**A DNA Structural Atlas of Escherichia coli and other microbial genomes**

David Ussery Anders Gorm Pedersen Lars Juhl Jensen Hans Henrik Stræfeldt Søren Brunak

Center for Biological Sequence Analysis
Institute of Biotechnology
Technical University of Denmark
http://www.CBS.dtu.dk

Poster for the 2nd Annual TIGR conference on "Comparative Microbial Genomics", in Reston, Virginia, (Oct. 31 to Nov. 3, 1998).

ABSTRACT

The complete nucleotide sequence of the Escherichia coli genome was examined, in terms of a set of 6 different DNA structural parameters: base-stacking interactions, intrinsic DNA curvature, DNA flexibility, propeller twist (helix rigidity), chromatin compaction signals, and linguistic complexity. We have found preferential localisation of sequences prone towards unique structures within intergenic regions. A model for the possible relationship between DNA architecture in upstream regions and RNA polymerase binding is discussed. Furthermore, we have found a set of long DNA structural elements scattered throughout the Escherichia coli genome that could be involved in chromosomal organisation. The results from E.coli are extended and compared with 18 other sequenced microbial genomes.

Two different views of the DNA Structural Atlas:
1.

2.
Click to see a larger view of the E.coli genome

Organism # Type %AT Size
(Mbp) number
of
genes %
transcribed date
published

Escherichia coli
K-12 strain MG1665 1a Bacteria (Gm-) 49 4.64 4288 88% Oct,1997

Escherichia coli
K-12 strain W3110 1b Bacteria (Gm-) 49 4.64 4085 79% -

Haemophilus influenzae 2 Bacteria (Gm-) 62 1.83 1703 87% Aug, 1995

Helicobacter pylori 3 Bacteria (Gm-) 61 1.67 1590 90% Jun, 1997

Treponema pallidum 4 Bacteria (Gm-) 47 1.14 1041 93% Jul,1998

Borrelia burgdorferi 5 Bacteria (Gm-) 71 0.91 853 94% Jul,1997

Campylobacter jejuni 6 Bacteria (Gm-) 69 1.64 1731 94% Oct, 1998

Chlamydia trachomatis 7 Bacteria (Gm-) 59 1.04 938 91% Nov, 1998

Rickettsia prowazekii 8 Bacteria (Gm-) 71 1.11 834 76% Nov,1998

Rhizobium sp. NGR234
plasmid pNGR234a 9 Bacteria (Gm-) 42 0.54 483 71% 1998

Bacillus subtilis 10 Bacteria (Gm+) 56 4.20 4222 88% Nov,1997

Mycoplasma genitalium 11 Bacteria (Gm+) 68 0.58 470 89% Oct, 1995

Mycoplasma pneumoniae 12 Bacteria (Gm+) 60 0.82 677 87% Nov, 1996

Mycobacterium tuberculosis 13 Bacteria (Gm+) 34 4.41 3924 91% Jun,1998

Aquifex aeolicus 14 Eubacteria 57 1.55 1512 94% Mar,1998

Synechocystissp. 15 Bacteria
("blue-green algae") 52 3.57 3168 87% Sep, 1996

Archaeoglobus fulgidus 16 Archaebacteria 51 2.18 2436 91% Jun,1997

Methanococcus jannashchii 17 Archaebacteria 69 1.66 1738 88% Aug, 1996

Methanobacterium
thermoautotrophicum 18 Archaebacteria 50 1.75 1918 91% May,1997

Pyrococcus horikoshii 19 Archaebacteria 58 1.74 2022 88% Jan,1998

Saccharomyces cerevisiae 20 Eukaryotic
("baker's yeast") 62 12.07 5885 72% Jan, 1996

Link to an expanded table, with more boring statistics

Link to poster for the FEBS meeting in Copenhagen (July, 1998).
Back to Dave's homepage

981112 du

Organism	#	Type	%AT	Size (Mbp)	number of genes	% transcribed	date published
Escherichia coli K-12 strain MG1665	1a	Bacteria (Gm-)	49	4.64	4288	88%	Oct,1997
Escherichia coli K-12 strain W3110	1b	Bacteria (Gm-)	49	4.64	4085	79%	-
Haemophilus influenzae	2	Bacteria (Gm-)	62	1.83	1703	87%	Aug, 1995
Helicobacter pylori	3	Bacteria (Gm-)	61	1.67	1590	90%	Jun, 1997
Treponema pallidum	4	Bacteria (Gm-)	47	1.14	1041	93%	Jul,1998
Borrelia burgdorferi	5	Bacteria (Gm-)	71	0.91	853	94%	Jul,1997
Campylobacter jejuni	6	Bacteria (Gm-)	69	1.64	1731	94%	Oct, 1998
Chlamydia trachomatis	7	Bacteria (Gm-)	59	1.04	938	91%	Nov, 1998
Rickettsia prowazekii	8	Bacteria (Gm-)	71	1.11	834	76%	Nov,1998
Rhizobium sp. NGR234 plasmid pNGR234a	9	Bacteria (Gm-)	42	0.54	483	71%	1998
Bacillus subtilis	10	Bacteria (Gm+)	56	4.20	4222	88%	Nov,1997
Mycoplasma genitalium	11	Bacteria (Gm+)	68	0.58	470	89%	Oct, 1995
Mycoplasma pneumoniae	12	Bacteria (Gm+)	60	0.82	677	87%	Nov, 1996
Mycobacterium tuberculosis	13	Bacteria (Gm+)	34	4.41	3924	91%	Jun,1998
Aquifex aeolicus	14	Eubacteria	57	1.55	1512	94%	Mar,1998
Synechocystissp.	15	Bacteria ("blue-green algae")	52	3.57	3168	87%	Sep, 1996
Archaeoglobus fulgidus	16	Archaebacteria	51	2.18	2436	91%	Jun,1997
Methanococcus jannashchii	17	Archaebacteria	69	1.66	1738	88%	Aug, 1996
Methanobacterium thermoautotrophicum	18	Archaebacteria	50	1.75	1918	91%	May,1997
Pyrococcus horikoshii	19	Archaebacteria	58	1.74	2022	88%	Jan,1998
Saccharomyces cerevisiae	20	Eukaryotic ("baker's yeast")	62	12.07	5885	72%	Jan, 1996