Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (515K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (44)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by McClelland, M.
Right arrow Articles by Miller, W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by McClelland, M.
Right arrow Articles by Miller, W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 24 4974-4986
© 2000 Oxford University Press

Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi

Michael McClelland*, Liliana Florea1, Ken Sanderson2, Sandra W. Clifton3, Julian Parkhill4, Carol Churcher4, Gordon Dougan5, Richard K. Wilson3 and Webb Miller1

Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA, 1Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA, 2Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, 3Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, MO 63108, USA, 4Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and 5Department of Biochemistry, Imperial College of Science, Technology and Medicine, London, SW7 2AY, UK

The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL) and the genome of the close outgroup Klebsiella pneumoniae (KPN). There are at least 160 locations where sequences of >400 bp are absent from ECO but present in the genomes of all three SAL and 394 locations where sequences are present in ECO but close homologs are absent in all SAL genomes. The 394 sequences in ECO that do not occur in SAL contain 1350 (30.6%) of the 4405 ECO genes. Of these, 1165 are missing from both SAL and KPN. Most of the 1165 genes are concentrated within 28 regions of 10–40 kb, which consist almost exclusively of such genes. Among these regions were six that included previously identified cryptic phage. A hypothetical ancestral state of genomic regions that differ between ECO and SAL can be inferred in some cases by reference to the genome structure in KPN and the more distant relative Yersinia pestis. However, many changes between ECO and SAL are concentrated in regions where all four genera have a different structure. The rate of gene insertion and deletion is sufficiently high in these regions that the ancestral state of the ECO/SAL lineage cannot be inferred from the present data. The sequencing of other closely related genomes, such as S.bongori or Citrobacter, may help in this regard.

* To whom correspondence should be addressed. Tel: +1 858 410 4192; Fax: +1 858 550 3998; Email: mmcclelland{at}skcc.org


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
M. AbuOun, P. F. Suthers, G. I. Jones, B. R. Carter, M. P. Saunders, C. D. Maranas, M. J. Woodward, and M. F. Anjum
Genome Scale Reconstruction of a Salmonella Metabolic Model: COMPARISON OF SIMILARITY AND DIFFERENCES WITH A COMMENSAL Escherichia coli STRAIN
J. Biol. Chem., October 23, 2009; 284(43): 29480 - 29488.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Guillier and S. Gottesman
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator
Nucleic Acids Res., December 1, 2008; 36(21): 6781 - 6794.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J.-H. Jeong, M. Song, S.-I. Park, K.-O. Cho, J. H. Rhee, and H. E. Choy
Salmonella enterica Serovar Gallinarum Requires ppGpp for Internalization and Survival in Animal Cells
J. Bacteriol., October 1, 2008; 190(19): 6340 - 6350.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
Q.-R. Li, A.-R. Carvunis, H. Yu, J.-D. J. Han, Q. Zhong, N. Simonis, S. Tam, T. Hao, N. J. Klitgord, D. Dupuy, et al.
Revisiting the Saccharomyces cerevisiae predicted ORFeome
Genome Res., August 1, 2008; 18(8): 1294 - 1303.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
D. A. Rosen, J. S. Pinkner, J. M. Jones, J. N. Walker, S. Clegg, and S. J. Hultgren
Utilization of an Intracellular Bacterial Community Pathway in Klebsiella pneumoniae Urinary Tract Infection and the Effects of FimK on Type 1 Pilus Expression
Infect. Immun., July 1, 2008; 76(7): 3337 - 3345.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
D. A. Rosen, J. S. Pinkner, J. N. Walker, J. S. Elam, J. M. Jones, and S. J. Hultgren
Molecular Variations in Klebsiella pneumoniae and Escherichia coli FimH Affect Function and Pathogenesis in the Urinary Tract
Infect. Immun., July 1, 2008; 76(7): 3346 - 3356.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. C. Fink, M. R. Evans, S. Porwollik, A. Vazquez-Torres, J. Jones-Carson, B. Troxell, S. J. Libby, M. McClelland, and H. M. Hassan
FNR Is a Global Regulator of Virulence and Anaerobic Metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s)
J. Bacteriol., March 15, 2007; 189(6): 2262 - 2273.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. D. Loh, P. Gyaneshwar, E. Markenscoff Papadimitriou, R. Fong, K.-S. Kim, R. Parales, Z. Zhou, W. Inwood, and S. Kustu
From the Cover: A previously undescribed pathway for pyrimidine catabolism
PNAS, March 28, 2006; 103(13): 5114 - 5119.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
N. Suzuki, H. Nonaka, Y. Tsuge, M. Inui, and H. Yukawa
New Multiple-Deletion Method for the Corynebacterium glutamicum Genome, Using a Mutant lox Sequence
Appl. Envir. Microbiol., December 1, 2005; 71(12): 8472 - 8480.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
N. Suzuki, S. Okayama, H. Nonaka, Y. Tsuge, M. Inui, and H. Yukawa
Large-Scale Engineering of the Corynebacterium glutamicum Genome
Appl. Envir. Microbiol., June 1, 2005; 71(6): 3369 - 3372.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C.-P. Ren, S. A. Beatson, J. Parkhill, and M. J. Pallen
The Flag-2 Locus, an Ancestral Gene Cluster, Is Potentially Associated with a Novel Flagellar System from Escherichia coli
J. Bacteriol., February 15, 2005; 187(4): 1430 - 1440.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Washietl, I. L. Hofacker, and P. F. Stadler
From The Cover: Fast and reliable prediction of noncoding RNAs
PNAS, February 15, 2005; 102(7): 2454 - 2459.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
R. A. Helm, S. Porwollik, A. E. Stanley, S. Maloy, M. McClelland, W. Rabsch, and A. Eisenstark
Pigeon-Associated Strains of Salmonella enterica Serovar Typhimurium Phage Type DT2 Have Genomic Rearrangements at rRNA Operons
Infect. Immun., December 1, 2004; 72(12): 7338 - 7341.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
F. J. Fernandez, M. C. Vega, F. Lehmann, E. Sandmeier, H. Gehring, P. Christen, and M. Wilmanns
Structural Studies of the Catalytic Reaction Pathway of a Hyperthermophilic Histidinol-phosphate Aminotransferase
J. Biol. Chem., May 14, 2004; 279(20): 21478 - 21488.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. Porwollik, R. M.-Y. Wong, R. A. Helm, K. K. Edwards, M. Calcutt, A. Eisenstark, and M. McClelland
DNA Amplification and Rearrangements in Archival Salmonella enterica Serovar Typhimurium LT2 Cultures
J. Bacteriol., March 15, 2004; 186(6): 1678 - 1682.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. H. Sibley and E. A. Raleigh
Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives
Nucleic Acids Res., January 26, 2004; 32(2): 522 - 534.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. S. Tchufistova, A. V. Komarova, and I. V. Boni
A key role for the mRNA leader structure in translational control of ribosomal protein S1 synthesis in {gamma}-proteobacteria
Nucleic Acids Res., December 1, 2003; 31(23): 6996 - 7002.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
V. Seputiene, D. Motiejunas, K. Suziedelis, H. Tomenius, S. Normark, O. Melefors, and E. Suziedeliene
Molecular Characterization of the Acid-Inducible asr Gene of Escherichia coli and Its Role in Acid Stress Response
J. Bacteriol., April 15, 2003; 185(8): 2475 - 2484.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. A. Frazer, L. Elnitski, D. M. Church, I. Dubchak, and R. C. Hardison
Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
Genome Res., January 1, 2003; 13(1): 1 - 12.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Jahreis, L. Bentler, J. Bockmann, S. Hans, A. Meyer, J. Siepelmeyer, and J. W. Lengeler
Adaptation of Sucrose Metabolism in the Escherichia coli Wild-Type Strain EC3132{dagger}
J. Bacteriol., October 1, 2002; 184(19): 5307 - 5316.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Porwollik, R. M.-Y. Wong, and M. McClelland
Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis
PNAS, June 25, 2002; 99(13): 8956 - 8961.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. Kolisnychenko, G. Plunkett III, C. D. Herring, T. Feher, J. Posfai, F. R. Blattner, and G. Posfai
Engineering a Reduced Escherichia coli Genome
Genome Res., April 1, 2002; 12(4): 640 - 647.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
E. Diaz, A. Ferrandez, M. A. Prieto, and J. L. Garcia
Biodegradation of Aromatic Compounds by Escherichia coli
Microbiol. Mol. Biol. Rev., December 1, 2001; 65(4): 523 - 569.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
T. J. Goss, A. Perez-Matos, and R. A. Bender
Roles of Glutamate Synthase, gltBD, and gltF in Nitrogen Metabolism of Escherichia coli and Klebsiella aerogenes
J. Bacteriol., November 15, 2001; 183(22): 6607 - 6619.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
H. Ochman and N. A. Moran
Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis
Science, May 11, 2001; 292(5519): 1096 - 1099.
[Abstract] [Full Text]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.