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]. The most basic components of transcriptional regulatory networks are the transcription factors (TFs), TF binding sites at upstream and downstream of the target genes and the target genes. Among them, TFs play the crucial role by enhancing or inhibiting the target gene expression by means of binding to the promoter sequences. Studies on TFs are of extreme significance and can glean more information about the mechanism of transcriptional regulatory networks. Genome-wide analysis of completely sequenced genomes have revealed that TFs account for a large proportion of all encoded proteins [2-4]. Escherichia coli was one of the best-studied organisms and was revealed to have more than 271 TFs in its whole genome. Despite the divergent domain organizations and sequence identities, the TFs characterized to share a significant degree of structural similarity of the DNA-binding domain (DBD), which binds to the specific DNA region [5]. TFs can be classified into several families based on structure difference of DBD which include helix-turn-helix motif, Zinc fingers, Leucine zippers, and Basic-helix-loop-helix, etc. Helix-turn-helix motif is the most common structure of DBD in prokaryotes [3,4,6]. Cyanobacteria are an ancient group of gram-negative bacteria, which exhibit extraordinary diversity in physiological properties, ecological niches and morphology [7]. They survive in different environments, such as fresh and marine waters and extreme conditions. Different member of cyanobacteria shows a remarkable size variation ranging from about 1.6 to 9.1 Mb. For example, Prochlorococcus sp. 1986 is only 1.75 Mb in genome size which is supposed to be one of the smallest genomes and most compact oxyphototrophic organisms discovered to date [8]. Nostoc punctiforme has a large genome size and complicated ecological niches which may suggest a relatively sophisticated organization of this species [9]. Currently, 21 cyanobacterial genomes have been fully sequenced, representing a wide range of species from unicellular to filamentous ones. In addition, more than 20 members of cyanobacteria are in the process of in-finishing or being sequenced [10,11]. Such data resources undoubtedly provide an opportunity for genome-wide analysis of TFs in cyanobacteria.
To date, only a few numbers of TFs in cyanobacteria have been studied in detail. However, those studied provide useful insights into the crucial roles of TFs in biology, and further into their functions. NtcA, one of the extensively studied TF that mediates global nitrogen control and regulates many genes involved in nitrogen assimilation, was identified in all cyanobacteria [12]. FUR could regulate iron assimilation and storage, and modulate the expression of genes involved in the response to different environmental stresses [13]. NtcB, another member of TFs, was identified to activate nitrate assimilation [14]. 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. Whole genome comparative analysis revealed great variability of the TFs 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.
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