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Direct comparison of small RNA and transcription factor signaling
- Nucleic Acids Res
, 2012
"... Small RNAs (sRNAs) and proteins acting as tran-scription factors (TFs) are the principal components of gene networks. These two classes of signaling molecules have distinct mechanisms of action; sRNAs control mRNA translation, whereas TFs control mRNA transcription. Here, we directly compare the pro ..."
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Small RNAs (sRNAs) and proteins acting as tran-scription factors (TFs) are the principal components of gene networks. These two classes of signaling molecules have distinct mechanisms of action; sRNAs control mRNA translation, whereas TFs control mRNA transcription. Here, we directly compare the properties of sRNA and TF signaling using mathematical models and synthetic gene circuits in Escherichia coli. We show the abilities of sRNAs to act on existing target mRNAs (as opposed to TFs, which alter the production of future target mRNAs) and, without needing to be first translated, have surprisingly little impact on the dynamics. Instead, the dynamics are primarily determined by the clearance rates, steady-state concentrations and response curves of the sRNAs and TFs; these factors determine the time delay before a target gene’s expression can maximally respond to changes in sRNA and TF transcription. The findings are broadly applicable to the analysis of signaling in gene networks, and we demonstrate that they can be used to rationally reprogram the dynamics of synthetic circuits.
doi:10.5402/2012/697308 Research Article Antagonistic Roles for GcvA and GcvB in hdeAB Expression in Escherichia coli
"... Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In E. coli, the periplasmic proteins HdeA andHdeB have chaperone-like functions, suppressing aggregation of periplasmic proteins under acidic conditions. A ..."
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Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In E. coli, the periplasmic proteins HdeA andHdeB have chaperone-like functions, suppressing aggregation of periplasmic proteins under acidic conditions. Amicroarray analysis of RNA isolated from an E. coliwild type and aΔgcvB strain grown tomid-log phase in Luria-Bertani broth indicated the hdeAB operon, encoding the HdeA and HdeB proteins, is regulated by the sRNA GcvB. We wanted to verify that GcvB and its coregulator Hfq play a role in regulation of the hdeAB operon. In this study, we show that GcvB positively regulates hdeA::lacZ and hdeB::lacZ translational fusions in cells grown in Luria-Bertani broth and in glucose minimal media + glycine. Activation also requires the Hfq protein. Although many sRNAs dependent on Hfq regulate by an antisense mechanism, GcvB regulates hdeAB either directly or indirectly at the level of transcription. GcvA, the activator of gcvB, negatively regulates hdeAB at the level of transcription. Although expression of gcvB is dependent on GcvA, activation of hdeAB by GcvB occurs independently of GcvA’s ability to repress the operon. Cell survival and growth at low pH are consistent with GcvA negatively regulating and GcvB positively regulating the hdeAB operon. 1.
Ecole doctorale des Sciences de la Vie et de la Santé Option: Microbiologie
"... Repoila, qui ont accepté de corriger mon travail de thèse. ..."
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gu ich
"... vad c alt li ar e ac dec Hha and CspD are necessary for persister cell formation via MqsR overexpression. Surprisingly, Hfq, a of bac etic cha ionary includ ..."
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vad c alt li ar e ac dec Hha and CspD are necessary for persister cell formation via MqsR overexpression. Surprisingly, Hfq, a of bac etic cha ionary includ
doi:10.5402/2012/636273 Research Article The Escherichia coli GcvB sRNA Uses Genetic Redundancy to Control cycA Expression
, 2012
"... Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Escherichia coli sRNA GcvB regulates several genes involved in transport of amino acids and peptides (sstT, oppA, dppA, and cycA). Two regions of GcvB ..."
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Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Escherichia coli sRNA GcvB regulates several genes involved in transport of amino acids and peptides (sstT, oppA, dppA, and cycA). Two regions of GcvB from nt +124 to +161 and from nt +73 to +82 are complementary with essentially the same region of the cycA mRNA. Transcriptional fusions of cycA to lacZ showed the region of cycA mRNA that can pair with either region of GcvB is necessary for regulation by GcvB. However, mutations in either region of gcvB predicted to disrupt pairing between cycA mRNA and GcvB did not alter expression of a cycA-lacZ translational fusion. A genetic analysis identified nts in GcvB necessary for regulation of the cycA-lacZ fusion. The results show that either region of GcvB complementary to cycA mRNA can basepair with and independently repress cycA-lacZ and both regions need to be changed to cause a significant loss of repression. 1.
