Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.
BACKGROUND
Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment.


RESULTS
We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively.


CONCLUSIONS
This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism.
Institute for Systems Biology, Seattle, WA, USA. cplaisier@systemsbiology.org.
Christopher L
CL
Plaisier
Institute for Systems Biology, Seattle, WA, USA. fylo@systemsbiology.org.|Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. fylo@systemsbiology.org.
Fang-Yin
FY
Lo
Institute for Systems Biology, Seattle, WA, USA. justin.ashworth@systemsbiology.org.
Justin
J
Ashworth
Institute for Systems Biology, Seattle, WA, USA. abrooks@systemsbiology.org.|Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. abrooks@systemsbiology.org.
Aaron N
AN
Brooks
Institute for Systems Biology, Seattle, WA, USA. kbeer@systemsbiology.org.|Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. kbeer@systemsbiology.org.
Karlyn D
KD
Beer
Institute for Systems Biology, Seattle, WA, USA. amardeep.kaur@systemsbiology.org.
Amardeep
A
Kaur
Institute for Systems Biology, Seattle, WA, USA. min.pan@systemsbiology.org.
Min
M
Pan
Institute for Systems Biology, Seattle, WA, USA. david.reiss@systemsbiology.org.
David J
DJ
Reiss
Department of Biomedical Engineering, University of California, Davis, CA, USA. mtfacciotti@ucdavis.edu.|Genome Center, University of California, Davis, CA, USA. mtfacciotti@ucdavis.edu.
Marc T
MT
Facciotti
Institute for Systems Biology, Seattle, WA, USA. nitin.baliga@systemsbiology.org.|Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA. nitin.baliga@systemsbiology.org.|Department of Microbiology, University of Washington, Seattle, WA, USA. nitin.baliga@systemsbiology.org.|Department of Biology, University of Washington, Seattle, WA, USA. nitin.baliga@systemsbiology.org.
Nitin S
NS
Baliga
D000220:Adaptation, Biological / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D005075:Biological Evolution; D004777:Environment; D020440:Gene Duplication / Q000235:genetics*; D019848:Gene Expression Regulation, Archaeal / Q000235:genetics*; D019617:Halobacterium salinarum / Q000235:genetics* / Q000378:metabolism; D010269:Paraquat; D014157:Transcription Factors / Q000235:genetics*
D014157:Transcription Factors; D010269:Paraquat