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A FRET-based, continuous assay for the helicase activity of DEAD-box proteins.
Methods Mol Biol
September 2015
Institut de Biologie Physico-chimique, CNRS FRE3630, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, Paris, 75005, France,
Enzymes from cold-adapted organisms are generally endowed with lower activation enthalpies than their counterparts from organisms growing at higher temperatures, making them better catalysts in the cold. However, the enzymes of RNA metabolism have not been examined in this respect. A challenge for studying cold adaptation of DEAD-box RNA helicases is the low precision of the classical, discontinuous helicase assay based on electrophoretic separation of duplexes and isolated strands.
View Article and Find Full Text PDFFunctions of DEAD-box proteins in bacteria: current knowledge and pending questions.
Biochim Biophys Acta
August 2013
Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France.
DEAD-box proteins are RNA-dependent ATPases that are widespread in all three kingdoms of life. They are thought to rearrange the structures of RNA or ribonucleoprotein complexes but their exact mechanism of action is rarely known. Whereas in yeast most DEAD-box proteins are essential, no example of an essential bacterial DEAD-box protein has been reported so far; at most, their absence results in cold-sensitive growth.
View Article and Find Full Text PDFProbing ribosomal protein-RNA interactions with an external force.
Proc Natl Acad Sci U S A
November 2011
Laboratoire Nanobiophysique, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Unité Mixte de Recherche 7083 du Centre National de la Recherche Scientifique, 10 rue Vauquelin, 75005 Paris, France.
Ribosomal (r-) RNA adopts a well-defined structure within the ribosome, but the role of r-proteins in stabilizing this structure is poorly understood. To address this issue, we use optical tweezers to unfold RNA fragments in the presence or absence of r-proteins. Here, we focus on Escherichia coli r-protein L20, whose globular C-terminal domain (L20C) recognizes an irregular stem in domain II of 23S rRNA.
View Article and Find Full Text PDFIdentification of the sites of action of SrmB, a DEAD-box RNA helicase involved in Escherichia coli ribosome assembly.
Mol Microbiol
October 2011
Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197, Génomique Fonctionnelle, 46 Rue d'Ulm 75230 Paris Cedex 05, France.
Article Synopsis
- DEAD-box RNA-dependent ATPases, like SrmB in E. coli, are crucial for RNA processes, but their exact roles aren't fully understood.
- SrmB aids in assembling the large ribosomal subunit by helping incorporate the ribosomal protein L13 early in the process.
- Research identified specific rRNA mutations that can bypass the need for SrmB, indicating that its action sites are distinct from where it attaches to the ribosome.
Termination troubles in Escherichia coli K12.
Mol Microbiol
January 2011
CNRS UPR9073 associated with University Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie 75005 Paris, France.
In this issue of Molecular Microbiology, Schaub and Hayes report that, compared with other enterobacteria, Escherichia coli K12 carries two mutations - one in the prfB gene encoding the release factor RF2, and the other in the rpsG gene encoding r-protein S7 - that together concur in compromising translation termination at the essential rpsG gene. As a consequence, the growth of E. coli K12 is very sensitive to a further mutation (rluD(-) ) that depresses RF2 activity, whereas the growth of its close relative, E.
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