30431 Introduktion til Bioinformatik
David Ussery
Fredag, 12 November, 1999


A DNA Structural Atlas of Escherichia coli

Overview

This lecture is about DNA structural analysis of the Escherichia coli genome. In a real sense, it is a continuation of Tuesday's talk. In the first part, I will discuss the DNA Structural Atlas, and talk about the organisation of the E. coli chromosome. Then, in the second half, I will go into more detail about gene expression analysis within E. coli.



What is? Background - What is a "DNA Structural Atlas"?

DNA helix



three views of E. coli Three Views of Escherichia coli:


view 1 The DNA Structural Atlas     Structural Atlas

view 2 The Base-Composition Atlas     Base Atlas

view 3 The DNA Repeat Atlas     Repeat Atlas

      the combined view The Genome Atlas (combined view)     Genome Atlas



DNA structure & promoters DNA Structural Analysis of Promoters Escherichia coli



Transcription animation

E. coli gene expression Gene Expression in E. coli

Escherichia coli is probably the best characterised organism.

some numbers:

  • There are 4085 predicted genes in Escherichia coli strain K-12 isolate W3110.


  • There are 4289 predicted genes in Escherichia coli strain K-12 isolate MG1665.


  • There are about 5100 predicted genes in Escherichia coli strain O157:H7 isolate EDL933 (enterohemorrhagic pathogen).




  • Roughly 2600 genes have been found to be expressed in Escherichia coli strain K-12 cells, under standard laboratory growth conditions.



  • About 2100 spots can be seen on 2-D protein gels.




  • Very roughly 1000 different genes (only about 600 mRNA transcripts) are expressed at "detectable levels" in E. coli cells grown in LB media.



  • Only about 350 proteins exist at concentrations of > 100 copies per cell. (These make up 90% of the total protein in E.coli!)



    • What is the chromosomal location of the genes for the highly proteins?

    proteomatlas
    Most (>90%) of the proteins are present in very low amounts (less than 100 copies per cell).


    cluster analysis Cluster Analysis of E. coli Genes



    E. coli gene expression Analysis of Chromatin-Protein Binding Sites



    E. coli gene expression DNA Periodicity in E. coli and other bacterial genomes



    E. coli gene expression Analysis of Pathogenicity Islands and Plasmids





    Link to the "DNA Structural Atlas" electronic poster. (For the 3rd Annual Conference on Computational Genomics, held at the Renaissance Harborplace Hotel in Baltimore, Maryland, USA (18 - 21 November, 1999).

    Go to the E. coli atlas page Link to the E. coli GenomeAtlas page


    Back to the CBS homepage
    Back to Dave's Courses page

    Last modified Thursday, 11 November, 1999 by David Ussery