Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA.
The DEAD-box protein CYT-19 functions in the folding of several group I introns in vivo and a diverse set of group I and group II RNAs in vitro. Recent work using the Tetrahymena group I ribozyme demonstrated that CYT-19 possesses a second RNA-binding site, distinct from the unwinding active site, which enhances unwinding activity by binding nonspecifically to the adjacent RNA structure. Here, we probe the region of CYT-19 responsible for that binding by constructing a C-terminal truncation variant that lacks 49 amino acids and terminates at a domain boundary, as defined by limited proteolysis. This truncated protein unwinds a six-base-pair duplex, formed between the oligonucleotide substrate of the Tetrahymena ribozyme and an oligonucleotide corresponding to the internal guide sequence of the ribozyme, with near-wild-type efficiency. However, the truncated protein is activated much less than the wild-type protein when the duplex is covalently linked to the ribozyme or single-stranded or double-stranded extensions. Thus, the active site for RNA unwinding remains functional in the truncated CYT-19, but the site that binds the adjacent RNA structure has been compromised. Equilibrium binding experiments confirmed that the truncated protein binds RNA less tightly than the wild-type protein. RNA binding by the compromised site is important for chaperone activity, because the truncated protein is less active in facilitating the folding of a group I intron that requires CYT-19 in vivo. The deleted region contains arginine-rich sequences, as found in other RNA-binding proteins, and may function by tethering CYT-19 to structured RNAs, so that it can efficiently disrupt exposed, non-native structural elements, allowing them to refold. Many other DExD/H-box proteins also contain arginine-rich ancillary domains, and some of these domains may function similarly as nonspecific RNA-binding elements that enhance general RNA chaperone activity.
Grohman
Jacob K
JK
Department of Chemistry and Biochemistry, and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
Del Campo
Mark
M
Bhaskaran
Hari
H
Tijerina
Pilar
P
Lambowitz
Alan M
AM
Russell
Rick
R
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D053487:DEAD-box RNA Helicases / Q000378:metabolism*; D018832:Molecular Chaperones / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D010206:Papain / Q000378:metabolism; D015800:Protozoan Proteins / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D016337:RNA, Catalytic / Q000378:metabolism*; D016808:Tetrahymena thermophila / Q000201:enzymology*
D018832:Molecular Chaperones; D015800:Protozoan Proteins; D016337:RNA, Catalytic; D012313:RNA; D010206:Papain; D053487:DEAD-box RNA Helicases