Rule–based regulatory and metabolic model for Quorum sensing in P. aeruginosa

BackgroundIn the pathogen P. aeruginosa, the formation of virulence factors is regulated via Quorum sensing signaling pathways. Due to the increasing number of strains that are resistant to antibiotics, there is a high interest to develop novel antiinfectives. In the combat of resistant bacteria, selective blockade of the bacterial cell–to–cell communication (Quorum sensing) has gained special interest as anti–virulence strategy. Here, we modeled the las, rhl, and pqs Quorum sensing systems by a multi–level logical approach to analyze how enzyme inhibitors and receptor antagonists effect the formation of autoinducers and virulence factors.ResultsOur rule–based simulations fulfill the behavior expected from literature considering the external level of autoinducers. In the presence of PqsBCD inhibitors, the external HHQ and PQS levels are indeed clearly reduced. The magnitude of this effect strongly depends on the inhibition level. However, it seems that the pyocyanin pathway is incomplete.ConclusionsTo match experimental observations we suggest a modified network topology in which PqsE and PqsR acts as receptors and an autoinducer as ligand that up–regulate pyocyanin in a concerted manner. While the PQS biosynthesis is more appropriate as target to inhibit the HHQ and PQS formation, blocking the receptor PqsR that regulates the biosynthesis reduces the pyocyanin level stronger.

[1]  L. Rahme,et al.  Mutation analysis of the Pseudomonas aeruginosa mvfR and pqsABCDE gene promoters demonstrates complex quorum-sensing circuitry. , 2006, Microbiology.

[2]  D. Chopp,et al.  A mathematical model of quorum sensing in a growing bacterial biofilm , 2002, Journal of Industrial Microbiology and Biotechnology.

[3]  Michael Lees,et al.  Inhibition of quorum sensing in a computational biofilm simulation , 2012, Biosyst..

[4]  S. Kjelleberg,et al.  Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors , 2003, The EMBO journal.

[5]  J. Reiser,et al.  Autoinducer-mediated regulation of rhamnolipid biosurfactant synthesis in Pseudomonas aeruginosa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[6]  P. Seed,et al.  RsaL, a Novel Repressor of Virulence Gene Expression in Pseudomonas aeruginosa , 1999, Journal of bacteriology.

[7]  P. Seed,et al.  Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa , 1997, Journal of bacteriology.

[8]  R. Tompkins,et al.  Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[9]  C. Reimmann,et al.  The global activator GacA of Pseudomonas aeruginosa PAO positively controls the production of the autoinducer N‐butyryl‐homoserine lactone and the formation of the virulence factors pyocyanin, cyanide, and lipase , 1997, Molecular microbiology.

[10]  Michael P. Storz,et al.  Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors. , 2012, Journal of the American Chemical Society.

[11]  R. Hartmann,et al.  Discovery of antagonists of PqsR, a key player in 2-alkyl-4-quinolone-dependent quorum sensing in Pseudomonas aeruginosa. , 2012, Chemistry & biology.

[12]  R. Maier,et al.  Pseudomonas aeruginosa rhamnolipids: biosynthesis and potential applications , 2000, Applied Microbiology and Biotechnology.

[13]  R. Hartmann,et al.  Biosynthesis of 2‐Alkyl‐4(1H)‐Quinolones in Pseudomonas aeruginosa: Potential for Therapeutic Interference with Pathogenicity , 2011, Chembiochem : a European journal of chemical biology.

[14]  D. Thieffry,et al.  Modular logical modelling of the budding yeast cell cycle. , 2009, Molecular bioSystems.

[15]  J. King,et al.  Mathematical modelling of therapies targeted at bacterial quorum sensing. , 2004, Mathematical biosciences.

[16]  W. Blankenfeldt,et al.  Structure elucidation and preliminary assessment of hydrolase activity of PqsE, the Pseudomonas quinolone signal (PQS) response protein. , 2009, Biochemistry.

[17]  E. Greenberg,et al.  A second N-acylhomoserine lactone signal produced by Pseudomonas aeruginosa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Diggle,et al.  Cooperation and cheating in Pseudomonas aeruginosa: the roles of the las, rhl and pqs quorum-sensing systems , 2011, The ISME Journal.

[19]  J. Keener,et al.  A mathematical model for quorum sensing in Pseudomonas aeruginosa , 2001, Bulletin of mathematical biology.

[20]  S. Miller,et al.  The Multifaceted Proteins MvaT and MvaU, Members of the H-NS Family, Control Arginine Metabolism, Pyocyanin Synthesis, and Prophage Activation in Pseudomonas aeruginosa PAO1 , 2009, Journal of bacteriology.

[21]  B. Iglewski,et al.  Bacterial Quorum Sensing in Pathogenic Relationships , 2000, Infection and Immunity.

[22]  K. Juárez,et al.  The Pseudomonas aeruginosa rhlAB Operon Is Not Expressed during the Logarithmic Phase of Growth Even in the Presence of Its Activator RhlR and the Autoinducer N-Butyryl-Homoserine Lactone , 2003, Journal of bacteriology.

[23]  S. E. West,et al.  Vfr controls quorum sensing in Pseudomonas aeruginosa , 1997, Journal of bacteriology.

[24]  S. Diggle,et al.  Quinolones: from Antibiotics to Autoinducers , 2022 .

[25]  Chuan He,et al.  The Pseudomonas aeruginosa Global Regulator VqsR Directly Inhibits QscR To Control Quorum-Sensing and Virulence Gene Expression , 2012, Journal of bacteriology.

[26]  R. Hartmann,et al.  Identification of small-molecule antagonists of the Pseudomonas aeruginosa transcriptional regulator PqsR: biophysically guided hit discovery and optimization. , 2012, ACS chemical biology.

[27]  L. Rahme,et al.  A Quorum Sensing Regulated Small Volatile Molecule Reduces Acute Virulence and Promotes Chronic Infection Phenotypes , 2011, PLoS pathogens.

[28]  D. Thieffry,et al.  A logical analysis of the Drosophila gap-gene system. , 2001, Journal of theoretical biology.

[29]  K. M. Lee,et al.  QscR, a modulator of quorum-sensing signal synthesis and virulence in Pseudomonas aeruginosa , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Ilya Shmulevich,et al.  Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks , 2006, Signal Process..

[31]  Andre Levchenko,et al.  A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies , 2010, PLoS Comput. Biol..

[32]  Richard Banks,et al.  Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets , 2006, CMSB.

[33]  T. B. Rasmussen,et al.  Quorum-sensing inhibitors as anti-pathogenic drugs. , 2006, International journal of medical microbiology : IJMM.

[34]  M. Gambello,et al.  Expression of Pseudomonas aeruginosa virulence genes requires cell-to-cell communication. , 1993, Science.

[35]  P. Seed,et al.  Activation of the Pseudomonas aeruginosa lasI gene by LasR and the Pseudomonas autoinducer PAI: an autoinduction regulatory hierarchy , 1995, Journal of bacteriology.

[36]  E. Pesci,et al.  PqsE Functions Independently of PqsR-Pseudomonas Quinolone Signal and Enhances the rhl Quorum-Sensing System , 2008, Journal of bacteriology.

[37]  M. Gambello,et al.  Cloning and characterization of the Pseudomonas aeruginosa lasR gene, a transcriptional activator of elastase expression , 1991, Journal of bacteriology.

[38]  Marina S. Kuznetsova,et al.  Functions Required for Extracellular Quinolone Signaling by Pseudomonas aeruginosa , 2002, Journal of bacteriology.

[39]  P. Williams,et al.  Transcriptomic analysis reveals a global alkyl-quinolone-independent regulatory role for PqsE in facilitating the environmental adaptation of Pseudomonas aeruginosa to plant and animal hosts , 2010, Environmental microbiology.

[40]  Luis Mendoza,et al.  A Boolean network model of the FA/BRCA pathway , 2012, Bioinform..

[41]  F. Fogelman-Soulié,et al.  Random Boolean Networks , 1981 .

[42]  Marian Gheorghe,et al.  Quorum sensing P systems , 2007, Theor. Comput. Sci..

[43]  E. Greenberg,et al.  Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[44]  L. Thomashow,et al.  Functional Analysis of Genes for Biosynthesis of Pyocyanin and Phenazine-1-Carboxamide from Pseudomonas aeruginosa PAO1 , 2001, Journal of bacteriology.

[45]  B. Finlay,et al.  Quorum sensing in bacterial virulence. , 2010, Microbiology.

[46]  J. Reiser,et al.  Isolation, characterization, and expression in Escherichia coli of the Pseudomonas aeruginosa rhlAB genes encoding a rhamnosyltransferase involved in rhamnolipid biosurfactant synthesis. , 1994, The Journal of biological chemistry.