52 4 Rational Efforts to Streamline the Escherichia coli Genome
provides regulatory and other functions (~11%). The genome is thus nearly fully
loaded with information-bearing sequences, leaving very little room for appar-
ently useless, intergenic DNA with no obvious function. The largest group of
genes codes for transport and binding proteins, reflecting the wide variety of
substrates the bacterium can utilize. Surprisingly, despite the long laboratory
history of E. coli, 38% of the genes had no experimentally verified function at the
time of sequencing, and even today this number stands about 20% [31].
As more genome sequences of E. coli strains became available, a peculiar,
mosaic-like genome structure was revealed. The genomes share a common,
homologous colinear backbone sequence, interrupted by hundreds of strain-
specific genomic islands. Typically, these genomic islands carry marks of rela-
tively recent horizontal transfer events and are characterized by a higher than
average number of unknown genes, mobile genetic elements, and a relatively
high A+T content. Since the basic cellular functions seem to be coded on the
backbone sequences and, less importantly, life style-specific genes reside onOriTerK-12
MG16551 2 3 4 5 61500000(^10)
(^00)
(^00)
0
(^500)
(^00)
0
4500000
40
00
00
0
35
00
00
0
Ri
gh
t (^) m
ac
ro
do
m
ai
n
Unstru
cture
d (^) re
gio
n
Or
i^ m
acr
odo
main
Left
(^) mac
rodoma
in
Un
st
ru
ct
ur
ed
(^) re
gi
on
Te
r^ m
ac
ro
do
m
ai
n
(^2500)
(^000)
20000
00
(^30)
(^00)
(^00)
0
Figure 4.1 Schematic map of selected features of the E. coli K-12 MG1655 genome, numbered
on the perimeter in base pair. Outward from the center, rings depict (1) strain-specific K-12
genomic islands longer than 4 kbp [29], (2) essential genes (www.shigen.nig.ac.jp/ecoli/pec/
index.jsp), (3) ribosomal RNA operons, (4) IS elements, (5) prophages [18], and (6)
macrodomains [30]. Ori and ter indicate the origin and terminus of replication, respectively.