Abstract

Summary: MtbRegList is a database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain predicted and characterized regulatory DNA motifs cross-referenced with corresponding transcription factor(s), and experimentally identified transcription start sites. MtbRegList can also handle flexible and complex genomic search requests, besides having a noteworthy browsing capability.

Availability: MtbRegList is freely available at http://www.USherbrooke.ca/vers/MtbRegList

Contact:Ryszard.Brzezinski@USherbrooke.ca

Supplementary information: On the MtbRegList website.

Environmental adaptation is essential to the establishment of successful infection by bacterial pathogens. In most cases, adaptation greatly depends on transcriptional regulation. In prokaryotes, promoter recognition is effected by a sigma factor that binds the catalytic core RNA polymerase and initiates transcription (Gruber and Gross, 2003). Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis, has one principal and 12 alternative sigma factors (Cole et al., 1998), all with potentially different promoter-recognition properties. It is presumed that each sigma factor controls diverse sets of genes in response to specific environmental conditions. Furthermore, at least 200 regulatory proteins also modulate gene expression profiles in Mtb.

Despite the use of the BCG vaccine and antibiotic treatments, it is currently estimated that Mtb infects one-third of the human population, killing nearly 2 million people each year (Frieden et al., 2003). Since the publication of its entire genome sequence (Cole et al., 1998), data regarding gene expression regulation in Mtb has accumulated at a significant rate. The identification and understanding of gene regulatory networks could lead to the discovery of new drugs and better vaccines. Compiling transcription start sites (tss), promoters and transcription factor binding sites is the first step to rationally initiating this approach. Some compilation studies already exist for other micro-organisms (Makita et al., 2004; Salgado et al., 2004). However, no database is currently available to structure our knowledge of gene regulation in this threatening pathogen. In order to facilitate access to this data, we have organized it in a relational database complete with a web-based search form and a graphical visualization tool. MtbRegList is freely accessible at http://www.USherbrooke.ca/vers/MtbRegList.

Genome annotations found in MtbRegList have been extracted from the frequently updated TubercuList database (http://genolist.pasteur.fr/TubercuList/) (Camus et al., 2002). Where applicable, we provide hyperlinks to COG numbers from the GenBank annotation (Tatusov et al., 2003), gene information from TubercuList, protein information from the Mtb Structural Genomics Consortium and relevant references from PubMed (National Library of Medicine). The first release of MtbRegList contains 315 annotated DNA motifs (72 tss, 119 promoters, 121 transcription factor binding sites and 3 terminators) described in 56 research papers. Among annotated DNA motifs, some are predicted or deduced sites (14), and some are experimentally derived from mycobacteria other than Mtb (24). The database will be kept up-to-date in future releases with data from the literature. Researchers requiring access to the most recent features and data can access the development version following a dedicated link provided in the main page of our database.

MtbRegList has two main search pages. The first allows requests on genome information while the second focuses on annotated DNA motifs. Genome information is categorized as intergenic regions (IRs), genes and gene products (proteins and untranslated RNAs). A functional status is given to each IR based on the orientation of its flanking genes. If both genes have the same orientation, the ‘IR status’ is Promoter (P if genes are encoded on the positive strand, Q if encoded on the negative strand); Divergent (D) where they are in opposite orientations; and Terminator (T) in the case of opposite convergent orientations. The unique gene identifiers, and gene products, are identical to those found in TubercuList. However, the name of an IR is composed of ‘ir’ followed by a letter representing its status (P, Q, D or T), and by the upstream and downstream gene identifier (e.g. irD_Rv1737c_Rv1738). Typical queries regarding genome information search pages could be to list all divergent and promoter IRs >55 bp or to identify all proteins from the ‘Regulatory’ functional category with a molecular mass >32 kDa.

The second main search page regards annotated motifs (including tss, promoters and transcription factor binding sites). Motifs are classified as either ‘Root pattern’ or ‘DNA motif’. Each annotated DNA motif (characterized or predicted) is derived from a Root pattern. Root patterns, akin to consensus sequences, are obtained from the literature or derived from experimentally identified DNA motifs. We also use the concept of ‘signature’, which allows users to view the information concerning several motifs at a glance. A Root pattern is represented by a signature such as S[/minSP – maxSP/S] where S stands for sequence box, SP for spacing, and what is inside brackets can be omitted or repeated depending on the number of pattern boxes. An annotated DNA motif is similarly represented by a signature such as S@m[/SP/S@m] where m stands for mismatch count relative to its respective Root pattern. For example, the Root pattern ‘GGRAAC/15−19/SGTTG’ (R = A or G; S = C or G) could have the following associated DNA motif instances: GGGATC@1/16/CGTTG@0 and GGTAAC@1/18/AGTTG@1. A Root pattern is mainly described by its signature, a category, the regulatory protein that recognizes it and relevant references from the literature. Categories of Root patterns include promoters, regulators, terminators and tss. A DNA motif is described by features such as its signature, the associated Root signature, the genomic region where it is found, the strand, 5′ and 3′ distances, experimental evidences and relevant references from the literature. The ‘experimental evidence’ field content distinguishes experimentally verified motifs from the predicted ones, as does the graphical view. A typical query could be to list all annotated DNA motifs formally identified by DNA-binding analysis or site-directed mutagenesis. The Root pattern and DNA motif search pages are dedicated exclusively to annotated motifs.

For each search page, the result columns displayed can be customized. Moreover, the results are displayed in tables that allow users to sort them according to any attribute. Hyperlinks are provided to navigate from results to definitions or associated components (for example regulatory proteins or genomic regions). Results can be saved in XML or tab delimited text format. An example of MtbRegList's browsing capability is shown in Figure 1, which simulates a sequence of operations from the Root pattern search page to the visualization of a particular IR.

In addition, it is possible to graphically navigate the genome. One can choose to view a genomic region according to its coordinates, or centered on a gene of interest. It is possible to zoom in or out of the generated view. Nucleotide sequences are shown whenever they would be readable. The view is ‘clickable’ and linked to relevant records of MtbRegList.

MtbRegList runs on an open source web platform (LAMP: Linux, Apache, MySQL, PHP). The design adopted for this database will allow, in subsequent versions, the support of large scale studies of DNA microarrays. For instance, it will allow users to establish links between a subset of differentially expressed genes and a particular annotated DNA motif (characterized or predicted). Moreover, the framework developed can be adapted for use with other completely sequenced bacterial genomes with minimal modifications.

Fig. 1

An example of the browsing capability of MtbRegList. From the Root pattern search page (A), list all Root of the ‘Regulator’ category, click on the signature of the LexA Root pattern (B) to access all annotated DNA motifs recognized by this regulatory protein (C) and visualize the IR irD_Rv2719c_Rv2720 that possesses a LexA annotated DNA motif (D).

Fig. 1

An example of the browsing capability of MtbRegList. From the Root pattern search page (A), list all Root of the ‘Regulator’ category, click on the signature of the LexA Root pattern (B) to access all annotated DNA motifs recognized by this regulatory protein (C) and visualize the IR irD_Rv2719c_Rv2720 that possesses a LexA annotated DNA motif (D).

The authors would like to thank Sébastien Rodrigue, Benoît Leblanc, Jean-François Jacques and Daniel Lafontaine for their valuable comments on the database and the manuscript. This work was supported by NSERC grants to R.B., L.G. and J.G. L.G. holds a Canada Research Chair on mechanisms of gene transcription, and is a Chercheur boursier Junior II of the FRSQ. P.-É.J. holds a FQRNT PhD scholarship.

REFERENCES

Camus, J.C., et al.
2002
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.
Microbiology
 
148
2967
–2973
Cole, S.T., et al.
1998
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature
 
393
537
–544
Frieden, T.R., et al.
2003
Tuberculosis.
Lancet
 
362
887
–899
Gruber, T.M. and Gross, C.A.
2003
Multiple sigma subunits and the partitioning of bacterial transcription space.
Ann. Rev. Microbiol.
 
57
441
–466
Makita, Y., et al.
2004
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
Nucleic Acids Res.
 
32
D75
–D77
Salgado, H., et al.
2004
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
Nucleic Acids Res.
 
32
D303
–D306
Tatusov, R.L., et al.
2003
The COG database: an updated version includes eukaryotes.
BMC Bioinformatics
 
4
41

Comments

0 Comments