Nucleic Acids Research, 2001, Vol. 29, No. 1 277-00
© 2001 Oxford University Press
PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
Department of Molecular Genetics and Biotechnology and 1School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel and 2Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
Received September 13, 2000; Accepted October 3, 2000.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONDATABASE CONTENT AND...AVAILABILITY OF THE DATABASEREFERENCES |
|---|
PromEC is an updated compilation of Escherichia coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E.coli chromosome, as well as the actual sequences in the promoter region. The database was updated as of July 2000 and includes 472 entries. PromEC is accessible at http://bioinfo.md.huji.ac.il/marg/promec
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONDATABASE CONTENT AND...AVAILABILITY OF THE DATABASEREFERENCES |
|---|
We announce the availability of an updated compilation of Escherichia coli mRNA promoter sequences (as of July 2000). The database extends our previous compilation (1), and as in the original compilation, contains only promoter sequences with experimentally identified transcriptional start sites. The original database has been used extensively both by researchers who are studying the properties of promoter sequences and their relationship to gene expression, and by computational biologists who have used it as a benchmark for testing newly developed prediction algorithms on a reliable data set. We believe that the updated database will be as valuable to both communities.
|
DATABASE CONTENT AND ORGANIZATION |
|---|
|
TOPABSTRACTINTRODUCTIONDATABASE CONTENT AND...AVAILABILITY OF THE DATABASEREFERENCES |
|---|
The added promoter sequences are based on three sources: the documentation in the E.coli genome file (2), the RegulonDB database (3) and an updated literature search (covering the years 1993–2000). Only promoters with documented transcriptional start sites were extracted from the genome file and the RegulonDB database. Promoters that were compiled following the literature search were those for which the transcriptional start sites were identified experimentally, either by primer extension or by S1 nuclease mapping. RegulonDB database has also incorporated these updates based on the literature search. The promoters in our original compilation were also re-examined in view of the documentation in the E.coli genome file and the RegulonDB database. As a result, a few sequences, deemed as incorrect, were removed or corrected. In most cases, those involved second or third mRNA start sites of the same gene.
The updated database currently includes 472 entries: 275 sequences from the original compilation, 157 promoters collected from the other two databases and 40 additional promoters that were found in publications dated between the years 1993 and 2000. The database documents the gene name, the position of the transcriptional start site on the E.coli genome, the reference paper and the sequence itself (spanning nucleotides –75 to +25 relative to the transcriptional start site). If more than one start site was documented for a single gene, the most prominent one is recorded in the position field (if such information is available), while all start sites are marked in the sequence record.
|
AVAILABILITY OF THE DATABASE |
|---|
|
TOPABSTRACTINTRODUCTIONDATABASE CONTENT AND...AVAILABILITY OF THE DATABASEREFERENCES |
|---|
The database is available at http://bioinfo.md.huji.ac.il/marg/promec, where a flat file containing all promoter sequences may also be extracted. When citing the database please cite this reference, along with the RegulonDB database (3). We expect the database to grow as new transcriptional start sites are determined. It is also probable that we have missed some already known transcriptional start sites. Any information of that kind would be very much appreciated and should be sent to promec{at}md2.huji.ac.il
|
ACKNOWLEDGEMENTS |
|---|
We thank Julio Collado-Vides and Heladia Salgado for their help. This study was supported by grants from the Human Frontiers Science Program (H.M.), and from the Ministry of Science, Israel (G.B.).
|
FOOTNOTES |
|---|
* To whom correspondence should be addressed at: Department of Molecular Genetics and Biotechnology, The Hebrew University—Hadassah Medical School, POB 12272 Jerusalem 91120, Israel. Tel.: +972 2 6758614; Fax: +972 2 6784010; Email: hanah{at}md2.huji.ac.il
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONDATABASE CONTENT AND...AVAILABILITY OF THE DATABASEREFERENCES |
|---|
-
1 Lisser,S. and Margalit,H. (1993) Compilation of Escherichia coli mRNA promoter sequences. Nucleic Acids Res., 21, 1507–1516.
2 Blattner,F.R., Plunkett,G.,III, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F., Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J., Mau,B. and Shao,Y. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453–1474.
3 Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Blattner,F.R. and Collado-Vides,J. (2000) RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res., 28, 65–67. Updated article in this issue: Nucleic Acids Res. (2001), 29, 72–74.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. L. Turnbough Jr. and R. L. Switzer Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors Microbiol. Mol. Biol. Rev., June 1, 2008; 72(2): 266 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Sinoquet, S. Demey, and F. Braun Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes Nucleic Acids Res., June 1, 2008; 36(10): 3332 - 3340. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G.-Q. Hu, X. Zheng, Y.-F. Yang, P. Ortet, Z.-S. She, and H. Zhu ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D114 - D119. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. S. Rani, S. D. Bhavani, and R. S. Bapi Analysis of E.coli promoter recognition problem in dinucleotide feature space Bioinformatics, March 1, 2007; 23(5): 582 - 588. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. K. Shultzaberger, Z. Chen, K. A. Lewis, and T. D. Schneider Anatomy of Escherichia coli {sigma}70 promoters Nucleic Acids Res., February 16, 2007; 35(3): 771 - 788. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Mallik, B. J. Paul, S. T. Rutherford, R. L. Gourse, and R. Osuna DksA Is Required for Growth Phase-Dependent Regulation, Growth Rate-Dependent Control, and Stringent Control of fis Expression in Escherichia coli. J. Bacteriol., August 1, 2006; 188(16): 5775 - 5782. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Rawal, V. B. R. Kummarasetti, J. Ravindran, N. Kumar, K. Halder, R. Sharma, M. Mukerji, S. K. Das, and S. Chowdhury Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation. Genome Res., May 1, 2006; 16(5): 644 - 655. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kanhere and M. Bansal Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes Nucleic Acids Res., June 6, 2005; 33(10): 3165 - 3175. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. A. Walker, P. Mallik, T. S. Pratt, and R. Osuna The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP J. Biol. Chem., December 3, 2004; 279(49): 50818 - 50828. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Lacour and P. Landini {sigma}S-Dependent Gene Expression at the Onset of Stationary Phase in Escherichia coli: Function of {sigma}S-Dependent Genes and Identification of Their Promoter Sequences J. Bacteriol., November 1, 2004; 186(21): 7186 - 7195. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Wang, M. Noordewier, and C. J. Benham Stress-Induced DNA Duplex Destabilization (SIDD) in the E. coli Genome: SIDD Sites Are Closely Associated With Promoters Genome Res., August 1, 2004; 14(8): 1575 - 1584. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Paredes, I. Rigoutsos, and E. T. Papoutsakis Transcriptional organization of the Clostridium acetobutylicum genome Nucleic Acids Res., April 1, 2004; 32(6): 1973 - 1981. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Repoila and S. Gottesman Temperature Sensing by the dsrA Promoter J. Bacteriol., November 15, 2003; 185(22): 6609 - 6614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Walker and R. Osuna Factors Affecting Start Site Selection at the Escherichia coli fis Promoter J. Bacteriol., September 1, 2002; 184(17): 4783 - 4791. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Tobes and J. L. Ramos AraC-XylS database: a family of positive transcriptional regulators in bacteria Nucleic Acids Res., January 1, 2002; 30(1): 318 - 321. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||