Analysis of key cyclic-di-GMP signalling systems that control wheat rhizosphere colonisation by Pseudomonas fluorescens
Lead Research Organisation:
John Innes Centre
Department Name: UNLISTED
Abstract
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Technical Summary
Biocontrol agents, soil microorganisms that suppress pathogens and/or promote plant growth, represent an attractive potential alternative to chemical pesticides. Pseudomonas fluorescens functions as an effective biocontrol agent, positively affecting plant health and nutrition and exhibiting antimicrobial capabilities via the production of diverse antibiotics and through direct competition with pathogens in the rhizosphere. The effectiveness of biocontrol is directly related to the effectiveness of bacterial rhizosphere colonisation. However, the intracellular signalling pathways that control rhizosphere colonisation and communication between Pseudomonas, its plant host, and the surrounding soil microbiota are currently poorly defined.
Recent work has identified a key role for cyclic-di-GMP (cdG) signalling in the control of rhizosphere colonisation by P. fluorescens. CdG is a ubiquitous bacterial second messenger that controls processes involved in the switch between sessile, communal and motile, single-celled lifestyles. In-vitro expression technology (IVET) has identified 146 genes in the model P. fluorescens strain SBW25 that are up-regulated in the rhizosphere and phyllosphere. Our analysis of the IVET data suggests that at least seven cdG systems are specifically up-regulated in the SBW25 plant environment. In this project, we aim to functionally characterise those cdG signalling proteins that contribute to SBW25 wheat rhizosphere colonisation using a combination of genetics, molecular microbiology, cell biology and biochemical approaches. We will determine the effects of these cdG systems on global gene expression during colonisation with soil microarrays, and identify the cdG output systems that function during rhizosphere colonisation. Finally, we will analyse the interactions between different cdG-related systems, and how they coordinate their activities to effect an integrated colonisation response.
Recent work has identified a key role for cyclic-di-GMP (cdG) signalling in the control of rhizosphere colonisation by P. fluorescens. CdG is a ubiquitous bacterial second messenger that controls processes involved in the switch between sessile, communal and motile, single-celled lifestyles. In-vitro expression technology (IVET) has identified 146 genes in the model P. fluorescens strain SBW25 that are up-regulated in the rhizosphere and phyllosphere. Our analysis of the IVET data suggests that at least seven cdG systems are specifically up-regulated in the SBW25 plant environment. In this project, we aim to functionally characterise those cdG signalling proteins that contribute to SBW25 wheat rhizosphere colonisation using a combination of genetics, molecular microbiology, cell biology and biochemical approaches. We will determine the effects of these cdG systems on global gene expression during colonisation with soil microarrays, and identify the cdG output systems that function during rhizosphere colonisation. Finally, we will analyse the interactions between different cdG-related systems, and how they coordinate their activities to effect an integrated colonisation response.
Planned Impact
unavailable
Publications
Caly DL
(2012)
Socializing, networking and development: a report from the second 'Young Microbiologists Symposium on Microbe Signalling, Organization and Pathogenesis'.
in Molecular microbiology
Caly DL
(2014)
Communication, cooperation, and social interactions: a report from the third Young Microbiologists Symposium on microbe signalling, organisation, and pathogenesis.
in Journal of bacteriology
Campilongo R
(2017)
One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas.
in PLoS genetics
Grenga L
(2017)
Quick change: post-transcriptional regulation in Pseudomonas.
in FEMS microbiology letters
Kirkpatrick C
(2017)
Interaction and signalling networks: a report from the fourth 'Young Microbiologists Symposium on Microbe Signalling, Organisation and Pathogenesis'
in Microbiology
Lammertz M
(2019)
Widely Conserved Attenuation of Plant MAMP-Induced Calcium Influx by Bacteria Depends on Multiple Virulence Factors and May Involve Desensitization of Host Pattern Recognition Receptors.
in Molecular plant-microbe interactions : MPMI
Little R
(2019)
Differential Regulation of Genes for Cyclic-di-GMP Metabolism Orchestrates Adaptive Changes During Rhizosphere Colonization by Pseudomonas fluorescens
in Frontiers in Microbiology
Little RH
(2016)
Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation.
in PLoS genetics
Malone JG
(2015)
Role of small colony variants in persistence of Pseudomonas aeruginosa infections in cystic fibrosis lungs.
in Infection and drug resistance
| Description | We have mapped the expression of several signalling pathways that control colonisation of plants by beneficial microbes. We show how these signalling proteins control plant colonisation and determine their relative importance for the control of different plant-interaction phenotypes. Based on our fundamental research into how plant bacteria colonise and infect their host plants and animals, we have identified and characterised potential new antimicrobial drug targets in the important human pathogen P. aeruginosa, and the plant pathogenic P. syringae. This research is still at the fundamental stage, but ultimately could lead to the development of new anti-infective drugs, and/or plant protection products that will replace harmful pesticides in the future. By looking at the population of a key soil microbe and examining how it changes with the environment, we have identified important pathways for plant colonisation, including a number of potentially useful antimicrobial gene clusters. By increasing our understanding of how changes in the plant/soil environment affects important bacterial populaitons, we hope to improve the consistency of farming techniques and enable a reduction in agricultural inputs. |
| Exploitation Route | These findings could be used in the pharma industry to develop new antimicrobials that target pathogen infectivity, rather than killing bacteria outright. This in turn would delay the rise of antibiotic resistance, and prolong the useful lifetime of the drug. As our findings apply to both plant and human pathogens, there is also potential for this work to be exploited to produce new plant-protection compounds. Our soil microbiology research is looking promising as a way to identify new, biologically relevant antimicrobial compounds. We also hope to use the findings of this work to improve agronomic advice to farmers, by increasing the consistency of suppressive soil generation and reducing inputs such as water and fertilisers. |
| Sectors | Agriculture Food and Drink Environment Healthcare Pharmaceuticals and Medical Biotechnology |
| URL | http://jic.ac.uk/directory/jacob-malone/ |
| Description | BBSRC NProNet Proof of Concept grant |
| Amount | £54,544 (GBP) |
| Funding ID | POC021 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2016 |
| End | 12/2016 |
| Description | DTP PhD Studentship |
| Amount | £76,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2015 |
| End | 09/2019 |
| Description | DTP PhD Studentship |
| Amount | £76,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2021 |
| Description | DTP PhD Studentship |
| Amount | £76,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2013 |
| End | 09/2017 |
| Description | iCASE PhD Studentship |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2017 |
| End | 09/2021 |
| Description | Formal Research collaboration - Rafael Rivilla, Marta Martin and Jacob Malone |
| Organisation | Autonomous University of Madrid |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | My research group has provided technical advice and support for the biochemistry of cyclic-di-GMP signalling analysis in Pseudomonas, including protein-nucleotide binding assays, ITC, nucleotide quantificaiton by LC/MS. We have hosted two researchers for summer visits to JIC |
| Collaborator Contribution | My research partners are conducting molecular microbiology experiments into Pseudomonas fluorescens plant colonisation, that are informed by the biochemistry from my lab. |
| Impact | One paper has been published so far from this collaboration: Muriel C., Arrebola E., Redondo-Nieto M., Martínez-Granero F., Jalvo B., Pfeilmeier S., Blanco-Romero E., Baena I., Malone J. G., Rivilla R., Martín M. (2018) AmrZ is a major determinant of c-di-GMP levels in Pseudomonas fluorescens F113. Scientific reports 8 p1979 |
| Start Year | 2015 |
| Description | Population genomics of the take-all/wheat/Pseudomonas biosphere |
| Organisation | Rothamsted Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My team works closely with Dr Tim Mauchline and Prof Kim Hammond Kosack at RR to examine the population structure of Pseudomonas fluorescens isolates in wheat fields that have been infected with the pathogenic fungal disease take-all. We hope to understand the microbiological underpinnings of the phenomenon of take-all suppressive soils. |
| Collaborator Contribution | Prof Hammond-Kosack provides access to her ongoing wheat field trial sites. Dr Mauchline isolates Pseudomonas and other soil microbial samples and does much of the phylogenetic analysis and plant-microbe assays associated with the study. |
| Impact | To date, we have published two research papers (TH Mauchline, et al. Environmental microbiology 17 (11), 4764-4778, and DD Nguyen, et al. Nature Microbiology 2 (1), 16197) and a review (see URL above) based on this collaboration. A PhD student is now working on downstream elements of this project, and we have applied for follow-on research funding. |
| Start Year | 2013 |
| Description | Educational film (UEA) |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Contributed to an educational film showing A-level students how mathematics is used in the world of science. |
| Year(s) Of Engagement Activity | 2016 |