Elucidating molecular level details of the plant Borate transporter structure and function.

Lead Research Organisation: Imperial College London
Department Name: Life Sciences

Abstract

All cells are surrounded by a membrane made up of fatty lipid molecules. This membrane acts as an effective barrier separating the contents of the cell from the external environment. The lipid membrane itself is impermeable to all but a limited number of molecules, however cells need to have a means of taking up key nutrients and removing waste products. The import and export of a wide range of molecules across the membrane is mediated via a system of specialized proteins called membrane transporters, which are embedded into the lipid layer. These transporter proteins bind a specific substrate or cargo on one side of the membrane, undergo a reconfiguration and then release the substrate on the other side of the membrane. The ability to transport key nutrients into and out of plant cells is fundamental to healthy plant growth and development. However, our current understanding of how plants take up minerals and precisely regulate their concentration inside cells is very limited due to a lack of detailed information on the transport proteins responsible for their uptake and distribution. One key nutrient is boron which is taken up from the soil by the roots and has essential roles in the formation and strength of the plant cell wall. Plants are tolerant of a very narrow range between deficient and toxic soil solution concentration. Boron deficiency causes reduced plant size and impaired seed production, both of which have a major impact on crop yield. Boron toxicity also results in compromised plant growth and development. Vast areas of agricultural land in China and West and Central Africa have poor fertility as a result of boron deficiency, while land in Australia, Turkey and Chile is affected by boron toxicity. BOR1 is a membrane transporter with roles in boron distribution from plant roots to other growing tissues. It is very important to understand precisely in what form and how boron is taken up into cells through BOR1. Central to increasing understanding of the operation of BOR1 is a technique called X-ray crystallography which allows us to obtain very detailed information on the arrangement of the atoms within a protein structure. Obtaining such detailed structures of membrane proteins such as transporters remains very challenging as it is necessary to remove the proteins from their membrane environment into a detergent containing solution so they can be isolated and crystallised. We have made substantial progress towards obtaining a detailed structure of BOR1 having obtained well diffracting crystals of BOR1 from both the model plant, mouse-ear cress, and the important crop, rice. We will additionally complement the structural studies with analysis of the protein in plant cells and whole plants. The techniques we will use allow us to study the protein in a native environment and also assess the functionality of a range of mutant BOR1s. Taken together with the structure, the plant based functional analysis will provide an opportunity to build a uniquely detailed picture of how BOR1 works. This should form the basis of future studies attempting to generate plants with improved tolerance to suboptimal soil boron concentrations.

Technical Summary

Boron (B) is an essential plant nutrient with a key role in the generation of ester cross-linked rhamnogalacturonan II through the formation of apisoyl dimers, essential for structure and function of the extracellular matrix. B deficiency and toxicity are major barriers to efficient crop growth in many parts of the world. B uptake, efflux and distribution are mediated by a complex system of integral membrane channels and transporters, one of which, BOR1, is a membrane transporter with important roles in the active transport of B for xylem loading. Despite the importance of this protein in the effective delivery of B to developing and growing plant tissues, remarkably little is known about its mechanism of action. The precise chemical nature of the substrate and molecular basis of BOR1 energisation are key unknowns. In order to investigate these and other key questions we will employ a combination of high-resolution X-ray crystallographic and plant functional studies. The research leading to this proposal has made significant progress towards the objectives through growth of well diffracting crystals of BOR1 from both the model plant Arabidopsis thaliana, and rice, Oryza sativa. In addition, we have a complete native diffraction dataset for the Oryza sativa BOR1. We aim to optimize the current crystals and solve the high resolution structure of at least one plant BOR1. The structural studies will be complemented with plant cell and whole plant studies aiming to identify and characterize key functional regions of the protein. Taken together with the structure, the plant based functional analysis will provide an opportunity to build a uniquely detailed picture of how BOR1 works. This should form the basis of future studies attempting to generate plants with improved tolerance to suboptimal soil B concentrations.

Planned Impact

The main objective of the proposal is to gain highly detailed insight into the mechanism of action of a plant transporter protein through a combination of high resolution structural studies and plant functional analysis. Given that this is very much a basic science project the immediate impact of the results will be in scientific advancement in the areas of membrane transporter biology, structural biology and plant mineral nutrition. However in the longer term the research findings should be of major interest for plant breeders and plant producers having implications for crop productivity. The research undertaken will also have significant impact through the strengthening of collaborative links between the applicants based at Imperial and Warwick. The results of our research will be disseminated to the wider scientific community through the publication of manuscripts in high impact journals and presentations at national and international meetings. Key findings will also be promoted through press releases to the media and through the Imperial College and University of Warwick websites. Where there is scope for further exploitation of the research findings, we will take advantage of the resources at both Imperial and Warwick to protect arising IP. We will additionally use the research findings to establish further collaborations with Industry. We will also undertake public engagement activities in a variety of formats and at both institutions with the aim of making our research findings available and accessible to the general public as well as inspiring the new generation of scientists. The PDRAs funded by the proposal will benefit by developing high quality research skills in world-class research environments as well as having the opportunity to build networks with complementary researchers. It is anticipated that they will also gain significant experience of presenting data at conferences and writing manuscripts. As a member of the Imperial College Post-doc Centre or the Warwick Learning and Development Centre they will also gain training in more generic professional development skills including CV preparation and interview training to facilitate their next step in academia, industry or other relevant careers.

Publications

10 25 50
 
Description As part of our work on the plant BOR transporters we identified a number of different residues in the protein that might be important for function/stability. We generated mutants and performed functional analysis using a functional complementation assay. What we found was that none of the residues we thought might be interesting did anything in the protein. This indicated that it is not always possible to predict what might stabilise the protein. We subsequently identified an additional set of residues that might be important for stability and and can now report that two of these thermostabilse the protein. We successfully isolated and obtained crystals of one of the proteins (the other is yet to assessed fully) and although these crystals diffract X-rays, the resolution is too low to provide successful structure determination. We have however managed to successfully obtain a large cryo-EM dataset of the BOR3 protein from rice, using the LonCEM facility at The Crick Institute. Our cryo-EM structure from this data was generated although as a result of COVID, this was limited to a resolution of about 6 Angstroms. This did confirm the overall subunit orgnisation of the protein and that the protein forms a closely associated dimer. These findings together with functional and plant studies carried out at both Imperial and University of Warwick have been submitted for publication.
We have developed a number of different purification protocols for the production and isolation of the BOR transporters and some of these have been published, with another under review.
We have also used the purified BOR protein to screen and characterise a number of novel detergents. Three manuscripts have now been published describing this work and there are a couple more in the pipeline
Additionally we used a homologue of the plant BOR proteins from the yeast, Saccharomyces cerevisiae, to explore the role that membrane lipids have on BOR structure and function and showed that lipids are critical for maintaining the dimeric structure of the protein but that the monomeric form can still exhibit transport function. A paper describing these findings has been published in Analytical Chemistry.
We also established a collaboration with Molecular Dimentions to develop a lipid screen. A paper describing this research is also currently under review and a grant applicaiton to Innovate UK to continue this work through to commercialisaiton is underway.
Exploitation Route This findings are likely to be relevant for other researchers working with this type of transporter. HOpefully once we have the structure we will be able to give a much clearer explanation for the results we have obtained so far. The lipid screen we have developed shoudl be useful for many researchers working in teh field and will contribute to the portfolio of products that Molecular Dimensions currently sell to support membrane protein research
Sectors Agriculture, Food and Drink,Education,Manufacturing, including Industrial Biotechology

 
Description Prof Byrne has given several talks to a variety of audiences. We have published a paper discussing issues associated with dimerisation of integral membrane transporters. Prof Byrne did an outreach event at a Primary School in Reading. Our research describing a lipid screen is of interest to a Biotech company and we hope to continue to work with them to deliver a product to market.
First Year Of Impact 2019
Sector Education
Impact Types Societal

 
Title A novel screen for identification of lipids that stabilise detergent purified membrane proteins 
Description This is a 96 well plate screen containing 32 different lipid conditions. The screen is set up in such a way as to allow both assessment of membrane protein stability and potentially as a source of lipids for crystallisation screening and nanodisc reconstitution. The ability to screen a wide lipid space in this way makes identificaiton of key lipids easier and more cost effective. Our preliminary analysis showed this screen successfully identified cholesterol hemisuccinate as stabilising teh human adenosine A2A receptor, validating its use as a tool. However we also identified completely novel lipids which were stabilising both teh A2A receptor and UapA, a eukaryotic transporter protein. We developed this in collaboration with Molecular Dimensions and Anatrace and are continuing to work with Molecular Dimensions in order to develop the product further with a view to making this commercially available. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact None so far as we are just trying to get additional funding to optimise and develop the tool prior to making it commercially available. 
 
Description Collaboration with Molecular Dimensions 
Organisation Molecular Dimensions Ltd
Country United Kingdom 
Sector Private 
PI Contribution We designed a lipid screen and worked with MD to generate this in a form for lab testing. Both IMperial and the University of Leeds were involved in optimising and testing teh screen, a process that involved production of multiple high quality membrane proteins. The results were very promising and we hope that these can form the basis of an application for further funding to Innovate UK with a view to producing the screen commercially.
Collaborator Contribution Molecular Dimensions generate the screen in a usable format.
Impact One manuscript submitted so far
Start Year 2018
 
Description Collaboration with Molecular Dimensions 
Organisation University of Leeds
Department Faculty of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We designed a lipid screen and worked with MD to generate this in a form for lab testing. Both IMperial and the University of Leeds were involved in optimising and testing teh screen, a process that involved production of multiple high quality membrane proteins. The results were very promising and we hope that these can form the basis of an application for further funding to Innovate UK with a view to producing the screen commercially.
Collaborator Contribution Molecular Dimensions generate the screen in a usable format.
Impact One manuscript submitted so far
Start Year 2018
 
Description Collaboration with Warwick 
Organisation University of Warwick
Department Centre for Mechanochemical Cell Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution We have expertise in the production of membrane proteins for structural studies as well as their functional analysis. Our aim is to crystallise the plant Boron transport proteins so we can obtain information their precise molecular mechanism of action. We will complement this with functional analysis of mutants.
Collaborator Contribution Dr Alexander Cameron is a world-leading expert in membrane protein crystallography. Dr Alexandra Jones is a plant biologist with an interest in plant mineral nutrition. Together they will provide additional expertise to help us solve the structure of the protein and carry out complementary plant based studies.
Impact None as yet.
Start Year 2016
 
Description RAMP-MCSA EU H2020 
Organisation University of Wales Trinity Saint David
Department Trinity College Carmarthen
Country United Kingdom 
Sector Academic/University 
PI Contribution We will prepare protein and cell pellet samples of AtBOR1 so we can set up lipidic cubic phase crystallisation trials using the equiment and expertise in Prof Martin Caffrey's lab at Trinity College Dublin.
Collaborator Contribution Equipment and expertise and training in the use of LCP crystallisation in Prof Martin Caffrey's lab.
Impact The exchange visit will only start in mid-May, so no outputs yet.
Start Year 2018
 
Description Hosting an A-level student 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact We hosted an A-level student in the laboratory for a few days. They got the opportunity to observe activities in the laboratory and to also try some hands on activities. This was part of a widening participation initiative focussed on talented students from the local area from low income families.
Year(s) Of Engagement Activity 2017
 
Description School Visit (reading) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk and demonstration to primary school students on protein structure and behaviour.
Year(s) Of Engagement Activity 2019