RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs.

Ribonuclease E (RNase E) of Escherichia coli, which is the founding member of a widespread family of proteins in bacteria and chloroplasts, is a fascinating enzyme that still has not revealed all its secrets. RNase E is an essential single-strand specific endoribonuclease that is involved in the processing and degradation of nearly every transcript in E. coli.

Single-molecule FRET characterization of RNA remodeling induced by an antitermination protein.

Single-molecule Förster Resonance Energy Transfer (smFRET) is a useful technique to probe conformational changes within bio-macromolecules. Here, we introduce how to perform smFRET measurements in solution to investigate RNA remodeling and RNA-protein interactions. In particular, we focus on how the close-to-open transition of an antiterminator hairpin is influenced by the binding of the antitermination protein and the competition by oligonucleotides.

RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains.

RNase E of Escherichia coli is a membrane-associated endoribonuclease that has a major role in mRNA degradation. The enzyme has a large C-terminal noncatalytic region that is mostly intrinsically disordered (ID). Under standard growth conditions, RhlB, enolase and PNPase associate with the noncatalytic region to form the multienzyme RNA degradosome.

Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria.

The degradosome is a multienzyme complex involved in mRNA degradation in Escherichia coli. The essential endoribonuclease RNase E contains a large noncatalytic region necessary for protein-protein interactions with other components of the RNA degradosome. Interacting proteins include the DEAD-box RNA helicase RhlB, the glycolytic enzyme enolase, and the exoribonuclease PNPase.

Co-immunopurification of multiprotein complexes containing RNA-degrading enzymes.

Co-immunopurification is a classical technique in which antiserum raised against a specific protein is used to purify a multiprotein complex. We describe work from our laboratory in which co-immunopurification was used to characterize the RNA degradosome of Escherichia coli, a multiprotein complex involved in RNA processing and mRNA degradation. Polyclonal rabbit antibodies raised against either RNase E or PNPase, two RNA degrading enzymes in the RNA degradosome, were used in co-immunopurification experiments aimed at studying the assembly of the RNA degradosome and mapping protein-protein interactions within the complex.