Proteomics and Metabolomics at the John Innes Centre

JIC has established state-of-the-art proteomic and metabolomic technologies, and supporting expertise, that enable us to identify the entire protein (proteome) or low molecular weight chemical (metabolome) complement of a sample, whether from a cell or whole organism.

The genome sequences for several organisms of particular relevance to JIC (Arabidopsis, Streptomyces, E. coli) have been completed. The genome sequence enables us to predict the sequences of all unmodified proteins that could potentially be present in an organism.

Proteomics

Comparing a partial amino acid sequence for a protein with an organism's genome sequence immediately enables recognition of both the corresponding gene and the protein's complete amino acid sequence. Proteomics links the static information contained in the organism's DNA (its genotype) to the dynamic physiology of the whole-cell and/or whole-organism (its phenotype).

By analyzing the abundance of proteins under different physiological conditions, or in different mutants, it is possible to identify groups of proteins that are important under those particular physiological conditions or are affected by that specific mutation. The amino acid sequence of the proteins identifies the genes involved. On-going advances in automated sample preparation, mass spectrometry and bio-informatics are making it possible to quickly and accurately relate proteins to genes.

The joint JIC-IFR proteomics facility includes three state-of-the-art mass spectrometers, a Bruker UltraFlex™ MALDI-ToF/ToF, a modified Micromass Q-ToF2 and a Thermo Scientific Orbitrap XL. All the machines are coupled to nanoLC systems and can be accessed through the proteomics facility in the Department of Biological Chemistry at JIC. Duplicate sets of sample preparation robots for 2-D gel electrophoresis, gel-imaging, spot-picking, proteolytic digestion and MALDI-plate loading are located at JIC and IFR.

The joint facility is funded by BBSRC through core support to IFR and JIC, three 'Joint Research Equipment Initiative' grants and SRIF2 HEFCE money from the University of East Anglia. Bruker, Micromass and Genomic Solutions have also made financial contributions. Unilever and Syngenta contributed to the cost of the Q-ToF mass spectrometer and also funded a five year post-doctoral fellowship in proteomics. A key interface is with JIC’s Computational Biology Users Supports group in terms of implementation of new tools for data analysis.

Metabolomics

An organism's "metabolome" is its full complement of metabolites, in the same way that its genome is all the genetic information it contains. Metabolomics is the study of all the low molecular weight chemicals in an organism. These chemicals are key to a better understanding of how an organism works.

The reactions of plants and microbes to changes in their environments can be followed, and better understood, by tracking changes in the low molecular weight chemicals they produce. These are the signals, and the intermediates, in all the chemistry that is going on as part of the organism reaction to environmental stimuli.

A mutation, or genetic change as a result of a breeding programme, will alter the basal levels of metabolites in a plant. We would like to be able to link these differences to the genetic differences which, indirectly, caused them. Establishing links between the genome, proteome and metabolome is one of the current major areas of interest in plant science.

JIC Metabolite Service serves the analytical needs of the Centre and its collaborators. We are able to handle both broad and narrowly targeted metabolomic approaches using our main technologies:- a single quad GC-MS gas chromatograph, and several liquid chromatography/mass spectrometry (LC-MS) instruments. We have a single quad LC-MS, an ion-trap LC-MS and an LTQ Orbi-trap™ LC-MS-MS all capable of identifying, quantifying and providing chemical structure of metabolites.

We have links with other UK centres with complementary interests and play an active role in the Norwich Research Park metabolomics group.

For more information about metabolite work at the JIC visit the JIC metabolite services web-pages.