The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA.
RNase R and RNase II are the two representatives from the RNR family of processive, 3' to 5' exoribonucleases in Escherichia coli. Although RNase II is specific for single-stranded RNA, RNase R readily degrades through structured RNA. Furthermore, RNase R appears to be the only known 3' to 5' exoribonuclease that is able to degrade through double-stranded RNA without the aid of a helicase activity. Consequently, its functional domains and mechanism of action are of great interest. Using a series of truncated RNase R proteins we show that the cold-shock and S1 domains contribute to substrate binding. The cold-shock domains appear to play a role in substrate recruitment, whereas the S1 domain is most likely required to position substrates for efficient catalysis. Most importantly, the nuclease domain alone, devoid of the cold-shock and S1 domains, is sufficient for RNase R to bind and degrade structured RNAs. Moreover, this is a unique property of the nuclease domain of RNase R because this domain in RNase II stalls as it approaches a duplex. We also show that the nuclease domain of RNase R binds RNA more tightly than the nuclease domain of RNase II. This tighter binding may help to explain the difference in catalytic properties between RNase R and RNase II.
Vincent
Helen A
HA
Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101.
Deutscher
Murray P
MP
Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101. Electronic address: mdeutsch@med.miami.edu.
D002384:Catalysis; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D005095:Exoribonucleases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000502:physiology; D020365:RNA Helicases / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional / Q000502:physiology*; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; C489683:rnr protein, E coli; D005095:Exoribonucleases; C022535:exoribonuclease II; D020365:RNA Helicases