NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE100022 Query DataSets for GSE100022
Status Public on Jun 01, 2019
Title A natively unstructured RNA/protein-recognition core in the E. coli RNA degradosome facilitates riboregulation
Platform organism Escherichia coli K-12
Sample organism Escherichia coli BL21(DE3)
Experiment type Expression profiling by array
Summary The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. The core of the assembly is provided by the endoribonuclease RNase E, one of the largest E. coli proteins. The C-terminal half of RNase E is predicted to be predominantly unstructured and is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We demonstrate that a subassembly of the degradosome - comprising a 248-residue segment of the C-terminal part of RNase E, the DEAD-box helicase RhlB, and the glycolytic enzyme enolase - serves as a flexible recognition centre that can co-recruit small regulatory RNA (sRNA) molecules and the RNA chaperone Hfq into an effector complex. The association of enolase with the degradosome impacts on carbon utilisation pathways under changing metabolic conditions, most likely by facilitating recruitment and the activity of sRNAs. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition core, facilitates pairing to cognate transcripts, and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.
 
Overall design In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5-fold change expression cut-off for ratio experiments was applied together with anti-correlation of color-swapped ratio profiles was applied, rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.
 
Contributor(s) Mollenkopf H, Papenfort K
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 14, 2017
Last update date Jul 25, 2021
Contact name Hans-Joachim Mollenkopf
E-mail(s) mollenkopf@mpiib-berlin.mpg.de
Phone +49 30 28460 482
Organization name Max-Planck-Institute for Infection Biology
Lab Microarray/Genomics Core Facility
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platforms (1)
GPL23500 MPIIB MWG-Ocimum Biosolutions E.coli K12 array
Samples (8)
GSM2668023 rne flag1 vs. pept1
GSM2668024 rne pept1 vs. flag1
GSM2668025 rne flag2 vs. pept2
Relations
BioProject PRJNA390515

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE100022_RAW.tar 18.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.