Abstract
BackgroundComprehensive 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.DescriptionIn 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.ConclusioncTFbase 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 and will be continuously updated when the newly sequenced cyanobacterial genomes are available.
Highlights
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
In order to make all the putative TFs in cyanobacteria available to the scientific community and fill in the gap without online databases, we present cTFbase, which will be a valuable resource for further research of TFs and transcriptional regulatory networks in cyanobacteria
We identified 1288 putative TFs from 21 cyanobacterial genomes, among which 404 genes have not been annotated as transcriptional factor in its original annotation in the IMG database
Summary
Deciphering and reconstructing gene transcriptional regulatory networks are important for better understanding the fundamental cellular processes, such as cell division, growth control and gene expression by which cells can adapt to environment more effectively [1]. Collection of TFs The amino acid sequences of the protein-encoding genes of 21 cyanobacterial genomes were retrieved from the IMG database (version 2.0). We identified 1288 putative TFs from 21 cyanobacterial genomes, among which 404 genes have not been annotated as transcriptional factor (including neither shown the function of regulation, nor possessing the helix-turn-helix motif) in its original annotation in the IMG database. Through links to inner section and other databases, it would be a platform in which information on putative TFs in cyanobacteria has highly integrated and will be a centralized warehouse for the comparative genomic analysis We expect that this database will help to further understand the transcriptional regulatory networks of microbiology.
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