Entrainment to periodic initiation and transition rates in a computational model for gene translation

Entrainment to periodic initiation and transition rates in a computational model for gene translation. Margaliot, M., Sontag, E., & Tuller, T. PLoS ONE, 9(5):e96039, 2014.

Paper doi abstract bibtex

A recent biological study has demonstrated that the gene expression pattern entrains to a periodically varying abundance of tRNA molecules. This motivates developing mathematical tools for analyzing entrainment of translation elongation to intra-cellular signals such as tRNAs levels and other factors affecting translation. We consider a recent deterministic mathematical model for translation called the Ribosome Flow Model (RFM). We analyze this model under the assumption that the elongation rate of the tRNA genes and/or the initiation rate are periodic functions with a common period T. We show that the protein synthesis pattern indeed converges to a unique periodic trajectory with period T. The analysis is based on introducing a novel property of dynamical systems, called contraction after a short transient (CAST), that may be of independent interest. We provide a sufficient condition for CAST and use it to prove that the RFM is CAST, and that this implies entrainment. Our results support the conjecture that periodic oscillations in tRNA levels and other factors related to the translation process can induce periodic oscillations in protein levels, and suggest a new approach for engineering genes to obtain a desired, periodic, synthesis rate.

@ARTICLE{margaliot_sontag_tuller_ribosome_flow_2013,
   AUTHOR       = {M. Margaliot and E.D. Sontag and T. Tuller},
   JOURNAL      = {PLoS ONE},
   TITLE        = {Entrainment to periodic initiation and transition rates 
      in a computational model for gene translation},
   YEAR         = {2014},
   OPTMONTH     = {},
   OPTNOTE      = {},
   NUMBER       = {5},
   PAGES        = {e96039},
   VOLUME       = {9},
   KEYWORDS     = {ribosomes, entrainment, nonlinear systems, stability, 
      contractions, contractive systems},
   URL          = {http://dx.doi.org/10.1371%2Fjournal.pone.0096039},
   PDF          = {../../FTPDIR/margaliot_sontag_tuller_translation_plosone2014_include_grant_correction.pdf},
   ABSTRACT     = {A recent biological study has demonstrated that the gene 
      expression pattern entrains to a periodically varying abundance of 
      tRNA molecules. This motivates developing mathematical tools for 
      analyzing entrainment of translation elongation to intra-cellular 
      signals such as tRNAs levels and other factors affecting translation. 
      We consider a recent deterministic mathematical model for translation 
      called the Ribosome Flow Model (RFM). We analyze this model under the 
      assumption that the elongation rate of the tRNA genes and/or the 
      initiation rate are periodic functions with a common period T. We 
      show that the protein synthesis pattern indeed converges to a unique 
      periodic trajectory with period T. The analysis is based on 
      introducing a novel property of dynamical systems, called contraction 
      after a short transient (CAST), that may be of independent interest. 
      We provide a sufficient condition for CAST and use it to prove that 
      the RFM is CAST, and that this implies entrainment. Our results 
      support the conjecture that periodic oscillations in tRNA levels and 
      other factors related to the translation process can induce periodic 
      oscillations in protein levels, and suggest a new approach for 
      engineering genes to obtain a desired, periodic, synthesis rate.},
   DOI          = {10.1371/journal.pone.0096039}
}

Downloads: 0

{"_id":"RBvhFpwCMsGKE9cfB","bibbaseid":"margaliot-sontag-tuller-entrainmenttoperiodicinitiationandtransitionratesinacomputationalmodelforgenetranslation-2014","downloads":0,"creationDate":"2018-10-18T05:07:05.918Z","title":"Entrainment to periodic initiation and transition rates in a computational model for gene translation","author_short":["Margaliot, M.","Sontag, E.","Tuller, T."],"year":2014,"bibtype":"article","biburl":"http://www.sontaglab.org/PUBDIR/Biblio/complete-bibliography.bib","bibdata":{"bibtype":"article","type":"article","author":[{"firstnames":["M."],"propositions":[],"lastnames":["Margaliot"],"suffixes":[]},{"firstnames":["E.D."],"propositions":[],"lastnames":["Sontag"],"suffixes":[]},{"firstnames":["T."],"propositions":[],"lastnames":["Tuller"],"suffixes":[]}],"journal":"PLoS ONE","title":"Entrainment to periodic initiation and transition rates in a computational model for gene translation","year":"2014","optmonth":"","optnote":"","number":"5","pages":"e96039","volume":"9","keywords":"ribosomes, entrainment, nonlinear systems, stability, contractions, contractive systems","url":"http://dx.doi.org/10.1371%2Fjournal.pone.0096039","pdf":"../../FTPDIR/margaliot_sontag_tuller_translation_plosone2014_include_grant_correction.pdf","abstract":"A recent biological study has demonstrated that the gene expression pattern entrains to a periodically varying abundance of tRNA molecules. This motivates developing mathematical tools for analyzing entrainment of translation elongation to intra-cellular signals such as tRNAs levels and other factors affecting translation. We consider a recent deterministic mathematical model for translation called the Ribosome Flow Model (RFM). We analyze this model under the assumption that the elongation rate of the tRNA genes and/or the initiation rate are periodic functions with a common period T. We show that the protein synthesis pattern indeed converges to a unique periodic trajectory with period T. The analysis is based on introducing a novel property of dynamical systems, called contraction after a short transient (CAST), that may be of independent interest. We provide a sufficient condition for CAST and use it to prove that the RFM is CAST, and that this implies entrainment. Our results support the conjecture that periodic oscillations in tRNA levels and other factors related to the translation process can induce periodic oscillations in protein levels, and suggest a new approach for engineering genes to obtain a desired, periodic, synthesis rate.","doi":"10.1371/journal.pone.0096039","bibtex":"@ARTICLE{margaliot_sontag_tuller_ribosome_flow_2013,\n AUTHOR = {M. Margaliot and E.D. Sontag and T. Tuller},\n JOURNAL = {PLoS ONE},\n TITLE = {Entrainment to periodic initiation and transition rates \n in a computational model for gene translation},\n YEAR = {2014},\n OPTMONTH = {},\n OPTNOTE = {},\n NUMBER = {5},\n PAGES = {e96039},\n VOLUME = {9},\n KEYWORDS = {ribosomes, entrainment, nonlinear systems, stability, \n contractions, contractive systems},\n URL = {http://dx.doi.org/10.1371%2Fjournal.pone.0096039},\n PDF = {../../FTPDIR/margaliot_sontag_tuller_translation_plosone2014_include_grant_correction.pdf},\n ABSTRACT = {A recent biological study has demonstrated that the gene \n expression pattern entrains to a periodically varying abundance of \n tRNA molecules. This motivates developing mathematical tools for \n analyzing entrainment of translation elongation to intra-cellular \n signals such as tRNAs levels and other factors affecting translation. \n We consider a recent deterministic mathematical model for translation \n called the Ribosome Flow Model (RFM). We analyze this model under the \n assumption that the elongation rate of the tRNA genes and/or the \n initiation rate are periodic functions with a common period T. We \n show that the protein synthesis pattern indeed converges to a unique \n periodic trajectory with period T. The analysis is based on \n introducing a novel property of dynamical systems, called contraction \n after a short transient (CAST), that may be of independent interest. \n We provide a sufficient condition for CAST and use it to prove that \n the RFM is CAST, and that this implies entrainment. Our results \n support the conjecture that periodic oscillations in tRNA levels and \n other factors related to the translation process can induce periodic \n oscillations in protein levels, and suggest a new approach for \n engineering genes to obtain a desired, periodic, synthesis rate.},\n DOI = {10.1371/journal.pone.0096039}\n}\n\n","author_short":["Margaliot, M.","Sontag, E.","Tuller, T."],"key":"margaliot_sontag_tuller_ribosome_flow_2013","id":"margaliot_sontag_tuller_ribosome_flow_2013","bibbaseid":"margaliot-sontag-tuller-entrainmenttoperiodicinitiationandtransitionratesinacomputationalmodelforgenetranslation-2014","role":"author","urls":{"Paper":"http://dx.doi.org/10.1371%2Fjournal.pone.0096039"},"keyword":["ribosomes","entrainment","nonlinear systems","stability","contractions","contractive systems"],"downloads":0,"html":""},"search_terms":["entrainment","periodic","initiation","transition","rates","computational","model","gene","translation","margaliot","sontag","tuller"],"keywords":["ribosomes","entrainment","nonlinear systems","stability","contractions","contractive systems"],"authorIDs":[],"dataSources":["DKqZbTmd7peqE4THw"]}