How comparative genomics has been used to analyse the genomes of prokaryotes such as E. coli · Genetic analysis in E. coli and comparative genomics of E. coli o E. coli are important organisms used frequently in labs (e.g., Melanie Lee used them to maintain her human gene libraries in her experiments) o However, they also cause some diseases such as the Uropathogenic strain, which causes urinary tract infections, or the enteropathogenic strain, that causes diarrhoea o The experiment below shows comparisons of the commensal strain (also causes tummy upsets, but also used in lab). o The genomes of the strains below were sequenced and compared - it was found that there are lots of genes unique to each strain (1350 for enteropathogenic, 1500 for Uropathogenic, and 600 for commensal). Some genes are shared between 2 strains but not all 3 (shown in overlaps between just 2 circles), and a core set of genes are shared between E. coli (300 genes) o This shows that there's a core set of genes that's shared among all E. coli, but there are many genes that determine the particular features of each strain. This is particularly important for the pathogenesis and phenotype of the diseases you get for E. coli o It's also important bc people have been using E. coli in forward genetic screens (genetic analysis) for decades. This involves: " 1) Make random mutations & screen for interesting phenotypes (like a nutritional requirement) (you grow them on an agar plate w a missing nutrient, and find E. coli w a mutation that allows them to survive) " 2) Map the mutation, identify the gene that is disrupted and study the function of the gene o The functions of 2000 E. coli genes were discovered and characterised in this way o Comparative genomics of E. coli (sequencing the genome then comparing it to other E. coli) revealed: " 1) The genome sequence of E. coli reveals ~4300 genes (on average, each E. coli has 4300) and a core genome of ~3000 genes - many chromosome regions are particular to each strain " 2) Many mutant phenotypes are not accessible to forward genetics
Commensal strain (K-12 MG1655) - found in gastrointestinal tract, but also use widely in lab 600 Uropathogenic strain (CFT073) - causes urinary tract infections 200 1500 3000 500 200 1350 Enteropathogenic strain (O157:H7) - found in intestines and cause diarrhoea - one of the most important pathogens infection children worldwide · Forward genetic analysis of E. coli - conclusion: o 2300 genes are not detectable by their mutant phenotype and the function of these genes is unknown o Possible explanations: · The mutagenesis screen was incomplete? " Are more extensive screens required? · More screens might identify more mutations? " Might some mutations may be lethal? · Most probable explanation: o The phenotype of some mutants was not revealed, or was not detectable in the conditions of the screen (the experiment was not conducted in the natural environment of E.