A Database ofPromoters and Transcription
Factors

B: subtilis

Takahiro Ishii

Kenta Nakai

ishii@imcb.osaka-u.ac.jp

nakai@imcb.osaka-u.ac.jp

Institute for Molecular and Cellular Biology, Osaka University
1-3 Yamada-oka, Suita, Osaka 565-0871, Japan

1 Introduction
Although the number of bacteria with their entire genomic sequence known is increasing, it is essential
to study well-known genomes for understanding the 'blueprint` of bacteria more precisely. For thispurpose, E. coli and B. subtilis are especially suitable because of their long history of research. Amongvarious information coded in bacterial genomes, we are interested in the analysis of transcriptional
regulation network. One of our ultimate goal is to predict the expression condition of given ORFs fromtheir upstream sequences. For example, we have developed a prediction system of sigma-dependencyof ORFs found in B. subtilis [6] and in E. coli (unpublished). However, to understand the detailed
mechanism of transcription regulation, the knowledge of other transcription factors is also crucial.
For E. coli, there is such a database called RegulonDB [3] but there is no databases containing
comprehensive information of transcription in B. subtilis. Thus, we constructed a database which will
be useful not only for our theoretical study but also for the works of experimental researchers.

2 Database
Basically, our database has inter-related components for promoters and for transcription factors. Theformer is a collection of 313 characterized promoters and its most important information is the positionsof known cis-elements in each promoter. These positions are shown both in a table format and in apicture. In contrast, the transcription factor module is a set of entries corresponding to the names of76 transcription factors including 10 sigma factors. Its main feature is the collection of known bindingsites for each factor (consensus pattern is highlighted in red if any). The information of experimental
techniques used for the characterization of each site is also noted. The main source of our database is
the literature survey of 298 references but the bene t of other pioneering works such as the compilation
by Helmann [4] is also used. Since the database is constructed on WWW, all references cited are linked
to the PubMed database in NCBI, enabling the one-click check of their abstracts. In addition, theentries are also linked to other databases such as SWISS-PROT [1]. Currently, our database is released
to limited users for beta-testing. One who wants to use it before its ocial release should ask theauthors by e-mail.

3 Analyses
We took some statistics on B. subtilis  A -dependent promoters and compared them with those on70E. coli  -dependent promoters [2] to see if there are some speci c features of B. subtilis promoters.
The ratio of repressible promoters and activatable ones is about 6:4, which is similar to the valueof E. coli. But it appears that the number of promoters with repeated homologous binding sites is351

signi cantly fewer in B. subtilis than in E. coli. In addition, we noticed that, unlike E. coli promoters,
B. subtilis promoters can have some binding regions of activators even at the downstream regions oftranscriptional initiation sites.
The amino acid similarity between transcription factors was also examined. We aligned 33 of thembased on the regions corresponding to the helix-turn-helix motif. It was found that the classi cationof factors based on our alignment does not precisely correspond to the traditional family classi cation,
described in SubtiList [5]. Since the traditional classi cation might be biased from historical reasons,further studies seems necessary to reconsider the classi cation.
Anyway, we hope that our database will become a useful resource for researchers of bacterialtranscription as well as for our own study. We plan to release our database free of charge before long.

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas, GenomeScience, from the Ministry of Education, Science, and Culture of Japan. KN was also supportedby Special Coordination Funds for Promoting Science and Technology from Science and Technology
Agency and by Research for the Future Program of JSPS.

References[1] Bairoch, A, and Apweiler, R., The SWISS-PROT protein sequence data bank and its supplement
TrEMBL in 1998., Nucleic Acids Res., 26:38-42, 1998.
[2] Gralla, J.D., and Collado-Vides, J., Organization and function of transcription regulatory elements, In Neidhardt, F.C. et al. (eds), Cellular and Molecular Biology: Eschericha coli andSalmonella, 2nd edn. American Society for Microbiology, Washington, DC, 1232{1245, 1996.
[3] Huerta, A.M., Salgado, H., Thie ry, D., and Collado-Vides, J., RegulonDB: a database on transcriptional regulation in Escherichia coli, Nucleic Acids Res., 26:55{59, 1998.
[4] Helmann, J.D., Compilation and analysis of Bacillus subtilis A -dependent promoter sequences:evidence for extended contact between RNA polymerase and upstream promoter DNA, NucleicAcids Res., 23:2351{2360, 1995.
[5] Moszer, I., Glaser, P., and Danchin, A., SubtiList: a relational database for the Bacillus subtilis
genome, Microbiology, 141:261{268, 1995.
[6] Yada, T., Totoki, Y., Ishii, T., and Nakai, K., Functional prediction of B. subtilis genes from theirregulatory sequences, Proc. Intell. Syst. Mol. Biol., 5:354{357, 1997.

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