Carbohydrate microarray printer for plant and microbial glycomics for food, nutrition and health research

Plants, yeasts and bacteria cells are all surrounded by a cell wall, which is made up of a complex mixtures of carbohydrates. The cell wall determines many of the important properties of biological products and so is an excellent target for genetic improvement. However, these carbohydrate networks are very complex to analyse, and hundreds of genes are needed for their construction. To understand these structures properly generally requires time consuming and expensive chemical analyses, which can make it difficult to collect enough data to match modern genetic technologies.

To address this we have developed a 'carbohydrate microarray-based' method which is able to analyse thousands of microscopic carbohydrate spots printed onto special microscope slides. Fine tuning of this approach has enabled us to collect cell wall carbohydrate data from hundreds of cultivars/strains (same species, different genetics) and has allowed us to match these differences to differences in genetics. Applying this technology to yeast strains housed at the National Collection of Yeast Cultures at IFR has led to exciting new research, working with other teams across the Norwich Research Park. We are also working with The University of York to apply this technology in plants. Overall, our current work has enormous potential to support a whole range of activities on existing projects and beyond which focus on improving Human Health, using microbes for industry (Industrial Biotechnology), and renewable energy from plants (Bioenergy).

Unfortunately, the current microarray printing equipment we rely on is old and cannot be maintained. The printer was built in 2004 to print DNA microarrays and so relies on old software and parts. Modern carbohydrate microarray printers are also much more accurate and produce better quality spots. Also, our Institute (Institute of Food Research) is moving to a new building called the Quadram Institute in 2018. It has been decided that our current microarray printer, which is the size of a room, cannot be moved and so this important tool will be lost.

The aim of this proposal is to seek funding for a new state-of-the-art carbohydrate microarray printer which will enable our 'Glycomics' research to continue and accelerate in the new QI.

Planned Research:
Our focus will reflect the strategies of the QI and the BBSRC and will concentrate on plant, yeast and other microbial cell walls relevant to food and health and industrial applications. Using genetic sequence data collected from yeasts (NCYC at IFR/QI)), oilseed rape and wheat (at University of York) and prokaryotic microbes (with University of East Anglia [UEA] and Bactevo Ltd), the array-based research will be targeted towards the use of plant and microbial cell walls for creating biochemicals and 'bioactives' which can improve our health, and understanding how microbes create carbohydrate structures (biofilms) which protect them from current anti-microbials used in medicine.

The main areas of research to be explored will include:
(a) Revealing the genetic basis for carbohydrate variation (structure and function) in yeasts, continuing and building on current research concerning yeast and other microbe interactions, including those found in the gut; the intention is to understand the behaviour of yeasts and other microbes (also with UEA) which can harm humans;
(b) Exploring the genetic basis for carbohydrate variations in structure and functionality in cell walls of plants (with University of York) for production of new biological polymers for biomedical use. For example controlled drug delivery and wound coverings;
(c) Unravelling the biology of 'biofilms' from yeasts and other microbes with a focus on medical safety (with industry, the QI and UEA).

Future areas of research under consideration include development of other fast and informative tools related to cell wall carbohydrate composition, structure and use.

The proposal seeks funding to replace the now obsolete, and soon to be decommissioned, microarray printer which is central to the high throughput glycomics research at the Institute of Food Research (IFR).

The aim of the proposed work is to extend the glycomics research at the IFR/QI, expanding collaborations with the University of East Anglia (UEA), University of York (UY) and industry (letters of support attached). Specifically, we will target the exploitation of plant and microbial biomass for creating functional biochemicals and bioactives, elucidate the development of microbial biofilms relevant to microbial infection, food safety, and gut health, and enhance the opportunities to exploit the NCYC yeast collection for bioactive and functional polysaccharides.

The main areas of research to be explored will include:

(a) Elucidating the genetic basis for polysaccharide variation in structure and functionality in yeasts, evaluating large glycomics datasets through genome-wide association studies (GWAS) and identifying opportunities to tailor yeast biology relevant to bioactivity and yeast-prokaryote and gut microbiome interactions; the intention is to understand the behaviour of yeasts and selected prokaryotes (with UEA and industry);
(b) Elucidating the genetic basis for polysaccharide variation in structure and functionality in cell walls of higher plants (GWAS with University of York on Brassica and wheat collections) for production of functional polysaccharides for biomedical use for example controlled drug delivery and sterile barriers;
(c) Unravelling the biology of biofilms from yeasts (using GWAS) and prokaryotes with a focus on microbiological safety (with industry, the QI and UEA).

Future areas of research under consideration include development of microfermentation and reaction systems making special use of the controlled environmental conditions in the array printer to develop micro-laboratory tools.

Background

The aim of the project is to advance and develop recently established rapid methods for glycomic phenotyping in order to evaluate the genomics of plant and microbial extracellular polysaccharides relevant to cell walls and biofilms from plants, yeasts and selected prokaryotes. This will involve the innovative use of state-or-the-art carbohydrate microarray printing technology in conjunction with advanced, rapid throughput compositional analysis using immuno-cytochemical and novel spectroscopic screening methods. Due to the heterogeneous nature of polysaccharides and the time-consuming and costly approaches for quantitative analysis of their complex structures, there is a paucity in our understanding of the genetic basis for their synthesis, and functionality in cell walls and biofilms.

Who will benefit and how they will benefit:

(i) Society
Society will benefit predominantly from the downstream benefits resulting from research and development relevant to health and environment (see below). These will include improved opportunities to produce renewable biochemicals from crop and agrifood chain field wastes, and improved health care in relation to reducing microbial infection through biofilms.

(ii) Industry (biomedical and industrial biotechnology)
Rapid throughput glycomics will be of considerable benefit to biomedical industries understanding the genetics of infection resistance through biofilms. This will have knock-on benefits to society through enhanced understanding of infectious diseases, and the development of improved medical treatments for pathogens protected in biofilm structures in tissues and within medical devices. Special benefit is foreseen in elucidating the glycomics of pathogenic yeasts (e.g. Candida species).

(iii) Environment
The economically viable production of platform chemicals and fuels from renewable biomass is a considerable challenge due to the extensive requirement for improved and more efficient industrial biotechnological processes. The targeted improvement in biomass cell wall composition and structure is likely to enhance its economic exploitation via the production of novel materials (fibres and functional polysaccharides) and greater ease of hydrolysis for the release of low cost sugars for fermentation. At the same time the improvement in yeast biotechnology, particularly concerning the control of biofilm production and flocculation during fermentation, will augment the efficiency of the fermentation process relevant to production of platform and bioactive chemicals.

(iv) Technologists (Academic and Industrial):
Technologists, academics, chemical engineers and process designers will benefit from a phenotyping technology that can relate polysaccharide structure and function through to the controlling genetics. This will augment the benefits in (i) - (iii) by facilitating a direct "system dynamics" approach to exploiting the technology. Carbohydrate microarrays are one of the only methodologies that can collect glycan data with sufficient throughput and precision to match genomic resources, suitable for association mapping.