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Title: DNA Recognition by a σ 54 Transcriptional Activator from Aquifex aeolicus

Transcription initiation by bacterial σ 54-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain. The structurally characterized DNA-binding domains from activators all belong to the Factor for Inversion Stimulation (Fis) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DNA-binding domain of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ 54 activators. Two NtrC4 binding sites were identified upstream (-145 and -85 base pairs) from the start of the lpxC gene, which is responsible for the first committed step in Lipid A biosynthesis. This is the first experimental evidence for σ 54 regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145 binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homologue, Fis. Ultimately, the greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base specific contacts contributing to affinity than for Fis.
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [1] ;  [2] ;  [1] ;  [4]
  1. Univ. of California, Berkeley, CA (United States)
  2. Univ. of California, Los Angeles, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231; FG05-86ER75281
Type:
Accepted Manuscript
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 426; Journal Issue: 21; Journal ID: ISSN 0022-2836
Publisher:
Elsevier
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DNA complex; DNA-binding domain; sequence-specific recognition; NtrC; Fis
OSTI Identifier:
1257831
Alternate Identifier(s):
OSTI ID: 1407256

Vidangos, Natasha K., Heideker, Johanna, Lyubimov, Artem, Lamers, Meindert, Huo, Yixin, Pelton, Jeffrey G., Ton, Jimmy, Gralla, Jay, Berger, James, and Wemmer, David E.. DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus. United States: N. p., Web. doi:10.1016/j.jmb.2014.08.009.
Vidangos, Natasha K., Heideker, Johanna, Lyubimov, Artem, Lamers, Meindert, Huo, Yixin, Pelton, Jeffrey G., Ton, Jimmy, Gralla, Jay, Berger, James, & Wemmer, David E.. DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus. United States. doi:10.1016/j.jmb.2014.08.009.
Vidangos, Natasha K., Heideker, Johanna, Lyubimov, Artem, Lamers, Meindert, Huo, Yixin, Pelton, Jeffrey G., Ton, Jimmy, Gralla, Jay, Berger, James, and Wemmer, David E.. 2014. "DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus". United States. doi:10.1016/j.jmb.2014.08.009. https://www.osti.gov/servlets/purl/1257831.
@article{osti_1257831,
title = {DNA Recognition by a σ54 Transcriptional Activator from Aquifex aeolicus},
author = {Vidangos, Natasha K. and Heideker, Johanna and Lyubimov, Artem and Lamers, Meindert and Huo, Yixin and Pelton, Jeffrey G. and Ton, Jimmy and Gralla, Jay and Berger, James and Wemmer, David E.},
abstractNote = {Transcription initiation by bacterial σ54-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain. The structurally characterized DNA-binding domains from activators all belong to the Factor for Inversion Stimulation (Fis) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DNA-binding domain of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ54 activators. Two NtrC4 binding sites were identified upstream (-145 and -85 base pairs) from the start of the lpxC gene, which is responsible for the first committed step in Lipid A biosynthesis. This is the first experimental evidence for σ54 regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145 binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homologue, Fis. Ultimately, the greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base specific contacts contributing to affinity than for Fis.},
doi = {10.1016/j.jmb.2014.08.009},
journal = {Journal of Molecular Biology},
number = 21,
volume = 426,
place = {United States},
year = {2014},
month = {8}
}