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Title: Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Moreover, calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. Our results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor producedmore » by P. aeruginosa.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [3];  [4];  [5];  [1]
  1. Hospital for Sick Children, Toronto, ON (Canada); Univ. of Toronto, ON (Canada)
  2. Brookhaven National Lab. (BNL), Upton, NY (United States)
  3. Hospital for Sick Children, Toronto, ON (Canada);
  4. Hospital for Sick Children, Toronto, ON (Canada)
  5. Virginia Commonwealth Univ. Medical Center and McGuire Veterans Affairs Medical Center, Richmond, VA (United States)
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1237169
Report Number(s):
BNL-108277-2015-JA
Journal ID: ISSN 0021-9258; R&D Project: LS001
Grant/Contract Number:  
SC00112704
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 290; Journal Issue: 20; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE

Citation Formats

Whitney, John C., Robinson, Howard, Whitfield, Gregory B., Marmont, Lindsey S., Yip, Patrick, Neculai, A. Mirela, Lobsanov, Yuri D., Ohman, Dennis E., and Howell, P. Lynne. Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa. United States: N. p., 2015. Web. doi:10.1074/jbc.M115.645051.
Whitney, John C., Robinson, Howard, Whitfield, Gregory B., Marmont, Lindsey S., Yip, Patrick, Neculai, A. Mirela, Lobsanov, Yuri D., Ohman, Dennis E., & Howell, P. Lynne. Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa. United States. https://doi.org/10.1074/jbc.M115.645051
Whitney, John C., Robinson, Howard, Whitfield, Gregory B., Marmont, Lindsey S., Yip, Patrick, Neculai, A. Mirela, Lobsanov, Yuri D., Ohman, Dennis E., and Howell, P. Lynne. Fri . "Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa". United States. https://doi.org/10.1074/jbc.M115.645051. https://www.osti.gov/servlets/purl/1237169.
@article{osti_1237169,
title = {Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa},
author = {Whitney, John C. and Robinson, Howard and Whitfield, Gregory B. and Marmont, Lindsey S. and Yip, Patrick and Neculai, A. Mirela and Lobsanov, Yuri D. and Ohman, Dennis E. and Howell, P. Lynne},
abstractNote = {Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Moreover, calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. Our results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor produced by P. aeruginosa.},
doi = {10.1074/jbc.M115.645051},
journal = {Journal of Biological Chemistry},
number = 20,
volume = 290,
place = {United States},
year = {Fri May 15 00:00:00 EDT 2015},
month = {Fri May 15 00:00:00 EDT 2015}
}

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Cited by: 60 works
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Table 1 Table 1: X-ray data collection and refinement statistics.

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Works referenced in this record:

Vibrio cholerae VpsT Regulates Matrix Production and Motility by Directly Sensing Cyclic di-GMP
journal, February 2010


The PilZ Domain Is a Receptor for the Second Messenger c-di-GMP
journal, August 2006

  • Ryjenkov, Dmitri A.; Simm, Roger; Römling, Ute
  • Journal of Biological Chemistry, Vol. 281, Issue 41
  • DOI: 10.1074/jbc.C600179200

ExsE, a secreted regulator of type III secretion genes in Pseudomonas aeruginosa
journal, May 2005

  • Rietsch, A.; Vallet-Gely, I.; Dove, S. L.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 22
  • DOI: 10.1073/pnas.0503005102

Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria
journal, February 2013


Structural polymorphism of c-di-GMP bound to an EAL domain and in complex with a type II PilZ-domain protein
journal, September 2012

  • Chin, Ko-Hsin; Kuo, Wei-Ting; Yu, Yu-Jen
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 10
  • DOI: 10.1107/S0907444912030594

The c-di-GMP recognition mechanism of the PilZ domain of bacterial cellulose synthase subunit A
journal, February 2013

  • Fujiwara, Takaaki; Komoda, Keisuke; Sakurai, Naofumi
  • Biochemical and Biophysical Research Communications, Vol. 431, Issue 4
  • DOI: 10.1016/j.bbrc.2012.12.103

A cyclic-di-GMP receptor required for bacterial exopolysaccharide production
journal, September 2007


Crystallographic snapshot of cellulose synthesis and membrane translocation
journal, December 2012

  • Morgan, Jacob L. W.; Strumillo, Joanna; Zimmer, Jochen
  • Nature, Vol. 493, Issue 7431
  • DOI: 10.1038/nature11744

Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein–protein interaction
journal, November 2012

  • Steiner, Samuel; Lori, Christian; Boehm, Alex
  • The EMBO Journal, Vol. 32, Issue 3
  • DOI: 10.1038/emboj.2012.315

Structural Analysis of the GGDEF-EAL Domain-Containing c-di-GMP Receptor FimX
journal, August 2009


FimX, a Multidomain Protein Connecting Environmental Signals to Twitching Motility in Pseudomonas aeruginosa
journal, December 2003


Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Dali server: conservation mapping in 3D
journal, May 2010

  • Holm, Liisa; Rosenstr�m, P�ivi
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq366

Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP
journal, April 2014

  • Morgan, Jacob L. W.; McNamara, Joshua T.; Zimmer, Jochen
  • Nature Structural & Molecular Biology, Vol. 21, Issue 5
  • DOI: 10.1038/nsmb.2803

The response threshold of Salmonella PilZ domain proteins is determined by their binding affinities for c-di-GMP : c-di-GMP binding affinities of PilZ domain proteins
journal, November 2012

  • Pultz, Ingrid Swanson; Christen, Matthias; Kulasekara, Hemantha Don
  • Molecular Microbiology, Vol. 86, Issue 6
  • DOI: 10.1111/mmi.12066

Solution Structure of the PilZ Domain Protein PA4608 Complex with Cyclic di-GMP Identifies Charge Clustering as Molecular Readout
journal, February 2011

  • Habazettl, Judith; Allan, Martin G.; Jenal, Urs
  • Journal of Biological Chemistry, Vol. 286, Issue 16
  • DOI: 10.1074/jbc.M110.209007

PilZ domain is part of the bacterial c-di-GMP binding protein
journal, October 2005


Phosphorylation-Independent Regulation of the Diguanylate Cyclase WspR
journal, March 2008


Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


Allosteric Control of Cyclic di-GMP Signaling
journal, August 2006

  • Christen, Beat; Christen, Matthias; Paul, Ralf
  • Journal of Biological Chemistry, Vol. 281, Issue 42
  • DOI: 10.1074/jbc.M603589200

The structural basis of cyclic diguanylate signal transduction by PilZ domains
journal, November 2007


Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3'-5')-cyclic-GMP in virulence
journal, February 2006

  • Kulasakara, H.; Lee, V.; Brencic, A.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 8
  • DOI: 10.1073/pnas.0511090103

Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor
journal, July 2008


Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
journal, October 2010

  • Winsor, G. L.; Lam, D. K. W.; Fleming, L.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq869

Oligomer Formation of the Bacterial Second Messenger c-di-GMP: Reaction Rates and Equilibrium Constants Indicate a Monomeric State at Physiological Concentrations
journal, December 2011

  • Gentner, Martin; Allan, Martin G.; Zaehringer, Franziska
  • Journal of the American Chemical Society, Vol. 134, Issue 2
  • DOI: 10.1021/ja207742q

The bacterial second messenger c-di-GMP: mechanisms of signalling: c-di-GMP signalling
journal, June 2011


Structural basis of activity and allosteric control of diguanylate cyclase
journal, November 2004

  • Chan, C.; Paul, R.; Samoray, D.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 49
  • DOI: 10.1073/pnas.0406134101

Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis
journal, February 2011


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients
journal, January 2007


Roles of Cyclic Diguanylate in the Regulation of Bacterial Pathogenesis
journal, October 2007


Polysaccharides serve as scaffold of biofilms formed by mucoid Pseudomonas aeruginosa
journal, July 2012


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms
journal, June 2003

  • Wozniak, D. J.; Wyckoff, T. J. O.; Starkey, M.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 13
  • DOI: 10.1073/pnas.1231792100

Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins
journal, April 2010


Type IV Pilus Assembly in Pseudomonas aeruginosa over a Broad Range of Cyclic di-GMP Concentrations
journal, June 2012

  • Jain, R.; Behrens, A. -J.; Kaever, V.
  • Journal of Bacteriology, Vol. 194, Issue 16
  • DOI: 10.1128/JB.00803-12

A new modification of the carbazole analysis: Application to heteropolysaccharides
journal, September 1968


Membrane topology and roles of Pseudomonas aeruginosa Alg8 and Alg44 in alginate polymerization
journal, June 2008


Structure of E. coli 5′-methylthioadenosine/S-adenosylhomocysteine Nucleosidase Reveals Similarity to the Purine Nucleoside Phosphorylases
journal, October 2001


c-di-GMP-binding protein, a new factor regulating cellulose synthesis in Acetobacter xylinum
journal, October 1997


PilZ Domain Proteins Bind Cyclic Diguanylate and Regulate Diverse Processes in Vibrio cholerae
journal, February 2007

  • Pratt, Jason T.; Tamayo, Rita; Tischler, Anna D.
  • Journal of Biological Chemistry, Vol. 282, Issue 17
  • DOI: 10.1074/jbc.M611593200

Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl
journal, January 2011

  • Franklin, Michael J.; Nivens, David E.; Weadge, Joel T.
  • Frontiers in Microbiology, Vol. 2
  • DOI: 10.3389/fmicb.2011.00167

Allosteric Control of Cyclic di-GMP Signaling
journal, October 2006


Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen
journal, August 2020

  • Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6
  • DOI: 10.1007/s00775-020-01814-y

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021


Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.
journalarticle, January 2008

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • International Union of Crystallography (IUCr)
  • DOI: 10.17863/cam.52329

Structural basis of activity and allosteric control of diguanylate cyclase
text, January 2004


PilZ domain proteins bind cyclic diguanylate and regulate diverse processes in Vibrio cholerae
text, January 2007

  • A. D., Tischler,; R., Tamayo,; A., Camilli,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/d8zs-5j32

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Works referencing / citing this record:

Recent advances in understanding Pseudomonas aeruginosa as a pathogen
journal, January 2017


Oxygen-dependent regulation of c-di-GMP synthesis by SadC controls alginate production in P seudomonas aeruginosa: SadC regulates alginate production
journal, February 2016

  • Schmidt, Annika; Hammerbacher, Anna Silke; Bastian, Mike
  • Environmental Microbiology, Vol. 18, Issue 10
  • DOI: 10.1111/1462-2920.13208

Tlr1612 is the major repressor of cell aggregation in the light-color-dependent c-di-GMP signaling network of Thermosynechococcus vulcanus
journal, March 2018


AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production
journal, May 2017

  • Schäper, Simon; Steinchen, Wieland; Krol, Elizaveta
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 24
  • DOI: 10.1073/pnas.1702435114

Biological function of a polysaccharide degrading enzyme in the periplasm
journal, November 2016

  • Wang, Yajie; Moradali, M. Fata; Goudarztalejerdi, Ali
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep31249

Structures of the activator of K. pneumonia biofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding
journal, August 2016

  • Schumacher, Maria A.; Zeng, Wenjie
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 36
  • DOI: 10.1073/pnas.1607503113

Novel dual regulators of Pseudomonas aeruginosa essential for productive biofilms and virulence
journal, July 2018

  • Heacock-Kang, Yun; Zarzycki-Siek, Jan; Sun, Zhenxin
  • Molecular Microbiology, Vol. 109, Issue 3
  • DOI: 10.1111/mmi.14063

Activation Mechanism and Cellular Localization of Membrane-Anchored Alginate Polymerase in Pseudomonas aeruginosa
journal, March 2017

  • Moradali, M. Fata; Ghods, Shirin; Rehm, Bernd H. A.
  • Applied and Environmental Microbiology, Vol. 83, Issue 9
  • DOI: 10.1128/aem.03499-16

Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein
journal, November 2017

  • Yan, Xin-Fu; Xin, Lingyi; Yen, Jackie Tan
  • Journal of Biological Chemistry, Vol. 293, Issue 1
  • DOI: 10.1074/jbc.m117.815704

The Role of Alginate in Bacterial Biofilm Formation
book, January 2019


Orchestrated delivery of Legionella effectors by the Icm/Dot secretion system
posted_content, January 2019

  • Allombert, Julie; Jaboulay, Corentin; Michard, Céline
  • BioRxiv
  • DOI: 10.1101/754762

Structural conservation and diversity of PilZ-related domains
posted_content, October 2019

  • Galperin, Michael Y.; Chou, Shan-Ho
  • Journal of Bacteriology
  • DOI: 10.1101/814665

Cyclic dinucleotide (c-di-GMP, c-di-AMP, and cGAMP) signalings have come of age to be inhibited by small molecules
journal, January 2016

  • Opoku-Temeng, Clement; Zhou, Jie; Zheng, Yue
  • Chemical Communications, Vol. 52, Issue 60
  • DOI: 10.1039/c6cc03439j

Molecular aspects of bacterial nanocellulose biosynthesis
journal, March 2019

  • Jacek, Paulina; Dourado, Fernando; Gama, Miguel
  • Microbial Biotechnology, Vol. 12, Issue 4
  • DOI: 10.1111/1751-7915.13386

Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library
journal, January 2017


CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens
journal, November 2019

  • Noirot-Gros, Marie-Francoise; Forrester, Sara; Malato, Grace
  • Scientific Reports, Vol. 9, Issue 1
  • DOI: 10.1038/s41598-019-52400-5

The PilZ domain of MrkH represents a novel DNA binding motif
journal, September 2016


Analysis of the alginate O-acetylation machinery in Pseudomonas aeruginosa
journal, January 2020

  • Chanasit, Wankuson; Gonzaga, Zennia Jean C.; Rehm, Bernd H. A.
  • Applied Microbiology and Biotechnology, Vol. 104, Issue 5
  • DOI: 10.1007/s00253-019-10310-6

Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae
journal, June 2018

  • Severin, Geoffrey B.; Ramliden, Miriam S.; Hawver, Lisa A.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 26
  • DOI: 10.1073/pnas.1801233115

MotI (DgrA) acts as a molecular clutch on the flagellar stator protein MotA in Bacillus subtilis
journal, December 2017

  • Subramanian, Sundharraman; Gao, Xiaohui; Dann, Charles E.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 51
  • DOI: 10.1073/pnas.1716231114

Emerging paradigms for PilZ domain-mediated C-di-GMP signaling
journal, February 2019

  • Cheang, Qing Wei; Xin, Lingyi; Chea, Rachel Yuen Fong
  • Biochemical Society Transactions, Vol. 47, Issue 1
  • DOI: 10.1042/bst20180543

A Cyclic di-GMP-binding Adaptor Protein Interacts with Histidine Kinase to Regulate Two-component Signaling
journal, July 2016

  • Xu, Linghui; Venkataramani, Prabhadevi; Ding, Yichen
  • Journal of Biological Chemistry, Vol. 291, Issue 31
  • DOI: 10.1074/jbc.m116.730887

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms
journal, June 2015

  • Chou, Shan-Ho; Galperin, Michael Y.
  • Journal of Bacteriology, Vol. 198, Issue 1
  • DOI: 10.1128/jb.00333-15

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