Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli

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Show simple item record Arbel Goren, Rinat Tal, Asaf Parasar, Bibudha Dym, Alvah Costantino, Nina Muñoz-García, Javier Court, Donald L. Stavans, Joel 2019-07-15T08:05:38Z 2019-07-15T08:05:38Z 2016-08-19
dc.identifier.bibliographicCitation Arbel-Goren, R., Tal, A., Parasar, B., Dym, A., Costantino, N., Muñoz-García, J., Court, D. L. y Stavans, J. (2016). Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. Nucleic Acids Research. 44(14), pp.6707-6720.
dc.identifier.issn 0305-1048
dc.description.abstract Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli. In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. We observed a monotonic increase of noise with iron stress but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo RyhB-mediated transcript degradation rates. The transcripts' threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Strikingly, the bacterial cell response exhibits Furdependent, switch-like activation instead of a graded response to iron deprivation.
dc.description.sponsorship Israel Science Foundation [514415 to J.S.]; Feinberg Foundation Visiting Faculty Program ( to J.M.-G.); MICINN (Spain) [FIS2012-32349 to J.M.-G.]; Intramural Research Program of the National Institutes of Health (to D.L.C.); National Cancer Institute (to D.L.C.); Center for Cancer Research (to D.L.C.); Siegfried and Irma Ullman Professorial Chair ( to J. S.). Funding for open access charge: Israel Science Foundation.
dc.format.extent 14
dc.language.iso eng
dc.publisher Oxford University Press on behalf of Nucleic Acids Research
dc.rights © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
dc.rights Atribución 3.0 España
dc.title Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli
dc.type article
dc.subject.eciencia Matemáticas
dc.rights.accessRights openAccess
dc.relation.projectID Gobierno de España. FIS2012-32349
dc.type.version publishedVersion
dc.identifier.publicationfirstpage 6707
dc.identifier.publicationissue 14
dc.identifier.publicationlastpage 6720
dc.identifier.publicationtitle Nucleic Acids Research
dc.identifier.publicationvolume 44
dc.identifier.uxxi AR/0000018220
dc.contributor.funder Ministerio de Economía y Competitividad (España)
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