Analysis of DEAD-box proteins in mRNA export. 2012

Ben Montpetit, and Markus A Seeliger, and Karsten Weis
Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.

DEAD-box ATPases/helicases are a large family of enzymes (>35 in humans) involved in almost all aspects of RNA metabolism including ribosome biogenesis, RNA splicing, export, translation, and decay. Many members of this family are ATP-dependent RNA-binding proteins that interact with the RNA phosphodiester backbone and promote structural remodeling of target complexes through ATP binding and hydrolysis. Here, we describe the methods used in our laboratory to characterize the DEAD-box ATPase Dbp5 of Saccharomyces cerevisiae. Dbp5 is essential for the process of mRNA export in budding yeast and highly conserved orthologs can be found in all eukaryotes. Specifically, we describe enzyme assays to measure the catalytic activity of Dbp5 in association with RNA and known binding partners, as well as assays developed to measure the binding affinities and release kinetics of RNA and adenosine nucleotides from Dbp5. These assays have provided important information that has shaped our current models of Dbp5 function in mRNA export and should be useful for the characterization of other DEAD-box family members.

UI MeSH Term Description Entries
D012441 Saccharomyces cerevisiae A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement. Baker's Yeast,Brewer's Yeast,Candida robusta,S. cerevisiae,Saccharomyces capensis,Saccharomyces italicus,Saccharomyces oviformis,Saccharomyces uvarum var. melibiosus,Yeast, Baker's,Yeast, Brewer's,Baker Yeast,S cerevisiae,Baker's Yeasts,Yeast, Baker
D053487 DEAD-box RNA Helicases A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function. DEAD-box RNA Helicase,DEAD Box Helicase p68,p68 DEAD Box Protein,p68 RNA Helicase,DEAD box RNA Helicase,DEAD box RNA Helicases,Helicase, DEAD-box RNA,Helicase, p68 RNA,Helicases, DEAD-box RNA,RNA Helicase, DEAD-box,RNA Helicase, p68,RNA Helicases, DEAD-box
D021581 Active Transport, Cell Nucleus Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE. Nuclear Export,Nuclear Import,Nuclear Transport,Nucleocytoplasmic Transport,Nucleo-cytoplasmic Transport,Export, Nuclear,Import, Nuclear,Nucleo cytoplasmic Transport,Transport, Nuclear,Transport, Nucleo-cytoplasmic,Transport, Nucleocytoplasmic,Transports, Nucleo-cytoplasmic
D028861 Nuclear Pore Complex Proteins Proteins that form the structure of the NUCLEAR PORE. They are involved in active, facilitated and passive transport of molecules in and out of the CELL NUCLEUS. Nucleoporins,Nucleoporin
D029543 Nucleocytoplasmic Transport Proteins Proteins involved in the process of transporting molecules in and out the cell nucleus. Included here are: NUCLEOPORINS, which are membrane proteins that form the NUCLEAR PORE COMPLEX; KARYOPHERINS, which carry molecules through the nuclear pore complex; and proteins that play a direct role in the transport of karyopherin complexes through the nuclear pore complex. Transport Proteins, Nucleocytoplasmic
D029701 Saccharomyces cerevisiae Proteins Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes. Baker's Yeast Proteins,S cerevisiae Proteins
D034443 RNA Transport The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms. Messenger RNA Localization Processes, Cellular,Messenger RNA Sorting,RNA Localization Processes, Cellular,RNA Sorting,Ribonucleic Acid Transport,mRNA Localization Processes, Cellular,mRNA Sorting,Acid Transport, Ribonucleic,RNA Sorting, Messenger,Sorting, Messenger RNA,Sorting, RNA,Sorting, mRNA,Transport, RNA,Transport, Ribonucleic Acid

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