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Unformatted text preview: Notes 3/8/10 Bacterial chromosomes and plasmids: The higher order structure of genes on chromosomes: Genetic map of the E. coli chromosome Originally determined by conjugation and transduction - now sequenced Mapped in minutes, w/ zero arbitrarily set at thrABC genes E. coli as a model prokaryote Ease of growth and characterization o Agreement to focus on and completely characterize one organism Strain MG1655 4,639,221 bp of DNA o 4,288 open reading frames (ORFs), corresponding to 88% of genome o 1% rRNA (7 repeats) and tRNAs (86 isospecies) o 0.5% - noncoding repetitive sequences o 10% regulatory sequences: promoters, operators, ori, etc Arrangement and expression of genes some genes clustered for coordinate control of expression: operons others may be scattered but still coordinately controlled: regulons o 70% of transcriptional units contain a single gene highly expressed genes transcribed in same direction as the direction of the DNA replication fork. Nearly 2000 genes characterized by classical genetic analysis Of the 2000+ ORFs not previously characterized o Functions of some inferred by homology analysis o Others remain of currently unknown function or hypothetical average protein: ~300 amino acids largest ORF: 2,383 aas uncharacterized but comparative genomics indicates similarities to proteins found in pathogenic relatives of E. coli. Very few duplicated genes but many genes have arisen by gene duplication during evolutionary history Some large gene families encoding products with related functions o ~70 related membrane transport proteins Genomes are dynamic : Insertions in the chromosome 7 - IS2 elements 5 IS3 elements several defective prophages (integrated genomes of certain viruses) nearly 20% of DNA originated from lateral (horizontal) gene transfer o recognizable as regions of significantly different G+C ratio o different codon bias o pathogenicity islands: unstable regions genome size: species-specific trait in spite of potential lateral transfer The dynamic nature of bacterial genomes: E. coli 0157:H7 pathogenic strain causing hemorrhagic colitis and kidney failure 73,000 cases of infection and 61 deaths/year in USA (1999 estimate). produces two known toxins (Shiga toxins) - fatal kidney damage new genes, similar to known toxin genes in other pathogenic organisms, probably inserted by viruses. horizontal gene transfers Infection very difficult to treat - certain antibiotics actually stimulate virally infected bacteria to produce more viruses and viral toxins. potential for spread of antibiotic resistance and pathogenicity factors by conjugation....
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