Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

Yu Qiu, Harish Nagarajan, Mallory Embree, Wendy Shieu, Elisa Abate, Katy Juárez, Byung-Kwan Cho, James G. Elkins, Kelly P. Nevin, Christian L. Barrett, Derek R. Lovley, Bernhard O. Palsson and Karsten Zengler ()
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Yu Qiu: University of California, San Diego
Harish Nagarajan: University of California, San Diego
Mallory Embree: University of California, San Diego
Wendy Shieu: University of California, San Diego
Elisa Abate: University of California, San Diego
Katy Juárez: Instituto de Biotecnología, Universidad Nacional Autónoma de México
Byung-Kwan Cho: University of California, San Diego
James G. Elkins: University of California, San Diego
Kelly P. Nevin: University of Massachusetts
Christian L. Barrett: University of California, San Diego
Derek R. Lovley: University of Massachusetts
Bernhard O. Palsson: University of California, San Diego
Karsten Zengler: University of California, San Diego

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: Abstract Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σN being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.

Date: 2013
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms2743

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DOI: 10.1038/ncomms2743

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