A systems analysis of the AHL Quorum Sensing system in Pseudomonas aeruginosa

Sets of rules with input vectorsModules Quorum sensing is a cell density dependent gene regulation system whereby populations of bacteria communicate through small diffusible signalling molecules in order to coordinate the expression of specific genes such as virulence factors depending on the their numbers, exhibiting population-level behaviour.1 InfobioticsInfobiotics Francisco J. Romero-Campero1, Jonathan Blakes1, Miguel Cámara2, Natalio Krasnogor1 1ASAP Research Group, School of Computer Science and IT, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK. {fxc, jvb,nxk}@cs.nott.ac.uk 2The Pseudomonas Quorum Sensing Group, Institute of Infection, Immunity and Inflammation & School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham. [email protected] A systems analysis of the AHL Quorum Sensing system in Pseudomonas aeruginosa Funded by EPSRC & BBSRC grants EP/E017215/1& BB/F01855X/1 a → b [ ]label a2b3c Multisets of objectsPopulation of molecules MembranesCompartments Rewriting rules on objects Molecular interactions P system specification Biological entity c high cell densitylow cell density division & quoration ais transformed into bwith rate c Name({molecules,...}{constants,...}{labels}) Quorum sensing relies on the synthesis, accumulation and subsequent sensing of these signals, particularly N-acylhomoserine lactones (AHLs) in P. aeruginosa: Composing a quorum sensing module In our methodology a module is a set of rules that define a integrated biological function, such as unregulated gene expression consisting of production and degradation of the LasR protein from gene lasR: Modules can be assembled into larger modules. Here a LasI UnReg module, enzymatic 3OC12 synthesis and diffusion, complexation and positive gene regulation modules are composed into the quorum sensing module QS({LasR,...,RsaL·lasI},{c1,...,c24},{b}) = signalling molecule bacteria In most QS systems the signals, S, are synthesised by an Ienzyme encoded by a geneI. A receptor protein Rencoded by a geneR interacts with Sto form an active transcription factor R·Swhich binds to geneI amplifying the production of Iprotein and therefore synthesis of S. This transcription factor also regulates many other genes. N H O O N-butyryl homoserine lactone (C4) N H OO O N-3-oxo-dodecanoyl homoserine lactone (3OC12) O O • Virulence • Secondary Metabolites • Motility and Swarming • Conjugation • Biofilm Development • Growth Inhibition r i + R S In P. aeruginosa LasR stimulates LasI, and RsaL which supresses LasI. This ensures the rapid but controlled production of AHL- synthesis required to coordinate a population phenotype. References 1. Bernardini F, Gheorghe M, Krasnogor N. Quorum sensing P systems. Theor. Comput. Sci. 371(1-2): 20-33 (2007) 2. Romero Campero FJ. & Pérez Jiménez MJ. Modelling gene expression control using P systems: The Lac Operon, a case study 3. Alon U. Network motifs: theory and experimental approaches. Nature Reviews Genetics 8 (2007) BioSystems 91 (2008) When coupled to a negative gene regulation module through lasI a 3OC12 controlled type 1 incoherent feed-forward loop3emerges. Modelling quorum sensing therefore requires a colony-level view with many individual copies of the same quorum sensing gene network in different states. Ordinary differential equations are problematic for modelling gene networks, as low numbers of molecules decrease the signal to noise ratio due to the finite number effect (η~ 1/√N). P systems represent a novel discrete, stochastic and mesoscopic framework for modelling cellular systems2that facilitates the assembly of transcriptional modules, mass duplication of cells and realistic kinetics using the well-studied Gillespie algorithm, for the observation of emergent behaviours through simulation. A P system consists of a nested membrane structure (colonies, cells or intracellular compartments), containing multisets of objects (genes, complexes, metabolites) which are rewritten by rules (reactions). LasR RsaL LasI + − +speed up by LasR·3OC12 homeostasis by RsaL type 1 IFFL • Growth Inhibition IR R S+ s’ S