BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405_url.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=curation_image.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405.odehttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000405?filename=BIOMD0000000405.pngprimaryOK200William MatherManually curatedordinary differential equation modelL2V4https://www.ebi.ac.uk/biomodels/BIOMD000000040522186735falseBioModelsSBMLModelsCookson2011 EnzymaticQueueingCoupling2011MODEL1111150000Natalie A Cookson, William H Mather, Tal Danino, Octavio Mondragón-Palomino, Ruth J Williams, Lev S Tsimring, Jeff HastyNatalie A Cookson22186735, High-throughput technologies have led to the generation of complex wiring diagrams as a post-sequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how 'waiting lines' can lead to correlations between protein 'customers' that are coupled solely through a downstream set of enzymatic 'servers'. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links.. null, 7. Molecular Biology Section, Division of Biological Science, University of California, San Diego, CA, USA.wmather@ucsd.eduHasty Lab, UCSD BiologyBIOMD0000000405High-throughput technologies have led to the generation of complex wiring diagrams as a post-sequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how 'waiting lines' can lead to correlations between protein 'customers' that are coupled solely through a downstream set of enzymatic 'servers'. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links.Queueing up for enzymatic processing: correlated signaling through coupled degradation.Cookson Natalie A NA, Mather William H WH, Danino Tal T, Mondragón-Palomino Octavio O, Williams Ruth J RJ, Tsimring Lev S LS, Hasty Jeff Jbiochemical pathways, scale tissue, IPP2A2, Understanding., artificial sequence, single-organism developmental process, acetylglucosaminyltransferase-like protein, Processes, peltate hair, postnatal development, Mbp1, Gene, growth and development, protein, protein-containing complex, LARGE1, cellular catabolism, froggy, PHAPII, Gyltl1a, protrusion, 5730420M11Rik, Readability, Gene Products, cellular degradation, Enterococcus coli, synthetic genetic interaction (sensu inequality), protein aggregate, myd, Synthetic, SET, anatomical systems, Escherichia/Shigella coli, like-acetylglucosaminyltransferase, Biology, TAF-I, breakdown of chemical, catabolism, MDDGB6, plant peltate hair, ipp2a2, Mbp-1, 2pp2a, synthetic genetic interaction defined by inequality, LARGE, CG10574, E. coli, DmelCG4299, BPFD#36, IGAAD, set, 2PP2A, DmelCG10574, taf-ibeta, dSET, dSet, biotransformation, species, Behaviors, single-organism behavior, phapii, cellular breakdown, Bacterium coli, anatomical protrusion, degradation, Process, gyltl1b-b, protein complex, Biologies, Proteins, igaad, StF-IT-1, artificial gene, synthetic DNA, results, Acceptance Processes, group, development, Acceptance Process, native protein, I-2PP2A, Bacillus coli, MDDGA6, mKIAA0609, Protein, Dm I-2, I2PP2A, synthetic, secretion, scales, KIAA0609, acetylglucosaminyltransferase-like 1A, breakdown of molecule, fg, Acceptance, gyltl1b, HLA-DR-associated protein II, scale, biodegradation, ensemble, DI-2, I-2Dm, mdc1d, postnatal growth, common, CG4299, Understanding, LARGE_HUMAN, synthetic constructs, Protein Gene Products, I-2PP1, Gene Proteins, MDC1D, dSET/TAF-Ibeta, breakdown of substance, SYNTHETIC CONSTRUCT sequences, 2610030F17Rik, TAF-IBETA, like-glycosyltransferase, enr, Bacterium coli commune, spine, Synthetic Biologies, artificial, TAF-Ibeta, AA407739, growth, i2pp2a, glycosyltransferase-like protein LARGE1biochemical pathways, scale tissue, IPP2A2, artificial sequence, single-organism developmental process, acetylglucosaminyltransferase-like protein, RIFLE, postnatal development, NetrinA, AUTSX5, Mbp1, D430049E23Rik, growth and development, protein, NOVH, CCN3, QM, 5730420M11Rik, Readability, diseases, cellular degradation, diseases and disorders, protein aggregate, myd, fs(1)M104, SET, human disease, Elkh, TALDOR, like-acetylglucosaminyltransferase, Biology, TAF-I, catabolism, plant peltate hair, EK6, Mbp-1, SAP-2, Sap-2, DmelCG4063, DmelCG4299, IBP-9, neuroendocrine tumour, IGAAD, set, Solute carrier family 6 member 2, DmelCG10574, CT27014, NET1, SLC6A5, biotransformation, multi-synapse, Homo sapiens disease, Tbl1, TBL1, netA, NOVh, single organism signaling, single-organism behavior, phapii, Elk, ELK, anatomical protrusion, Process, gyltl1b-b, Neuronally-expressed EPH-related tyrosine kinase, TALH, Biologies, StF-IT-1, multisynapse, SAP2, 9330129L11, results, Acceptance Processes, neuroendocrine neoplasm, Acceptance Process, 154176_at, Norepinephrine transporter, MDDGA6, mKIAA0609, EPH-like kinase 6, secretion, NOV, KIAA0609, PlexA1, acetylglucosaminyltransferase-like 1A, fg, Plxn1, gyltl1b, HLA-DR-associated protein II, CG4063, DI-2, I-2Dm, mdc1d, common, nov, CG4299, hEK6, LARGE_HUMAN, CMT2P, E-2f, mKIAA4053, E-2g, fs(1)Y[b], I-2PP1, MDC1D, disease, SYNTHETIC CONSTRUCT sequences, DmelCG18657, TAF-IBETA, enr, spine, C130088N23Rik, Synthetic Biologies, artificial, TAF-Ibeta, PLXN1, DXS648E, i2pp2a, multiple synapse, AW488255, other disease, Tb11, YB, Processes, peltate hair, number, Gene, Copyrights, protein-containing complex, LARGE1, cellular catabolism, froggy, PHAPII, DOI, Gyltl1a, protrusion, FBXW4, netrin, Yb, Hek6, Gene Products, disease or disorder, Cek6, synthetic genetic interaction (sensu inequality), CG2827, CG2706, ENSMUSG00000074119, doi, Synthetic, ERP, APUDoma, Erp, anatomical systems, breakdown of chemical, MDDGB6, Ebi, EBI, ipp2a2, Tyrosine-protein kinase receptor EPH-2, 2pp2a, synthetic genetic interaction defined by inequality, LARGE, IGFBP9, CG10574, non-neoplastic, BPFD#36, Kiaa4053, Abstract, 2.7.10.1, 2PP2A, taf-ibeta, L10, Etrp, dSET, dSet, disorder, NAT1, species, Behaviors, NET, Net, TAL, CT9666, cellular breakdown, C130099E04Rik, degradation, protein complex, DmelCG2827, DmelCG2706, Proteins, igaad, disorders, EPH tyrosine kinase 2, DXS648, artificial gene, medical condition, SMAP55, synthetic DNA, neuroendocrine tumor, net, tal, group, presence., development, count in organism, native protein, I-2PP2A, IGFBP-9, Protein, Dm I-2, I2PP2A, synthetic, condition, scales, Data Base, breakdown of molecule, Acceptance, TAL-H, biodegradation, scale, ensemble, postnatal growth, Understanding, synthetic constructs, CG18657, l(2)k16213, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, breakdown of substance, 2610030F17Rik, signalling process, like-glycosyltransferase, EPHT2, EG:95B7.8, 2600013D04Rik, AA407739, growth, netrin A, glycosyltransferase-like protein LARGE1biochemical pathways, cellular breakdown, breakdown of substance, signalling process, biodegradation, degradation, breakdown of molecule., breakdown of chemical, catabolism, cellular degradation, biotransformation, secretion, cellular catabolism, single organism signalingfalseCookson2011_EnzymaticQueueingCoupling This model is from the article: Queueing up for enzymatic processing: correlated signaling through coupled degradation. Natalie A Cookson, William H Mather, Tal Danino, Octavio Mondragón-Palomino, Ruth J Williams, Lev S Tsimring, & Jeff Hasty Molecular Systems Biology2011; 7:561; DOI:10.1038/msb.2011.94 Abstract: High-throughput technologies have led to the generation of complex wiring diagrams as a post-sequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how ‘waiting lines’ can lead to correlations between protein ‘customers’ that are coupled solely through a downstream set of enzymatic ‘servers’. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links. Note: Individual stochastic trajectories for a queueing system in three different conditions, 1) Underloaded, 2) Balanced and 3) Overloaded, demonstrate correlation resonance. The parameter values in this model correspond to the Balanced Condition. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team. For more information see the terms of use. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. 2024-08-212024-09-022011-11-15BIOMD000000040522186735CHEBI:36080MODEL1111150000BIOMD0000000405GO:0050790GO:0043234131567