New approaches to resolving community metaproteomes: ComProt

Understanding interactions between organisms in an ecosystem is a critical part of ecological research and facilitates our understanding of how ecosystems function and this is particularly important for microorganisms and microarthropods as they are often difficult to study in situ in real time. Currently the natural environment faces many challenges and we need to be able to measure the impacts of changes in climate, pollutant levels, intensive farming and development of ley systems to understand how resilient communities are and how Carbon, nitrogen and phosphorous cycles are affected.
Microrganisms play a vital role in our environment they occupy a wide range of habitats from our gut and body surfaces all the way to hot vents under the sea, they are critical in the soil for recycling of nutrients and plant health and responsible for the essential digestion of cellulose from grass being broken down in the specialised stomach of the cow termed the rumen to the global cycling of carbon in the oceans via harvesting of sunlight as many bacteria can photosynthesize and thus harvest light energy to fix carbon dioxide. A major problem exists in our ability to study the physiology and overall activities of these microbes due to the fact that we cannot isolate and cultivate (yet) the vast majority (probably over 98%) of them in the laboratory. We know they exist because we have used methods similar to DNA forensic approaches to detect them solely based on their DNA using signature genes which allow us to identify and group them. Most of this diversity is bacterial but there are also several groups of fungi. New methods are being developed for the study of these microbial populations and this is called metagenomics and we are focused in this projects on the proteins produced termed metaproteomic. Proteins equate with activity as all enzymes are proteins and act as catalysts for reactions. Therefore, we can use the metagenomes to help in identifying which proteins are present because there is a relationship between the DAN code and the sequence of peptides in a protein. Making this link is challenging so we aim to improve the understanding of how to translate a series of peptide sequences into functioning proteins and recognise both their origins and putative function.
so that we study the microbial community as a population of many genomes rather than trying to isolate and study one. We can study this population in our guts or in the soil by extracting and analysing DNA for diversity analysis, RNA for gene expression and protein for confirmation of activities and metabolites to determine physiology. In addition we can extract DNA and express it in other bacteria which are culturable. This allows us to capture the DNA and express it thus gaining an insight into some functions such as specific enzymes or pigments with special properties. The imof the proposed work is to establish a network of academic partners to build capacity in this important area of science to ensure that we are able to study and exploit all the interesting and exciting attributes of bacterial populations and harness them for a sustainable future.

The research has relevance to the study of the microbiome and interactions between microbes and their hosts which will be important in wildlife health and physiology to study host protein production in the gut, in humans for immune reactions or overreactions in gut pathologies and really put a strong focus on the interactions between microbiomes and their environment whether it is a river bed, waste water treatment plant or plant rhizosphere. The study of protein provides an opportunity to understand physiology and nutritional interactions important in biogeochemical cycles, soil fertility, decomposition and molecular ecology.
The new approach to directly uncovering enzyme diversity has very significant impact on the potential for exploitation of these enzymes for a wide range of applications. Academia as well as the biotechnology industry that is involved in food and waste management is continuously in search of novel enzymes able to degrade recalcitrant natural polymers such as chitins and lignins, and/or polluting man-made compounds such as halogenated aliphatic and aromatic compounds. In particular, biochemical transformations that bring novel opportunities to key industries involved in environmental sanitation and in the agricultural / pharmaceutical / chemical / food areas are of interest. Thus, a strong demand has developed concerning the production of novel enzymes of several classes. Although this project is supporting science it is providing the scientific community with the tools to exploit new ultra sensitive MS-MS systems to provide spectral analysis of minute quantities of peptides and this will facilitate take-up of the technology and encourage the study of metaproteomics and metaexoproteomics as a stepping stone towards significant improved understanding of microbial diversity. Funding this research will mean that in the long term we will have access to untapped enzyme biodiversity for exploitation for pollution control, clean energy generation and improved waste water effluent to name just a few of the applications. Metagenomics has become widely accepted in all parts of environmental research so it is now timely and important to take the next level of analysis to function thus achieving by the use of appropriate bioinformatics the link between structure and function.