Niche adaptation by expansion and reprogramming of general transcription factors

Serdar Turkarslan, David J. Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J. Christopher Bare, Christopher Plaisier, Nitin S. Baliga

Research output: Contribution to journalArticle

22 Citations (Scopus)

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.

Original languageEnglish (US)
Article number554
JournalMolecular Systems Biology
Volume7
DOIs
StatePublished - Nov 30 2011
Externally publishedYes

Fingerprint

General Transcription Factors
Transcription factors
Niche
Transcription Factor
Archaea
niches
Transcription Factors
transcription factors
Fitness Landscape
Genes
Interaction
Halobacterium
Halobacterium salinarum
Gene
Gene Conversion
gene conversion
systems analysis
Regulatory Networks
Regulator Genes
Lakes

Keywords

  • evolution by gene family expansion
  • fitness
  • niche adaptation
  • reprogramming of gene regulatory network
  • transcription factor B

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

Turkarslan, S., Reiss, D. J., Gibbins, G., Su, W. L., Pan, M., Bare, J. C., ... Baliga, N. S. (2011). Niche adaptation by expansion and reprogramming of general transcription factors. Molecular Systems Biology, 7, [554]. https://doi.org/10.1038/msb.2011.87

Niche adaptation by expansion and reprogramming of general transcription factors. / Turkarslan, Serdar; Reiss, David J.; Gibbins, Goodwin; Su, Wan Lin; Pan, Min; Bare, J. Christopher; Plaisier, Christopher; Baliga, Nitin S.

In: Molecular Systems Biology, Vol. 7, 554, 30.11.2011.

Research output: Contribution to journalArticle

Turkarslan, Serdar ; Reiss, David J. ; Gibbins, Goodwin ; Su, Wan Lin ; Pan, Min ; Bare, J. Christopher ; Plaisier, Christopher ; Baliga, Nitin S. / Niche adaptation by expansion and reprogramming of general transcription factors. In: Molecular Systems Biology. 2011 ; Vol. 7.
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