Betaine production in diatoms - engineering more nutritious and salt tolerant crops
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
The quaternary nitrogen compound betaine is the most abundant osmolyte on Earth. Betaine production in organisms protects against osmotic, temperature and drought stresses and its release into the environment provides dissolved organic nitrogen. Also, it is desirable for crops to have high betaine levels due to its wide-ranging health benefits. Betaine synthesis is well understood in many organisms but there are no detailed studies on betaine synthesis in any marine eukaryotic phytoplankton - not a single synthesis gene is reported.
Using diatoms as model phytoplankton we have identified a betaine synthase gene that when cloned in Escherichia coli confers enhanced salt tolerance and the ability to produce betaine from glycine. With the need to maximize nutritional value and crop production in the modern world, science has successfully explored transgenic introduction of betaine synthesis genes into crop plants to enhance their stress tolerance and betaine production. Given that the diatom synthase has no significant identity to any characterised betaine synthesis enzyme, it is a good candidate for transgenic stress tolerance studies in higher plants.
This PhD aims to demonstrate the role of this betaine synthase in Thalassiosira pseudonana via overexpression and knocking down of the corresponding gene in this model diatom. We will study gene regulation and the physiology of transgenic diatoms under varied environmental conditions and monitor their osmolyte production by liquid chromatography/mass spectroscopy. To explore the potential of producing stress tolerant higher plants, the diatom betaine synthase will be introduced and expressed in Arabidopsis and wheat. Comprehensive training will be provided at UEA by Mock and Todd, and at JIC by Balk and Uauy.
Using diatoms as model phytoplankton we have identified a betaine synthase gene that when cloned in Escherichia coli confers enhanced salt tolerance and the ability to produce betaine from glycine. With the need to maximize nutritional value and crop production in the modern world, science has successfully explored transgenic introduction of betaine synthesis genes into crop plants to enhance their stress tolerance and betaine production. Given that the diatom synthase has no significant identity to any characterised betaine synthesis enzyme, it is a good candidate for transgenic stress tolerance studies in higher plants.
This PhD aims to demonstrate the role of this betaine synthase in Thalassiosira pseudonana via overexpression and knocking down of the corresponding gene in this model diatom. We will study gene regulation and the physiology of transgenic diatoms under varied environmental conditions and monitor their osmolyte production by liquid chromatography/mass spectroscopy. To explore the potential of producing stress tolerant higher plants, the diatom betaine synthase will be introduced and expressed in Arabidopsis and wheat. Comprehensive training will be provided at UEA by Mock and Todd, and at JIC by Balk and Uauy.
Organisations
- University of East Anglia (Lead Research Organisation)
- University of Technology Sydney (Collaboration)
- Ocean University of China (Collaboration)
- Australian Government (Collaboration)
- PLYMOUTH MARINE LABORATORY (Collaboration)
- University of East Anglia (Collaboration)
- University of Barcelona (Collaboration)
Publications
Pellicer Martinez MT
(2017)
Sensing iron availability via the fragile [4Fe-4S] cluster of the bacterial transcriptional repressor RirA.
in Chemical science
Sun H
(2021)
Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary.
in Environmental microbiology
Xue C
(2021)
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data
in Frontiers in Microbiology
Liu J
(2021)
Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea
in Microorganisms
Williams BT
(2019)
Bacteria are important dimethylsulfoniopropionate producers in coastal sediments.
in Nature microbiology
Curson AR
(2017)
Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process.
in Nature microbiology
Curson ARJ
(2018)
DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton.
in Nature microbiology
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 1654293 | Studentship | BB/M011216/1 | 01/10/2015 | 30/09/2019 | Ana Bermejo Martinez |
| Description | Community Resource for Wheat Transformation |
| Amount | £0 (GBP) |
| Organisation | National Institute Of Agricultural Botany |
| Sector | Private |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 09/2017 |
| Description | Collaboration with JB Raina at the University of Technology Sydney, Australia |
| Organisation | University of Technology Sydney |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Myself and my research team (including Dr Carrion, Dr Curson and Dr Pinchbeck; and PhD students Ana Bermejo Martinez and Beth Williams) collaborate with Dr Raina to carry out the localisation of isotopes within microbes using NANOSIMS technology. |
| Collaborator Contribution | We identified novel genes involved in the cycling of DMSP/DMS and of betaine in multiple different prokaryotic and eukaryotic microbes. We shared our data with Dr Raina who used his expertise to link our localisation work of key enzymes to the localisation of key labelled compounds within our model organisms. |
| Impact | Our most recent Nature Microbiology paper Curson et al., (2018) DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton, was an out put from this collaboration. The work is multidisciplinary involving: Molecular biology, Molecular Ecology, bioinformatics, algal physiology, NANOSIMS and ImmunoGold localisation for example. |
| Start Year | 2017 |
| Description | Microbial synthesis of dimethylsulphoniopropionate and dimethylsuphide (Prof. Xiao-Hua Zhang Ocean University, China) |
| Organisation | Ocean University of China |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Collaborating with Prof. Xiao-Hua Zhang (Ocean University, China) we are characterising the molecular genetic systems utilised by marine organisms in their catabolism and synthesis of dimethylsulphoniopropionate (DMSP). |
| Collaborator Contribution | Prof. Xiao-Hua Zhang (Ocean University, China) has isolated thousands of marine microbes and is screening them for their ability to produce and catabolise dimethylsulphoniopropionate (DMSP). Any positive strains are shipped to UEA for molecular characterisation. |
| Impact | There are no output as yet but a full NERC grant will be submitted on this subject in January 2015. |
| Start Year | 2013 |
| Description | Relating denitrification to DMSP cycling |
| Organisation | University of East Anglia |
| Department | Biomedical Research Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Through work on our current NERC grants, we collaborate with Prof. David Richardson, Dr Gary Rowley and Dr Andrew Gates on work relating the process of denitrification to DMSP cycling in important marine prokaryotes and eukaryotes. We provide expertise, bacterial and plankton model organisms and methods to characterise these processes in the marine environment. We cosupervise PhD students with these collaborators on this topic. |
| Collaborator Contribution | Prof. David Richardson, Dr Gary Rowley and Dr Andrew Gates provide expertise in the denitrification process. |
| Impact | 1 NERC EnvEast PhD studentiship and 1 UEA-funded PhD studentship. |
| Start Year | 2016 |
| Description | Subcellular localisation of DMSP and DMS-producing enzymes in eukaryotes and prokaryotes |
| Organisation | University of Barcelona |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Collaborating with Dr. Elena Mercade (University of Barcelona, Spain) we are growing eukaryotes and prokaryotes that produce DMSP and/or DMS and providing specific antibodies against the enzymes involved to localise them at a subcellular level. |
| Collaborator Contribution | Dr. Elena Mercade (University of Bacelona, Spain) has prepared samples for immunogold labelling with the specific antibodies provided by us and used Transmission Electronic Microcoscopy to localise the enzymes involved in DMSP and/or DMS synthesis in the cells. |
| Impact | The collaboration has successfully allowed the localisation of key enzymes involved in DMSP and/or DMS production in diatoms and bacteria. These results will be included in the forthcoming publications. |
| Start Year | 2014 |
| Description | The importance of bacterial DMSP production in coral reef environments. |
| Organisation | Australian Government |
| Department | Australian Institute of Marine Science |
| Country | Australia |
| Sector | Public |
| PI Contribution | We provide knowledge and expertise on bacterial DMSP production to enable an environmental microbiological study of the importance of bacteria in DMSP production in coral reefs. This involved us designing enrichment experiments for the isolation of DMSP-producing bacteria. We provided ratified gene probes and techniques to study the expression and abundance of key genes involved in DMSP production in environmental samples. Furthermore, we provided expertise in the analysis of metagenomic data generated from coral reef environmental samples. |
| Collaborator Contribution | Dr David Bourne and Dr Jean-Baptiste Raina obtained samples from coral reefs and conducted experiments to study the importance of bacteria in DMSP production under the guidance of our group. This involved the isolation of high quality DNA and RNA which is being analysed for the abundance and diversity of bacterial DMSP synthesis genes. Dr Raina is localising DMSP in model phytoplankton for our project using nanoSIMS. |
| Impact | None yet. |
| Start Year | 2015 |
| Description | The importance of bacterial DMSP production in coral reef environments. |
| Organisation | University of Technology Sydney |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We provide knowledge and expertise on bacterial DMSP production to enable an environmental microbiological study of the importance of bacteria in DMSP production in coral reefs. This involved us designing enrichment experiments for the isolation of DMSP-producing bacteria. We provided ratified gene probes and techniques to study the expression and abundance of key genes involved in DMSP production in environmental samples. Furthermore, we provided expertise in the analysis of metagenomic data generated from coral reef environmental samples. |
| Collaborator Contribution | Dr David Bourne and Dr Jean-Baptiste Raina obtained samples from coral reefs and conducted experiments to study the importance of bacteria in DMSP production under the guidance of our group. This involved the isolation of high quality DNA and RNA which is being analysed for the abundance and diversity of bacterial DMSP synthesis genes. Dr Raina is localising DMSP in model phytoplankton for our project using nanoSIMS. |
| Impact | None yet. |
| Start Year | 2015 |
| Description | The production of betaine by marine phytoplankton (Dr Ruth Airs PML) |
| Organisation | Plymouth Marine Laboratory |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | During our NERC grant (NE/J01138X/1) we identified candidate genes involved in the synthesis of betaine. We have shown that model diatoms make betaine and that our candidate genes when cloned and expressed confer the ability to produce betaine and confer salt tolerance to Escherichia coli. In collaboration with Dr Ruth Airs we have established liquid chromatography mass spectrometry methods to detect betaine and dimethylsulphoniopropionate (DMSP) from biological samples. |
| Collaborator Contribution | Dr Ruth Airs at PML helped us to develop and establish liquid chromatography mass spectrometry methods to detect betaine and dimethylsulphoniopropionate (DMSP) from biological samples. |
| Impact | My postdoctoral researcher Research technicians on the NERC Grant (NE/J01138X/1) have presented our findings at the research conferences detailed below: -The Molecular Life of Diatoms, Paris, Dr Andrew Curson (Tues 25th June) -MMEG Molecular Microbial Ecology Group 2013, University of Essex, Ana Bermejo Martinez (Tues 17th Dec 2013) -6th International symposium on biological and environmental chemistry of DMS(P) and related compounds, ICM-CSIC, Barcelona, Ana Bermejo Martinez (26th - Fri 30th May 2014) As a result of this work we put together a NERC ENVEAST PhD proposal with Dr Todd as PI, and Dr Ruth Airs and Prof, Mock as CoIs. The work is multi-disciplinary as it involves phytoplankton physiology, biogeochemistry, microbiology, biochemistry, molecular genetics, molecular ecology and analytical biology. |
| Start Year | 2013 |
| Description | 'DMSP production in marine bacteria and algae: idenitification of novel synthesis genes' research talk at Microbiology Society Annual Conference in Belfast April 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Research talk at Microbiology Society annual conference, presenting a summary of research work in Todd's lab. |
| Year(s) Of Engagement Activity | 2019 |
| Description | 'Marine Microbial DMSP Synthesis - from genes to microbes to pathways' at GEOMAR in Kiel, Germany in October 2018. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited research presentation at GEOMAR in Kiel Germany, presenting a summary of research work in Todd's lab. |
| Year(s) Of Engagement Activity | 2018 |
| Description | 'Marine Microbial DMSP Synthesis - from genes to microbes to pathways' at the Marine Microbes GRC 2018, Lucca, Italy, 1-6th July 2018. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited research talk at the Gordon Research Conference Marine Microbes conference, covering all research work from the Todd group. |
| Year(s) Of Engagement Activity | 2018 |
| Description | 'Surface marine sediments are factories for DMSP and the climate active gas DMS' at the ASM Microbe meeting, June 2019, San Francisco. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited reesearch presnetation at ASM conference in San Francisco, summarising the reseacrh from Todd's lab. |
| Year(s) Of Engagement Activity | 2019 |
| Description | BIO Research Colloquium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | I presented my research as a poster in the BIO Research Colloquium, a one day conference where PIs from the School of Biological Sciences present their research and posgraduates present posters. I obtained a second prize for poster presentation. |
| Year(s) Of Engagement Activity | 2017 |
| Description | European Nitrogen Cycle meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented my research as a poster at the European Nitrogen Cycle meeting. Experienced as well as early carreer researchers from around Europe attend to this conference. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Invited Oral presentation at Microbiology Society Annual meeting, April 2020, Edinburgh.The title of the talk was "Molecular insights into marine organosulfur cycling" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof Jon Todd presented research from his groups work as an invited speaker at the Microbiology Society Annual conference 2020 in Edinburgh. The title of the talk was "Molecular insights into marine organosulfur cycling". |
| Year(s) Of Engagement Activity | 2020 |
| Description | Jonathan Milner Talk |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | I took part in the organization and chaired a free lecture given by Jonathan Milner, CEO of ABCAM. Undergraduates, posgraduates and PIs from University of East Anglia from all backgrounds (predominantely business and sciences) attended. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Maintaining a 'Jonathan Todd Research Group' twitter page |
| 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 | We run a popular twitter group @ToddLabUEA where we post updates on our awards and successes, as well as retweet interesting or relevant articles and messages from other twitter accounts. We currently have 202 followers. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://twitter.com/ToddLabUEA |
| Description | Microbiology Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented my research as a guest speaker in the microbiology seminar held at the Kenyan Medical Research Centre-Wellcome Trust, Kilifi, Kenya. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Molecular Microbial Ecology Group (MMEG) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | I gave an oral presentation about my research to the Molecular microbial ecology group. Around 100 early carreer researchers and PIs attend to this meeting from around the UK. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Molecular Microbiology seminar series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Formal talk about my research to the Molecular Microbiology department at the School of Biological Sciences, University of East Anglia. Posgraduate students and PI from the department, as well as other interested audience from the university attend to this seminar series. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Nature Microbiology Community blog post |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A blog covering the research published in Nature Microbiology 2018 published in Nature Microbiology community blog. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://naturemicrobiologycommunity.nature.com/users/84434-andrew-curson/posts/30656-dmsp-synthesis-... |
| Description | Norwich Science Festival 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Norwich Science Festival is a big event organised by the Forum Trust focused on Science outreach to general public. In 2018, the Todd lab had a stand showcasing the research don in the lab with explanations and activities catered to all ages. During the day >100 people visited the stands and activities showing great engagement and interest. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Pint of Science |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | I was "Our Body" Event Manager for Pint of Science, a three day event with talks from researchers from Norwich Research Park to a general audience (delivered in a local pub). |
| Year(s) Of Engagement Activity | 2016 |
| Description | Posgraduate Colloquium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented a talk as part of the posgraduate colloqiuum held by the School of Biological Sciences. All posgraduate students from the school as wells as some PIs were present. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Present in the Pub |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | The talks was an engaging and informal presentation of the research carried our as part of my PhD. It took place in an informal setting at the Graduate Bar at the University of East Anglia. Attendees included posgraduate students from very different areas from humanities to sciences. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Press cover |
| 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 | Public/other audiences |
| Results and Impact | Publication in Nature Microbiology, 2017, was covered by Spanish regional newspaper "La Voz de Galicia" with a reach of thousands of people. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.lavozdegalicia.es/noticia/sociedad/2017/02/22/bacterias-marinas-producen-gas-influye-cli... |
| Description | Seminar & Journal Club |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | I gave a talk as part of a seminar series at the university of Kilifi, Kenya. This activity was aimed to undergraduate students from the Biotecnology and the Biology departments in order to expose them to international research. |
| Year(s) Of Engagement Activity | 2017 |