General transcription factor specified global gene regulation in archaea

Marc T. Facciotti, David J. Reiss, Min Pan, Amardeep Kaur, Madhavi Vuthoori, Richard Bonneau, Paul Shannon, Alok Srivastava, Samuel M. Donohoe, Leroy E. Hood, Nitin S. Baliga

Research output: Contribution to journalArticlepeer-review


Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, σ factors regulate much of this process, whereas in eukaryotes, four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, by using a systems approach, we provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution toward closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to use various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little has been previously known.

Original languageEnglish (US)
Pages (from-to)4630-4635
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number11
StatePublished - Mar 13 2007


  • Archaea
  • Regulatory networks
  • Systems biology

ASJC Scopus subject areas

  • General


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