skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria

Journal Article · · Journal of Biological Chemistry
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. North Dakota State Univ., Fargo, ND (United States)
+ Show Author Affiliations

Cell-surface signaling (CSS) in Gram-negative bacteria involves highly conserved regulatory pathways that optimize gene expression by transducing extracellular environmental signals to the cytoplasm via inner-membrane sigma regulators. The molecular details of ferric siderophore-mediated activation of the iron import machinery through a sigma regulator are unclear. Here, we present the 1.56 Å resolution structure of the periplasmic complex of the C-terminal CSS domain (CCSSD) of PupR, the sigma regulator in the Pseudomonas capeferrum pseudobactin BN7/8 transport system, and the N-terminal signaling domain (NTSD) of PupB, an outer-membrane TonB-dependent transducer. The structure revealed that the CCSSD consists of two subdomains: a juxta-membrane subdomain, which has a novel all-β-fold, followed by a secretin/TonB, short N-terminal subdomain at the C terminus of the CCSSD, a previously unobserved topological arrangement of this domain. Using affinity pulldown assays, isothermal titration calorimetry, and thermal denaturation CD spectroscopy, we show that both subdomains are required for binding the NTSD with micromolar affinity and that NTSD binding improves CCSSD stability. Our findings prompt us to present a revised model of CSS wherein the CCSSD:NTSD complex forms prior to ferric-siderophore binding. Upon siderophore binding, conformational changes in the CCSSD enable regulated intramembrane proteolysis of the sigma regulator, ultimately resulting in transcriptional regulation.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); USDOE Office of Science (SC); North Dakota EPSCoR; National Science Foundation (NSF)
Grant/Contract Number:
P41 GM103403; 9P41 GM103622; 1S10OD018090-01; AC02-06CH11357; 1R15 GM113227; 1R01 GM126207; P30 GM103332; FAR0025216; 1R15 GM122035; MCB-1413525
OSTI ID:
1616598
Journal Information:
Journal of Biological Chemistry, Vol. 295, Issue 17; ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular BiologyCopyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science

References (57)

SASBDB, a repository for biological small-angle scattering data journal October 2014
Cell-surface signaling in Pseudomonas : stress responses, iron transport, and pathogenicity journal July 2014
Signal transduction pathway of TonB-dependent transporters journal December 2006
Differential proteolysis of sigma regulators controls cell-surface signalling in Pseudomonas aeruginosa: Proteolysis in cell-surface signalling pathways journal November 2011
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal December 2007
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates journal December 1995
Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli: ECF-signalling domain of TonB-dependent receptors journal September 2005
Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface. journal April 1995
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions journal June 2017
PRIMUS: a Windows PC-based system for small-angle scattering data analysis journal September 2003
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination journal September 1998
The HMMTOP transmembrane topology prediction server journal September 2001
Analysis of the Ferric Citrate Transport Gene Promoter of Escherichia coli journal April 2003
SEDPHAT – A platform for global ITC analysis and global multi-method analysis of molecular interactions journal April 2015
Activation of a Cell Surface Signaling Pathway in Pseudomonas aeruginosa Requires ClpP Protease and New Sigma Factor Synthesis journal December 2017
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard journal May 2009
Interactions between an anti-sigma protein and two sigma factors that regulate the pyoverdine signaling pathway in Pseudomonas aeruginosa journal November 2014
DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma E-dependent extracytoplasmic stress response journal August 2002
JPred4: a protein secondary structure prediction server journal April 2015
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles journal May 2016
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin journal January 1993
Structural basis for the negative regulation of bacterial stress response by RseB journal March 2010
Scaling and assessment of data quality journal December 2005
Analysis of Protein Circular Dichroism Spectra Based on the Tertiary Structure Classification journal December 2001
XDS journal January 2010
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT journal January 2015
Mechanistic Implications of the Unique Structural Features and Dimerization of the Cytoplasmic Domain of the Pseudomonas Sigma Regulator, PupR journal September 2015
SMART, a simple modular architecture research tool: Identification of signaling domains journal May 1998
Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling journal January 2007
GNOM – a program package for small-angle scattering data processing journal October 1991
NMR assignments of the N-terminal signaling domain of the TonB-dependent outer membrane transducer PupB journal October 2017
Surface Signaling in Ferric Citrate Transport Gene Induction: Interaction of the FecA, FecR, and FecI Regulatory Proteins journal February 2000
Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions journal April 2016
Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering journal February 2015
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
Coot model-building tools for molecular graphics journal November 2004
The Prc and RseP proteases control bacterial cell-surface signalling activity: Prc and RseP proteases control CSS journal January 2014
Metal Import through Microbial Membranes journal January 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Processing of cell-surface signalling anti-sigma factors prior to signal recognition is a conserved autoproteolytic mechanism that produces two functional domains: Initial cleavage of CSS anti-sigma factors journal February 2015
Benchmarking fold detection by DaliLite v.5 journal July 2019
Interaction of a Partially Disordered Antisigma Factor with Its Partner, the Signaling Domain of the TonB-Dependent Transporter HasR journal April 2014
From the Periplasmic Signaling Domain to the Extracellular Face of an Outer Membrane Signal Transducer of Pseudomonas aeruginosa: Crystal Structure of the Ferric Pyoverdine Outer Membrane Receptor journal April 2007
Fitting two- and three-site binding models to isothermal titration calorimetric data journal April 2015
NMRPipe: A multidimensional spectral processing system based on UNIX pipes journal November 1995
Overcoming Expression and Purification Problems of RhoGDI Using a Family of “Parallel” Expression Vectors journal February 1999
Preparation of selenomethionyl proteins for phase determination book January 1997
Data processing and analysis with the autoPROC toolbox journal March 2011
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion journal March 2006
HingeProt: Automated prediction of hinges in protein structures journal September 2007
SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale journal December 2018
Self-cleavage of the Pseudomonas aeruginosa Cell-surface Signaling Anti-sigma Factor FoxR Occurs through an N-O Acyl Rearrangement journal March 2015
SMART: recent updates, new developments and status in 2015 journal October 2014
The Crystal Structure of the Pyoverdine Outer Membrane Receptor FpvA from Pseudomonas aeruginosa at 3.6Å Resolution journal March 2005
Isoform-Selective and Stereoselective Inhibition of Hypoxia Inducible Factor-2 journal July 2015
Phaser crystallographic software journal July 2007

Figures / Tables (12)

Figure 1(p. 2)figure Figure 1
Table 1(p. 2)table Table 1
Figure 2(p. 3)figure Figure 2
Figure 3(p. 4)figure Figure 3
Table 2(p. 4)table Table 2
Table 3(p. 4)table Table 3
Figure 4(p. 5)figure Figure 4
Table 4(p. 5)table Table 4
Figure 5(p. 6)figure Figure 5
Figure 6(p. 7)figure Figure 6
Figure 7(p. 8)figure Figure 7
Figure 8(p. 8)figure Figure 8

Similar Records

Mechanistic Implications of the Unique Structural Features and Dimerization of the Cytoplasmic Domain of the Pseudomonas Sigma Regulator, PupR
Journal Article · Tue Sep 29 00:00:00 EDT 2015 · Biochemistry · OSTI ID:1616598
+4 more
An unusual crystal structure of ferric-enterobactin bound FepB suggests novel functions of FepB in microbial iron uptake
Journal Article · Fri Sep 23 00:00:00 EDT 2016 · Biochemical and Biophysical Research Communications · OSTI ID:1616598
+4 more
Preliminary X-ray investigations of several crystal forms of the ferripyoverdine FpvA outer membrane receptor from Pseudomonas aeruginosa bound to ferripyoverdine
Journal Article · Mon May 01 00:00:00 EDT 2006 · Acta Crystallographica. Section F · OSTI ID:1616598
+1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
bacterial signal transduction
biophysics
metal homeostasis
protein structure
structural biology
X-ray crystallography
X-ray scattering
cell surface signaling
inner membrane sigma regulator
TonB-dependent transducer