Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB
Abstract
RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379–405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204–209, 2010,https://doi.org/10.1016/j.mib.2010.01.002; D. J. Clarke, Future Microbiol 5:1173–1184, 2010,https://doi.org/10.2217/fmb.10.83). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6–17, 2012,https://doi.org/10.1094/MPMI-08-11-0207). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allowsmore »
- Authors:
-
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
- Keck Biophysics Facility, Northwestern University, Evanston, Illinois, USA
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Illinois at Urbana-Champaign, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); NIAID; National Institutes of Health (NIH); HHS
- OSTI Identifier:
- 1493948
- Alternate Identifier(s):
- OSTI ID: 1499720
- Grant/Contract Number:
- SC0012443; NIH R01AI083640; NIH 2R01AI083640-06A1; R01AI083640; 2R01AI083640-06A1; AC02-06CH11357
- Resource Type:
- Journal Article: Published Article
- Journal Name:
- mBio
- Additional Journal Information:
- Journal Name: mBio Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2161-2129
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Filippova, Ekaterina V., Zemaitaitis, Bozena, Aung, Theint, Wolfe, Alan J., Anderson, Wayne F., and Hendrickson, ed., Wayne A. Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB. United States: N. p., 2018.
Web. doi:10.1128/mBio.01993-17.
Filippova, Ekaterina V., Zemaitaitis, Bozena, Aung, Theint, Wolfe, Alan J., Anderson, Wayne F., & Hendrickson, ed., Wayne A. Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB. United States. https://doi.org/10.1128/mBio.01993-17
Filippova, Ekaterina V., Zemaitaitis, Bozena, Aung, Theint, Wolfe, Alan J., Anderson, Wayne F., and Hendrickson, ed., Wayne A. 2018.
"Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB". United States. https://doi.org/10.1128/mBio.01993-17.
@article{osti_1493948,
title = {Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB},
author = {Filippova, Ekaterina V. and Zemaitaitis, Bozena and Aung, Theint and Wolfe, Alan J. and Anderson, Wayne F. and Hendrickson, ed., Wayne A.},
abstractNote = {RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379–405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204–209, 2010,https://doi.org/10.1016/j.mib.2010.01.002; D. J. Clarke, Future Microbiol 5:1173–1184, 2010,https://doi.org/10.2217/fmb.10.83). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6–17, 2012,https://doi.org/10.1094/MPMI-08-11-0207). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria.},
doi = {10.1128/mBio.01993-17},
url = {https://www.osti.gov/biblio/1493948},
journal = {mBio},
issn = {2161-2129},
number = 1,
volume = 9,
place = {United States},
year = {Wed Mar 07 00:00:00 EST 2018},
month = {Wed Mar 07 00:00:00 EST 2018}
}
Web of Science
Figures / Tables:
Works referenced in this record:
Salmonella Biofilm Development Depends on the Phosphorylation Status of RcsB
journal, May 2012
- Latasa, C.; Garcia, B.; Echeverz, M.
- Journal of Bacteriology, Vol. 194, Issue 14
Crystal structure of nonphosphorylated receiver domain of the stress response regulator RcsB from Escherichia coli : X-Ray Structure of the RcsB Receiver Domain
journal, October 2016
- Filippova, Ekaterina V.; Wawrzak, Zdzislaw; Ruan, Jiapeng
- Protein Science, Vol. 25, Issue 12
Regulation and mode of action of the second small RNA activator of RpoS translation, RprA: RprA regulation and mode of action
journal, October 2002
- Majdalani, Nadim; Hernandez, David; Gottesman, Susan
- Molecular Microbiology, Vol. 46, Issue 3
Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae
journal, July 2015
- Doi, Akihiro; Nakamura, Hiro; Shiro, Yoshitsugu
- Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 8
The RcsAB Box: CHARACTERIZATION OF A NEW OPERATOR ESSENTIAL FOR THE REGULATION OF EXOPOLYSACCHARIDE BIOSYNTHESIS IN ENTERIC BACTERIA
journal, March 2000
- Wehland, Markus; Bernhard, Frank
- Journal of Biological Chemistry, Vol. 275, Issue 10
RflM mediates target specificity of the RcsCDB phosphorelay system for transcriptional repression of flagellar synthesis in Salmonella enterica : Repression of
journal, June 2016
- Kühne, Caroline; Singer, Hanna M.; Grabisch, Eva
- Molecular Microbiology, Vol. 101, Issue 5
RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli: Regulation of flhDC by RcsB
journal, August 2003
- Francez-Charlot, Anne; Laugel, Bruno; Van Gemert, Alice
- Molecular Microbiology, Vol. 49, Issue 3
Nε−Lysine Acetylation of a Bacterial Transcription Factor Inhibits Its DNA-Binding Activity
journal, December 2010
- Thao, Sandy; Chen, Chien-Sheng; Zhu, Heng
- PLoS ONE, Vol. 5, Issue 12
Dali server: conservation mapping in 3D
journal, May 2010
- Holm, Liisa; Rosenstr�m, P�ivi
- Nucleic Acids Research, Vol. 38, Issue suppl_2
Transcriptional regulation by BglJ–RcsB, a pleiotropic heteromeric activator in Escherichia coli
journal, December 2013
- Salscheider, Silja Lucia; Jahn, Andreas; Schnetz, Karin
- Nucleic Acids Research, Vol. 42, Issue 5
DNA-binding proteins
journal, September 1983
- Takeda, Y.; Ohlendorf, D.; Anderson, W.
- Science, Vol. 221, Issue 4615
Structure of the Escherichia coli Response Regulator NarL † , ‡
journal, January 1996
- Baikalov, Igor; Schröder, Imke; Kaczor-Grzeskowiak, Maria
- Biochemistry, Vol. 35, Issue 34
An asymmetric heterodomain interface stabilizes a response regulator–DNA complex
journal, February 2014
- Narayanan, Anoop; Kumar, Shivesh; Evrard, Amanda N.
- Nature Communications, Vol. 5, Issue 1
Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation
journal, May 2013
- Leonard, P. G.; Golemi-Kotra, D.; Stock, A. M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 21
Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay
journal, August 2006
- Fredericks, Christine E.; Shibata, Satoshi; Aizawa, Shin-Ichi
- Molecular Microbiology, Vol. 61, Issue 3
Fine-structure mapping and identification of two regulators of capsule synthesis in Escherichia coli K-12.
journal, June 1988
- Brill, J. A.; Quinlan-Walshe, C.; Gottesman, S.
- Journal of Bacteriology, Vol. 170, Issue 6
The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae
journal, April 2008
- Hinchliffe, S. J.; Howard, S. L.; Huang, Y. H.
- Microbiology, Vol. 154, Issue 4
Genome Expression Analyses Revealing the Modulation of the Salmonella Rcs Regulon by the Attenuator IgaA
journal, January 2009
- Mariscotti, J. F.; Garcia-del Portillo, F.
- Journal of Bacteriology, Vol. 191, Issue 6
Signal transduction in bacteria: molecular mechanisms of stimulus—response coupling
journal, April 1998
- Goudreau, Paul N.; Stock, Ann M.
- Current Opinion in Microbiology, Vol. 1, Issue 2
Detecting Envelope Stress by Monitoring β-Barrel Assembly
journal, December 2014
- Cho, Seung-Hyun; Szewczyk, Joanna; Pesavento, Christina
- Cell, Vol. 159, Issue 7
Dimerization allows DNA target site recognition by the NarL response regulator
journal, September 2002
- Maris, Ann E.; Sawaya, Michael R.; Kaczor-Grzeskowiak, Maria
- Nature Structural Biology, Vol. 9, Issue 10
Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE
journal, February 2010
- Castanié-Cornet, Marie-Pierre; Cam, Kaymeuang; Bastiat, Bénédicte
- Nucleic Acids Research, Vol. 38, Issue 11
Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells
journal, November 2017
- Chakraborty, Smarajit; Winardhi, Ricksen S.; Morgan, Leslie K.
- Nature Communications, Vol. 8, Issue 1
Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA
journal, June 2002
- Zhang, Rong-guang; Pappas, Katherine M.; Brace, Jennifer L.
- Nature, Vol. 417, Issue 6892
Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis
journal, April 2016
- He, Xiaoyuan; Wang, Liqin; Wang, Shuishu
- Scientific Reports, Vol. 6, Issue 1
Interaction of the RcsB Response Regulator with Auxiliary Transcription Regulators in Escherichia coli
journal, December 2015
- Pannen, Derk; Fabisch, Maria; Gausling, Lisa
- Journal of Biological Chemistry, Vol. 291, Issue 5
Structural Analysis of the DNA-binding Domain of the Erwinia amylovora RcsB Protein and Its Interaction with the RcsAB Box
journal, March 2003
- Pristovšek, Primoz̆; Sengupta, Kaushik; Löhr, Frank
- Journal of Biological Chemistry, Vol. 278, Issue 20
Acetylation of the Response Regulator RcsB Controls Transcription from a Small RNA Promoter
journal, July 2013
- Hu, L. I.; Chi, B. K.; Kuhn, M. L.
- Journal of Bacteriology, Vol. 195, Issue 18
Identification of an RcsA/RcsB Recognition Motif in the Promoters of Exopolysaccharide Biosynthetic Operons from Erwinia amylovora and Pantoea stewartii Subspecies stewartii
journal, February 1999
- Wehland, Markus; Kiecker, Clemens; Coplin, David L.
- Journal of Biological Chemistry, Vol. 274, Issue 6