title: Niche adaptation by expansion and reprogramming of general transcription factors.
abstract: Numerous lineage-specific expansions of the transcription factor B (TFB) family in archaea suggests an important role for expanded TFBs in encoding environment-specific gene regulatory programs. Given the characteristics of hypersaline lakes, the unusually large numbers of TFBs in halophilic archaea further suggests that they might be especially important in rapid adaptation to the challenges of a dynamically changing environment. Motivated by these observations, we have investigated the implications of TFB expansions by correlating sequence variations, regulation, and physical interactions of all seven TFBs in Halobacterium salinarum NRC-1 to their fitness landscapes, functional hierarchies, and genetic interactions across 2488 experiments covering combinatorial variations in salt, pH, temperature, and Cu stress. This systems analysis has revealed an elegant scheme in which completely novel fitness landscapes are generated by gene conversion events that introduce subtle changes to the regulation or physical interactions of duplicated TFBs. Based on these insights, we have introduced a synthetically redesigned TFB and altered the regulation of existing TFBs to illustrate how archaea can rapidly generate novel phenotypes by simply reprogramming their TFB regulatory network.
authors: Baliga Lab, Institute for Systems Biology, Seattle, WA 98109, USA.
authors: Serdar
authors: S
authors: Turkarslan
authors: David J
authors: DJ
authors: Reiss
authors: Goodwin
authors: G
authors: Gibbins
authors: Wan Lin
authors: WL
authors: Su
authors: Min
authors: M
authors: Pan
authors: J Christopher
authors: JC
authors: Bare
authors: Christopher L
authors: CL
authors: Plaisier
authors: Nitin S
authors: NS
authors: Baliga
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D019848:Gene Expression Regulation, Archaeal; D019617:Halobacterium salinarum / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D055049:Salt Tolerance; D013312:Stress, Physiological; D035581:Transcription Factor TFIIB / Q000235:genetics* / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D011994:Recombinant Proteins; D035581:Transcription Factor TFIIB; C106466:transcription factor B, Archaea