The Escherichia coli RNA processing and degradation machinery is compartmentalized within an organized cellular network

2014 ◽  
Vol 458 (1) ◽  
pp. 11-22 ◽  
Author(s):  
Aziz Taghbalout ◽  
Qingfen Yang ◽  
Véronique Arluison
Keyword(s):  
Escherichia Coli ◽  
Rna Processing ◽  
Cellular Network ◽  
High Order ◽  
Cellular Structures ◽  
General Mechanism ◽  
Protein Networks ◽  
Macromolecular Assembly ◽  
Bacterial Rna

We have shown that the multiprotein network of the bacterial RNA processing and degradation is organized within high-order cellular structures. Macromolecular assembly of protein networks could provide a general mechanism to streamline specific pathways within the seemingly non-compartmentalized prokaryotic cytoplasm.

scholarly journals The extent of B-form structure in a 6S RNA variant that mimics DNA to bind to the Escherichia coli RNA Polymerase

2018 ◽  
Author(s):  
Nilesh K. Banavali
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Structural Analysis ◽  
Rna Polymerase ◽  
Rna Structure ◽  
Recent Article ◽  
Single Strand ◽  
Bacterial Rna ◽  
6S Rna

AbstractIn a recent article by Darst and coworkers, it was found that a non-coding 6S RNA variant regulates a bacterial RNA polymerase by mimicking B-Form DNA, and a few different nucleic acid duplex parameters were analyzed to understand the extent of B-form RNA structure. In this manuscript, a different structural analysis based on conformational distance from canonical A-form and B-form single-strand structures is presented. This analysis addresses the occurrence and extent of both local and global B-form structure in the published 6S RNA variant model.

Specificity in RNA Processing Reactions in Escherichia Coli

1988 ◽  
pp. 91-103 ◽  
Author(s):  
David Apirion ◽  
Geza Dallmann ◽  
Michael Gurevitz ◽  
Andras Miczak ◽  
Jozeff Szeberenyi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Processing

scholarly journals Substitution of a Highly Conserved Histidine in the Escherichia coli Heat Shock Transcription Factor, σ32, Affects Promoter Utilization In Vitro and Leads to Overexpression of the Biofilm-Associated Flu Protein In Vivo

2007 ◽  
Vol 189 (23) ◽  
pp. 8430-8436 ◽  
Author(s):  
Olga V. Kourennaia ◽  
Pieter L. deHaseth
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Rna Polymerase ◽  
Sigma Factor ◽  
Stable Complex ◽  
Tryptophan Residue ◽  
Specific Sequence ◽  
Bacterial Rna

ABSTRACT The heat shock sigma factor (σ32 in Escherichia coli) directs the bacterial RNA polymerase to promoters of a specific sequence to form a stable complex, competent to initiate transcription of genes whose products mitigate the effects of exposure of the cell to high temperatures. The histidine at position 107 of σ32 is at the homologous position of a tryptophan residue at position 433 of the main sigma factor of E. coli, σ70. This tryptophan is essential for the strand separation step leading to the formation of the initiation-competent RNA polymerase-promoter complex. The heat shock sigma factors of all gammaproteobacteria sequenced have a histidine at this position, while in the alpha- and deltaproteobacteria, it is a tryptophan. In vitro the alanine-for-histidine substitution at position 107 (H107A) destabilizes complexes between the GroE promoter and RNA polymerase containing σ32, implying that H107 plays a role in formation or maintenance of the strand-separated complex. In vivo, the H107A substitution in σ32 impedes recovery from heat shock (exposure to 42°C), and it also leads to overexpression at lower temperatures (30°C) of the Flu protein, which is associated with biofilm formation.

The X-ray Structure of Escherichia coli RraA (MenG), A Protein Inhibitor of RNA Processing

2003 ◽  
Vol 332 (5) ◽  
pp. 1015-1024 ◽  
Author(s):  
Arthur F. Monzingo ◽  
Junjun Gao ◽  
Ji Qiu ◽  
George Georgiou ◽  
Jon D. Robertus
Keyword(s):  
Escherichia Coli ◽  
Rna Processing ◽  
Protein Inhibitor ◽  
X Ray

scholarly journals The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome

2014 ◽  
Vol 34 (6) ◽  
Author(s):  
Feng Lu ◽  
Aziz Taghbalout
Keyword(s):  
Escherichia Coli ◽  
Rna Processing ◽  
Binding Sites ◽  
Rna Degradation ◽  
The Other ◽  
Polynucleotide Phosphorylase ◽  
Cell Extracts ◽  
Domains Of Life ◽  
Rna Degradosome ◽  
Rnase Ii

Multiprotein complexes that carry out RNA degradation and processing functions are found in cells from all domains of life. In Escherichia coli, the RNA degradosome, a four-protein complex, is required for normal RNA degradation and processing. In addition to the degradosome complex, the cell contains other ribonucleases that also play important roles in RNA processing and/or degradation. Whether the other ribonucleases are associated with the degradosome or function independently is not known. In the present work, IP (immunoprecipitation) studies from cell extracts showed that the major hydrolytic exoribonuclease RNase II is associated with the known degradosome components RNaseE (endoribonuclease E), RhlB (RNA helicase B), PNPase (polynucleotide phosphorylase) and Eno (enolase). Further evidence for the RNase II-degradosome association came from the binding of RNase II to purified RNaseE in far western affinity blot experiments. Formation of the RNase II–degradosome complex required the degradosomal proteins RhlB and PNPase as well as a C-terminal domain of RNaseE that contains binding sites for the other degradosomal proteins. This shows that the RNase II is a component of the RNA degradosome complex, a previously unrecognized association that is likely to play a role in coupling and coordinating the multiple elements of the RNA degradation pathways.

scholarly journals Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq

2021 ◽  
Author(s):  
Kumari Kavita ◽  
Aixia Zhang ◽  
Chin-Hsien Tai ◽  
Nadim Majdalani ◽  
Gisela Storz ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Binding ◽  
Class Ii ◽  
Rna Chaperone ◽  
Terminal Domain ◽  
C Terminus ◽  
Bacterial Rna ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD deletion in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.

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