Abstract
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
Highlights
Archaea, Bacteria, and Eukarya represent the three domains of life
Archaea include a purine-rich transcription factor B recognition element (BRE), which is recognized by the transcription factor TFIIB (TFB), immediately followed by a TATA box promoter sequence centered at a distance of 26/27 bp, upstream of the transcription start site (TSS) [5,6,7], a homologue of the transcription factor TFIIB (TFB), and an RNA polymerase that contains between
These steps allowed for the detection of 86 proteins as probable transcription factors (TFs) that represent the 4% of the total genes encoded in this archaeon
Summary
Bacteria, and Eukarya represent the three domains of life. Organisms included in the Archaea cellular domain are highly diverse in morphology, physiology, and natural habitats [1,2,3,4].An interesting feature associated with Archaea is their basal transcription machinery, which resembles that of eukaryotes.In this regard, Archaea include a purine-rich transcription factor B recognition element (BRE), which is recognized by the transcription factor TFIIB (TFB), immediately followed by a TATA box promoter sequence centered at a distance of 26/27 bp, upstream of the transcription start site (TSS) [5,6,7], a homologue of the transcription factor TFIIB (TFB), and an RNA polymerase that contains between8 and 13 subunits [8,9]. Archaeal mRNAs and DNA-binding transcription factors (TFs) are structurally similar to their bacterial counterparts [12,13] This regulatory organization raises basic questions with regard to the mechanisms of transcriptional regulation and the manner by which bacteria-like TFs may interact or interfere with the components of the eukaryotic-like basal transcriptional machinery within an archaeal cell. It is for this reason that archaeal DNA-binding
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