Investigating the regulation by O2 of the nif and fix genes in Rhizobia - AfS, ENWW
Lead Research Organisation:
University of Oxford
Department Name: Interdisciplinary Bioscience DTP
Abstract
Nif and fix genes are responsible for diazotrophic biological nitrogen fixation (BNF), the ability of specialised bacteria to convert atmospheric N2 into N-containing compounds utilisable by plants. BNF can enable plants to be grown without the application of artificial N containing fertilisers, providing the potential to greatly enhance crop yields in areas without ready fertiliser access. A better understanding of the regulation of these genes will allow the manipulation and possible transfer of BNF to other organisms. Low O2 is a known regulator of some nif and fix genes but not all of them. This work aims to discover the other regulators involved and use a proteomics-based approach to understand the metabolic processes that these regulators control.
Research themes:
Sustainably enhancing agricultural production.
Global food security
Research themes:
Sustainably enhancing agricultural production.
Global food security
People |
ORCID iD |
| Philip Poole (Primary Supervisor) | |
| Gail Preston (Primary Supervisor) |
Publications
Crang N
(2021)
Role and Regulation of Poly-3-Hydroxybutyrate in Nitrogen Fixation in Azorhizobium caulinodans
in Molecular Plant-Microbe Interactions®
Schulte CCM
(2021)
Metabolic control of nitrogen fixation in rhizobium-legume symbioses.
in Science advances
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011224/1 | 01/10/2015 | 31/03/2024 | |||
| 1810130 | Studentship | BB/M011224/1 | 01/10/2015 | 30/09/2019 |
| Description | It has been determined that the isocitrate dehydrogenase gene icd is solely responsible for the isocitrate dehydrogenase activity seen in Rhizobium leguminosarum bv. viciae 3841and it is essential for growth under all conditions. As a result of this discovery a statistical error in the Hidden Markov Model previously utilised during InSeq screenings by our group has been identified and corrected. PHB has been demonstrated to be per se non-essential for N2 fixation in Azorhizobium caulinodans ORS571. It does however, play a key role in the regulatory activities of phaR which can severely reduce growth and fixing ability when misregulated. The theoretical "Malonate Shunt" in Azorhizobium Caulinodans which allowed for generation of acetyl CoA from malate without a pyruvate intermediate, has been shown to be non-existent in the form first proposed by Pauling et. al 2001. Furthermore, any form of malonate semialdehyde dehydrogenase activity has been shown to be functionally irrelevant for growth and fixation on C4 dicarboxylates. Instead the two primary fluxes that enable acetyl CoA production and growth on C4 dicarboxylates are shown to operate via PEP carboxykinase and the malic enzyme pathways |
| Exploitation Route | The PHB findings have been written for publication after a second viewing by the reviewers. This work was important as A. caulinodans was exceptional amongst rhizobia in being unable to fix N2 in the absence of PHB production. Our findings were able to demonstrate that this is not due to a unique flux balancing effect observed only in this species but was entirely due to the misregulation of central carbon metabolism by phaR. The identification of the malonate shunt as functionally irrelevant has informed flux balance maps previously generated for A. caulinodans, allowing their metabolic models to be refined as has the demonstration that the primary and secondary metabolic fluxes to acetyl coA are via malic enzyme and PEP carboxykinase respectively. It is intended to publish this refined flux model as a paper and we are currently awaiting the refining of the flux map by our collaboration partner. |
| Sectors | Manufacturing, including Industrial Biotechology |
| Description | BBSRC Flexible Talent Mobility Account - Innovation Fellowship "Screening for bottlenecks of CO2 fixation in industrial autotrophs " |
| Amount | £120,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 02/2022 |
| Description | Metabolic bottlenecks in rhizobia affecting competitive nodulation during infection stages |
| Amount | SFr. 103,400 (CHF) |
| Funding ID | P400PB_183901 / 1 |
| Organisation | Swiss National Science Foundation |
| Sector | Public |
| Country | Switzerland |
| Start | 03/2019 |
| End | 02/2021 |
| Description | TEM imagining to help characterise PHB mutants |
| Organisation | James Hutton Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We produced a mutant strains of azorhizobium caulinodans with novel nitrogen fixing phenotypes. These mutant strains were applied to the host legume Sesbania Rostra and nodules were sent to our partner. |
| Collaborator Contribution | Our collaboration partner performed transmission electron microscopy nodules, allowing us to visualise clearly the phenotype of the bacteroids within |
| Impact | We will be using the images obtained as part of a publication |
| Start Year | 2017 |
| Description | 21st Congress on Nitrogen Fixation - 10th-15th Oct 2019, Wuhan, China - Philip Poole |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Phil gave a talk at this international conference. He had many questions on his work and spent time exchanging ideas with colleagues in this research area. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://2019icnf.csp.escience.cn/dct/page/65580 |
| Description | Development of Poole Lab website (Rhizosphere.org) |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The Rhizosphere website is used to describe work performed, profiles lab members, lists outreach activities and celebrates achievements. Also includes a list of Lab publications. |
| Year(s) Of Engagement Activity | 2014,2015,2016,2017,2018,2019,2020 |
| URL | https://rhizosphere.org |
| Description | Plant Sciences Masterclass |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | 30 Secondary school students between 14 and 17 years of age attended a lecture at the Oxford Museum of Natural History on the GM work on tomatoes by Professor Lee Sweetlove from the Oxford Department of Plant Sciences. Students were split into groups of around a dozen and discussed through the benefits of GM, how it differs to traditional agricultural breeding techniques and whether or not the results Professor Sweetlove had achieved could have been reached via conventional means. I was a discussion facilitator for one of the groups, answering questions, asking leading questions and trying my best to draw them out into the discussion. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Posters at ICNF, Granada, Spain, Sept. 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | International conference. 11 posters from Lab. 2 short presentations |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://rhizosphere.org/lab-news/ |
| Description | Rothamsted Research invited seminar - Phil Poole |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Phil gave a lunch-time research seminar. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://rhizosphere.org/lab-news/ |
| Description | Twitter account Rhizosphere @PooleLabOxford |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Twitter account to publicise the work of the Poole Lab |
| Year(s) Of Engagement Activity | 2017,2018,2019,2020 |
| URL | https://twitter.com |
| Description | World Science Day for Peace and Development 2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | As part of my internship at UNESCO Bangkok I organised, in collaboration with the Thai Ministry of Science and Technology as well as the Asian Institute of Technology (AIT), the World Science Day for Peace and Development event. This focused on the theme of plastic pollution and involved four international speakers, taking place across two days at UNESCO Bangkok and AIT. 100 guests from NGOs, the Thai government, universities, schools and industry attended the event, which included Q&A sessions plus poster presentations. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://bangkok.unesco.org/index.php/content/strategic-solutions-deal-global-deluge-plastic-pollutio... |