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New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex

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dc.contributor.author Doniselli, Nicola
dc.contributor.author Rodriguez-Aliaga, Piere
dc.contributor.author Amidani, Davide
dc.contributor.author Bardales, Jorge A.
dc.contributor.author Bustamante, Carlos
dc.contributor.author Guerra Giraldez, Daniel
dc.contributor.author Rivetti, Claudio
dc.date.accessioned 2019-02-06T14:53:08Z
dc.date.available 2019-02-06T14:53:08Z
dc.date.issued 2015
dc.identifier.uri https://hdl.handle.net/20.500.12866/5374
dc.description.abstract The stringent response modulators, guanosine tetraphosphate (ppGpp) and protein DksA, bind RNA polymerase (RNAP) and regulate gene expression to adapt bacteria to different environmental conditions. Here, we use Atomic Force Microscopy and in vitro transcription assays to study the effects of these modulators on the conformation and stability of the open promoter complex (RPo) formed at the rrnA P1, rrnB P1, its discriminator (dis) variant and lambda pR promoters. In the absence of modulators, RPo formed at these promoters show different extents of DNA wrapping which correlate with the position of UP elements. Addition of the modulators affects both DNA wrapping and RPo stability in a promoter-dependent manner. Overall, the results obtained under different conditions of ppGpp, DksA and initiating nucleotides (iNTPs) indicate that ppGpp allosterically prevents the conformational changes associated with an extended DNA wrapping that leads to RPo stabilization, while DksA interferes directly with nucleotide positioning into the RNAP active site. At the iNTPs-sensitive rRNA promoters ppGpp and DksA display an independent inhibitory effect, while at the iNTPs-insensitive pR promoter DksA reduces the effect of ppGpp in accordance with their antagonistic role. en_US
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartofseries Nucleic Acids Research
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Gene Expression Regulation, Bacterial en_US
dc.subject Promoter Regions, Genetic en_US
dc.subject Transcription Initiation, Genetic en_US
dc.subject Bacteriophage lambda/genetics en_US
dc.subject DNA-Directed RNA Polymerases/metabolism en_US
dc.subject DNA, Bacterial/chemistry/ultrastructure en_US
dc.subject Escherichia coli Proteins/metabolism en_US
dc.subject Escherichia coli/enzymology/genetics en_US
dc.subject Genes, rRNA en_US
dc.subject Guanosine Tetraphosphate/metabolism en_US
dc.subject Ribonucleotides/metabolism en_US
dc.subject Transcription, Genetic en_US
dc.title New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1093/nar/gkv391
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.07
dc.relation.issn 1362-4962


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