu, Leighton Pritchard, Paul Birch
The genome sequence of Pba strain SCRI1043 was obtained by SCRI in collaboration with the Sanger Institute in Cambridge. The sequence was published in 2004 in PNAS and was the first bacterial plant pathogen to be fully sequenced in the UK (and the first enterobacterial plant pathogen to be sequenced worldwide). The project was undertaken in parallel to a Dickeya dadantii (Dda) sequencing project at the University of Wisconsin under the supervision of Professor Nicole Perna, for which SCRI are collaborating partners. At SCRI we have used these sequences to develop the first genome-wide microarrays for this group of pathogens in association with Agilent Technologies. These arrays, which are now being used by a number of groups worldwide, are helping to inform our work on bacterial regulation and the Pba-plant interaction. We have also developed a mutation library of over 10,000 independent gene knock-outs for rapid selection of mutants.
Bioinformatics
Staff: Leighton Pritchard, Ian Toth, Paul Birch, Nicola Holden
At SCRI, we undertake comparisons between the genomes of bacterial plant (Pba) and human/animal (E. coli, Salmonella spp.)pathogens and, where applicable, their plant hosts. We have developed the GenomeDiagram package in order to visualise the relationships between hundreds of genome sequences simultaneously. Comparative analysis of the Pba genome and its bacterial relatives has revealed insights into its adaptation to an agricultural environmental niche, and informs our understanding of the evolution of pathogenicity. Recent comparisons between Pba, plant–associated bacteria (PAB) and animal pathogenic enterobacteria (APE) led to the identification of PAB-specific sequences in members of the APE that are potentially involved in plant colonisation and bacterial survival (see Environmental Pathology).
Pectobacterium-potato interaction
Staff: Ian Toth, Paul Birch, Hui Liu, Leighton Pritchard, Sonia Humphris
The excellent facilities at SCRI and the broad repertoire of skills within the plant pathology programme allow for in-depth investigation into the Pba-plant interaction. Our current research employs genomics approaches to identify and investigate pathogenicity determinants that are novel to this group of pathogens (particularly phytotoxins, regulators and secretion systems), and to determine regulatory networks involved in pathogenesis (including those associated with type III secretion and quorum sensing). We are also interested in how these determinants are used by the pathogen to interact with its host. For example, Pba is considered a necrotroph, an organism that kills part or all of another organism before deriving nutrients from it, in contrast to biotrophic pathogens such as Pseudomonas syringae, that derive nutrients from the living tissues of another organism. We are investigating the potential role of biotrophy in the interaction between Pba and potato by focusing on i) the type III secretion system and its effectors, ii) putative phytotoxic compounds such as coronafacic acid conjugates, and their effects on basal resistance in potato.
Host resistance
Staff: Paul Birch, Ian Toth, Hui Liu, Eleanor Gilroy, Sonia Humphris, Alison Lees
We are investigating how plants respond to attack by Pba and other bacterial pathogens. To assist in this investigation, we have developed a plant response microarray (in association with Agilent Technologies) with over 6,000 plant genes either known or thought to be associated with resistance. On challenge of the plant with wild type Pba, mutants disabled in phytotoxin production or type III secretion, or plant chemical signals such as salicylic acid and methyl jasmonate, we have identified a number of candidate defence genes and mechanisms involved in the early host response to Pba. One of these (encoding a DNA binding protein), believed to be a key regulator in the early plant response, has been constitutively expressed in a susceptible potato plant and this provides total resistance to Pba. High levels of expression of this gene have been observed naturally in a cultivated potato species with a high level of resistance to Pba and other plant pathogens. The link between this gene and resistance is now being investigated in association with the Genetics Programme.
Environmental pathology
Staff: Nicola Holden, Ian Toth, Leighton Pritchard, Paul Birch
Much of our research over the last four decades has focused on the role of Pba in the environment and the epidemiology and aetiology of disease, including recent work on the relationships between potato seed tuber contamination, blackleg development and progeny tuber contamination. Using information from the genome sequence, we are currently investigating mechanisms of attachment to the roots of potato and other plants in the environment, in order to identify alternative niches for this pathogen when it is not causing disease. This work will inform the development of methods to reduce contamination of high grade seed stocks.
Food poisoning outbreaks are increasingly associated with fruit and vegetables, and genomic comparisons have highlighted features within the genomes of human pathogens that may be important for their persistence in the environment. Many of the so-called virulence features that are known to be required for infection of either plant or animal hosts are shared by both Pba and human pathogens. Examples include flagella, type III secretion systems and fimbriae. The work carried out here aims to characterise more of the shared features to define their roles in the interaction of human pathogenic bacteria with plants. In parallel to this we aim to determine the association of human pathogenic bacteria with plants in an agricultural setting, by sampling from a number of different farms. This will yield information not only on the prevalence of these pathogens in the environment but also show whether there are any associations with particular plant species or farming practices.
Techniques and resources
SCRI has the collective expertise, facilities and techniques to enable high quality research to be conducted on most aspects of bacterial-plant biology. Examples of these are described below.
Genome sequence and bioinformatics: The genome sequence of Pba and bioinformatics tools, including GenomeDiagram.
Mutation libraries: Transposon-based mutation libraries of Pba allowing rapid identification and selection from over 10,000 mutants.
Microarrays: Whole genome microarrays for Pba and D. dadantii, as well as a microarray with over 6000 known or putative plant defence response genes.
Culture collection: One of the largest collections of Pectobacterium / Erwinia strainsworldwide, many of them characterised in terms of their genetic relatedness (through fingerprinting) and pathogenicity. In addition, a collection of human and other animal pathogens includes several of the well characterised strains of pathogenic Escherichia coli, Salmonella enterica serovars and Klebsiella pneumoniae.
Disease assays: Several assays have been developed at SCRI for assessing pathogenicity and in vivo gene expression.
