The E. coli Genome

Physical Characteristics of the E. coli genome:

  • single chromosome/cell (haploid)
  • 4.6 x 106 bp (4600 kilobases)
    • about 4300 potential coding sequences
    • only about 1800 known E. coli proteins
  • 70% is composed of single (monocistronic) genes
  • 6% is polycistronic
  • Roughly equal number of genes on each strand

About 30% of the sequenced ORF’s (Open Reading Frames, areas that look like they could be the start points of transcription) have unknown function.


The “100 minute map” is a time-based map of the E. coli genome. Based on the assumption/observation that it takes 100 minutes to replicate the genome, the map is a listing of at what points in time a particular gene is copied; in this case, it is looking at clusters of genes (it is important to note that most genes are not clustered).  From the map, we can say “At time X, genes for traits A, B, and C have been copied”; conversely, we can say “I need to wait X minutes for my desired trait to copy.”

The E.coli chromosome is shown above; notice how tightly wound it all is.  The DNA is supercoiled, and bound by H-like proteins (basically, they act like eukaryotic histones) into 50 separate supercoiled domains.  This serves to protect, condense, and organize the DNA.

Genotype vs. Phenotype

Genotype is the actual genetic makeup of an organism; phenotype is how that is expressed. When dealing with different strains of E. coli,the genotype tells us how the organism is different from wild-type E. coli; we usually have to determine the phenotype, how these mutations will be expressed. For instance:

E. coli CJ236 * pCJ105 F`

chr: dut-1, ung-1, thi-1, relA1
F`:  Camr, (wt: tra, pili)




no functional deoxyuridine triphosphatase, cannot degrade dUTP, and so it accumulates and becomes incorporated into DNA during replication.


no functional uracil-n-glycosylase, can’t remove U’s once they are incorporated into the DNA.


thiamine auxotroph, cannot produce its own thiamine, and thus must be supplied with it from the environment.


chloramphenicol resistance

wt: tra

wild type F` for transfer genes

wt: pili

wild type F` for pilus genes