Genome Research scroll

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Gur-Arie, R.
Right arrow Articles by Kashi, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gur-Arie, R.
Right arrow Articles by Kashi, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 10, Issue 1, 62-71, January 2000

LETTER
Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism

Riva Gur-Arie,3 Cyril J. Cohen,3 Yuval Eitan, Leora Shelef,1 Eric M. Hallerman,2 and Yechezkel Kashi4

Department of Food Engineering and Biotechnology, Technion-Israel Institute of Technology, Haifa 32000, Israel; 1 Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202 USA; 2 Department of Fisheries and Wildlife Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 USA

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF209020-209030 and AF209508-209518.]

3 These authors contributed equally to this work.

4 Corresponding author.

10:62-71 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Eukaryot CellHome page
M. GuhaMajumdar, E. Dawson-Baglien, and B. B. Sears
Creation of a Chloroplast Microsatellite Reporter for Detection of Replication Slippage in Chlamydomonas reinhardtii
Eukaryot. Cell, April 1, 2008; 7(4): 639 - 646.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
L. Diancourt, V. Passet, C. Chervaux, P. Garault, T. Smokvina, and S. Brisse
Multilocus Sequence Typing of Lactobacillus casei Reveals a Clonal Population Structure with Low Levels of Homologous Recombination
Appl. Envir. Microbiol., October 15, 2007; 73(20): 6601 - 6611.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
Y. Y. Broza, Y. Danin-Poleg, L. Lerner, M. Broza, and Y. Kashi
Vibrio vulnificus Typing Based on Simple Sequence Repeats: Insights into the Biotype 3 Group
J. Clin. Microbiol., September 1, 2007; 45(9): 2951 - 2959.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Mrazek, X. Guo, and A. Shah
Simple sequence repeats in prokaryotic genomes
PNAS, May 15, 2007; 104(20): 8472 - 8477.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
Z. Zhang, Y. Deng, J. Tan, S. Hu, J. Yu, and Q. Xue
A Genome-wide Microsatellite Polymorphism Database for the Indica and Japonica Rice
DNA Res, April 23, 2007; (2007) dsm005v1.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
Y. Danin-Poleg, L. A. Cohen, H. Gancz, Y. Y. Broza, H. Goldshmidt, E. Malul, L. Valinsky, L. Lerner, M. Broza, and Y. Kashi
Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats
J. Clin. Microbiol., March 1, 2007; 45(3): 736 - 746.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
C. W. Stratilo, C. T. Lewis, L. Bryden, M. R. Mulvey, and D. Bader
Single-Nucleotide Repeat Analysis for Subtyping Bacillus anthracis Isolates.
J. Clin. Microbiol., March 1, 2006; 44(3): 777 - 782.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
A. Shelenkov, K. Skryabin, and E. Korotkov
Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes
DNA Res, January 1, 2006; 13(3): 89 - 102.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. Lin, E. L. Civerolo, R. Hu, S. Barros, M. Francis, and M. A. Walker
Multilocus Simple Sequence Repeat Markers for Differentiating Strains and Evaluating Genetic Diversity of Xylella fastidiosa
Appl. Envir. Microbiol., August 1, 2005; 71(8): 4888 - 4892.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
L. Somer, Y. Danin-Poleg, E. Diamant, R. Gur-Arie, Y. Palti, and Y. Kashi
Amplified Intergenic Locus Polymorphism as a Basis for Bacterial Typing of Listeria spp. and Escherichia coli
Appl. Envir. Microbiol., June 1, 2005; 71(6): 3144 - 3152.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H. Karaoglu, C. M. Y. Lee, and W. Meyer
Survey of Simple Sequence Repeats in Completed Fungal Genomes
Mol. Biol. Evol., March 1, 2005; 22(3): 639 - 649.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
T. Coenye and P. Vandamme
Characterization of mononucleotide repeats in sequenced prokaryotic genomes.
DNA Res, January 1, 2005; 12(4): 221 - 233.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. N. Forbes, R. K. Valenzuela, P. Keim, and P. M. Service
Quantitative Trait Loci Affecting Life Span in Replicated Populations of Drosophila melanogaster. I. Composite Interval Mapping
Genetics, September 1, 2004; 168(1): 301 - 311.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
E. Diamant, Y. Palti, R. Gur-Arie, H. Cohen, E. M. Hallerman, and Y. Kashi
Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci
Appl. Envir. Microbiol., April 1, 2004; 70(4): 2464 - 2473.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. P. C. Rocha, I. Matic, and F. Taddei
Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?
Nucleic Acids Res., May 1, 2002; 30(9): 1886 - 1894.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
A. M. Klevytska, L. B. Price, J. M. Schupp, P. L. Worsham, J. Wong, and P. Keim
Identification and Characterization of Variable-Number Tandem Repeats in the Yersinia pestis Genome
J. Clin. Microbiol., September 1, 2001; 39(9): 3179 - 3185.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.