Structural Basis for Processivity and Single-Strand Specificity of RNase II

Zuo, Y.; Vincent, Helen A.; Zhang, Jianwei; Wang, Yong; Deutscher, Murray P.; Malhotra, Arun

doi:10.1016/j.molcel.2006.09.004

Cited by 84 publications

(110 citation statements)

References 33 publications

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“…coli RNase II is the model of the RNase II family of enzymes, whose homologues are present in all three domains of life (1,11,12,44,45). The resolution of the structure of E. coli RNase II in the RNA-free and bound complex constituted a significant breakthrough (22,24). The structural study together with biochemical analysis helped to explain certain aspects of the enzyme activity and led to the proposal of a model for RNA degradation by RNase II that can be extrapolated to other family members (13,15,22,26,41).…”

Section: Discussionmentioning

confidence: 99%

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Determination of Key Residues for Catalysis and RNA Cleavage Specificity

Barbas

Matos

Amblar

et al. 2009

Journal of Biological Chemistry

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RNase II is the prototype of a ubiquitous family of enzymes that are crucial for RNA metabolism. In Escherichia coli this protein is a single-stranded-specific 3-exoribonuclease with a modular organization of four functional domains. In eukaryotes, the RNase II homologue Rrp44 (also known as Dis3) is the catalytic subunit of the exosome, an exoribonuclease complex essential for RNA processing and decay. In this work we have performed a functional characterization of several highly conserved residues located in the RNase II catalytic domain to address their precise role in the RNase II activity. We have constructed a number of RNase II mutants and compared their activity and RNA binding to the wild type using different singleor double-stranded substrates. The results presented in this study substantially improve the RNase II model for RNA degradation. We have identified the residues that are responsible for the discrimination of cleavage of RNA versus DNA. We also show that the Arg-500 residue present in the RNase II active site is crucial for activity but not for RNA binding. The most prominent finding presented is the extraordinary catalysis observed in the E542A mutant that turns RNase II into a "super-enzyme."Exoribonuclease II (RNase II) 5 is one of the major exoribonucleases involved in the degradation of RNA (1). This protein degrades RNA hydrolytically in the 3Ј to 5Ј direction, releasing 5Ј-nucleotide monophosphates in a processive manner. Its activity is sequence independent but sensitive to secondary structures, and poly(A) is the preferential substrate for this enzyme (2-6). In Escherichia coli RNase II is responsible for 90% of the hydrolytic activity in crude extracts (7). Moreover, its expression is differentially regulated at the transcriptional and post-transcriptional levels (8 -10), and the protein can be regulated by environmental conditions (10). The E. coli enzyme is the prototype of a widespread family of exoribonucleases, and RNase II homologues can be found in prokaryotes and eukaryotes (11). In the nucleus and in the cytoplasm of eukaryotic cells, RNase II homologues (Rrp44/Dis3) are part of the exosome, an essential multiprotein complex of exoribonucleases involved in processing, turnover, and quality control of different types of RNAs (12). Rrp44 is the only catalytically active nuclease in the human and yeast core exosome (13,14). Moreover, it was recently demonstrated that apart from the RNB catalytic domain, Rrp44p has a second nuclease domain, the PINc domain, that confers endonucleolytic activity to the protein (15, 16). In prokaryotic cells, apart from RNase II, there is an additional RNase II-like enzyme, RNase R, that is involved in RNA degradation and RNA and protein quality control (17)(18)(19)(20). RNase R has also been shown to be required for virulence (21).The determination of E. coli RNase II structure (22-24) showed that, contrary to the sequence predictions, RNase II consisted of four domains; they are two N-terminal cold shock domains (CSD1 and CSD2) involved in RNA b...

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Section: Discussionmentioning

confidence: 99%

“…The determination of E. coli RNase II structure (22)(23)(24) showed that, contrary to the sequence predictions, RNase II consisted of four domains; they are two N-terminal cold shock domains (CSD1 and CSD2) involved in RNA binding, one central RNB catalytic domain, and a third RNA binding domain at the C terminus, the S1 domain (Fig. 1A).…”

mentioning

confidence: 98%

Determination of Key Residues for Catalysis and RNA Cleavage Specificity

Barbas

Matos

Amblar

et al. 2009

Journal of Biological Chemistry

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“…The catalytic activity is provided by a 10th essential subunit, Rrp44p (2,5,6). This protein is similar to RNase II in that it contains three putative RNA binding domains that flank an RNB domain (3,(7)(8)(9)(10). The RNB domain is responsible for the 3′ exonuclease activity of the exosome (3).…”

Section: Dis3 | Saccharomyces Cerevisiaementioning

confidence: 99%

Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs

Schaeffer

Hoof

2011

Proc. Natl. Acad. Sci. U.S.A.

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Two general pathways of mRNA decay have been characterized in yeast. In one pathway, the mRNA is degraded by the cytoplasmic form of the exosome. The exosome has both 3′ to 5′ exoribonuclease and endoribonuclease activity, and the available evidence suggests that the exonuclease activity is required for the degradation of mRNAs. We confirm here that this is true for normal mRNAs, but that aberrant mRNAs that lack a stop codon can be efficiently degraded in the absence of the exonuclease activity of the exosome. Specifically, we show that the endo-and exonuclease activities of the exosome are both capable of rapidly degrading nonstop mRNAs and ribozyme-cleaved mRNAs. Additionally, the endonuclease activity of the exosome is not required for endonucleolytic cleavage in no-go decay. In vitro, the endonuclease domain of the exosome is active only under nonphysiological conditions, but our findings show that the in vivo activity is sufficient for the rapid degradation of nonstop mRNAs. Thus, whereas normal mRNAs are degraded by two exonucleases (Xrn1p and Rrp44p), several endonucleases contribute to the decay of many aberrant mRNAs, including transcripts subject to nonstop and nogo decay. Our findings suggest that the nuclease requirements for general and nonstop mRNA decay are different, and describe a molecular function of the core exosome that is not disrupted by inactivating its exonuclease activity.Dis3 | Saccharomyces cerevisiae

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“…A clamp-like assembly in the RNA-binding domain of RNase II possibly allows single-stranded RNA 3Ј-ends to enter the catalytic center and blocks doublestranded RNA. During RNA digestion in vitro, RNase II progressively slows down at double-stranded structures, resulting in products that usually contain an average 7-9-nt singlestranded overhang at the 3Ј-end (22). In contrast to RNase II, E. coli RNase R is able to degrade double-stranded RNA effectively starting from a single-stranded 3Ј-overhang.…”

Section: Discussionmentioning

confidence: 99%

Novel One-step Mechanism for tRNA 3′-End Maturation by the Exoribonuclease RNase R of Mycoplasma genitalium

Alluri¹,

2012

Journal of Biological Chemistry

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Background: Mycoplasma genitalium lacks known ribonucleases for tRNA 3Ј-processing. The only identified exoribonuclease, RNase R, can carry out this function. Results: RNase R processes the tRNA 3Ј-end depending on the acceptor stem, discriminator, and CCA terminus. Conclusion: RNase R can process tRNA by recognizing features within the tRNA. Significance: M. genitalium may process tRNA 3Ј-end employing a unique single-step exonucleolytic pathway.

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Structural Basis for Processivity and Single-Strand Specificity of RNase II

Cited by 84 publications

References 33 publications

Determination of Key Residues for Catalysis and RNA Cleavage Specificity

Determination of Key Residues for Catalysis and RNA Cleavage Specificity

Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs

Novel One-step Mechanism for tRNA 3′-End Maturation by the Exoribonuclease RNase R of Mycoplasma genitalium

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