cTFbase: a database for comparative genomics of transcription factors in cyanobacteria

Abstract

Background: Comprehensive identification and classification of the transcription factors (TFs) in a given genome is an important aspect in understanding transcriptional regulatory networks of a specific organism. Cyanobacteria are an ancient group of gram-negative bacteria with strong variation in genome size ranging from about 1.6 to 9.1 Mb and little is known about their TF repertoires. Therefore, we constructed the cTFbase database to classify and analyze all the putative TFs in cyanobacterial genomes, followed by genome-wide comparative analysis.

Description: In the current release, cTFbase contains 1288 putative TFs identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domains and ortholog identification from any selected genomes. Comparative analysis revealed great variability of the TF sequences in cyanobacterial genomes. The high variance on the gene number and domain organization would be related to their diverse biological functions and their adaptation to various environmental conditions.

Conclusion: cTFbase provides a centralized warehouse for comparative analysis of putative TFs in cyanobacterial genomes. The availability of such an extensive database would be of great interest for the community of researchers working on TFs or transcriptional regulatory networks in cyanobacteria. cTFbase can be freely accessible at http://cegwz.com/ and will be continuously updated when the newly sequenced cyanobacterial genomes are available.

Figure 1

Flow-chart of method used to identify TFs.

Figure 2

Relationship between the number of TFs and the total number of ORFs in 21 cyanobacterial genomes. The total number of ORFs in each genome was plotted as a function against the number of TFs. Triangle indicates marine cyanobacteria, while square indicates fresh or soil cyanobacteria.

Figure 3

Domain architectures and classification scheme of TFs in the 21 cyanobacterial genomes. The methods classifying TFs into families and identifying the domains can be referred in Section 2. Green rectangles indicate the DBD domains, while red ellipses represent associated domains. The number on the right of the domain organization represents the number of sequences in the specific family.