Understanding the common gene expression in E.coli
serotypes
The School of Biosciences at the University of Birmingham is collaborating with OGT to develop a new generation of microarray to investigate a range of Escherichia coli genomes. The School has previously enjoyed a number of highly successful collaborations with OGT exploring various aspects of E. coli genomics, and has been keen to continue its close relationship with OGT for this new venture.
Professor Charles Penn explained: “The School of Biosciences has expertise in both pathogenesis and fundamental bacteriology, and has been interested in the functional genomics of E. coli for a number of years. Once the complete genomes of several strains of E. coli had been completed, it became apparent that there is a very large genetic variation between strains. This diversity is the result of over five million years of evolution, meaning two E. coli strains may have as much genetic divergence as humans and mice! We are now working with OGT to develop a ‘pan-E. coli‘ expression array, to assist in understanding the fundamental gene expression patterns linking, for example, the highly pathogenic serotypes and the cultivated laboratory strain.”
“This latest endeavour, funded by the BBSRC, is comparing the gene expression patterns of various E. coli strains. These include the K12 laboratory serotype and a number of pathogenic strains causing conditions such as haemorrhagic colitis, cystitis and the so called ‘travellers-tummy’, as well as an avian strain which is a significant problem in farmed chickens and turkeys. Each strain has approximately 5,000 genes, however there are over 12,000 known E. coli genes. The high resolution of OGT’s arrays allows us to create an array that should represent around 95 per cent of the genome of all E. coli strains, even if their genome hasn’t yet been sequenced.”
“Unlike the low resolution technologies we have used in the past, the OGT arrays allow us to generate the probes in situ on the array via a cyclical synthesis procedure. This is a very versatile system and allows optimisation of the probe for a specific gene, a process that was previously too expensive and cumbersome to be viable. Although the technology behind these arrays is very complex, we work closely with the scientists at OGT which significantly simplifies the array development process. Watertight communication is essential to a project like this, and we can meet with OGT whenever we need to.”