The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

Deana, Atilio; Čelešnik, Helena; Belasco, Joel G.

doi:10.1038/nature06475

Cited by 382 publications

(469 citation statements)

References 30 publications

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“…Previous studies have shown that mRNA degradation by a 5′-end-dependent pathway requires a single-stranded 5′ terminus in both B. subtilis and E. coli (7,10). However, the number of unpaired 5′-terminal nucleotides required for degradation by this mechanism had not been determined in these or any other species.…”

Section: Discussionmentioning

confidence: 89%

“…However, we have recently described an alternative degradation pathway in B. subtilis in which the decay of primary transcripts is triggered by the RNA pyrophosphohydrolase RppH (previously known as YtkD), a Nudix hydrolase that removes two of the three 5′-terminal phosphates to generate a full-length intermediate that is monophosphorylated and therefore vulnerable to rapid 5′-exonucleolytic digestion by RNase J (7). A related 5′-end-dependent pathway is also present in bacterial species that lack RNase J, such as E. coli, where pyrophosphate removal triggers rapid cleavage by RNase E, the endonucleolytic activity of which is stimulated by a 5′ monophosphate (8)(9)(10).…”

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confidence: 99%

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Specificity of RppH-dependent RNA degradation in Bacillus subtilis

Hsieh

Richards

Liu

et al. 2013

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

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Bacterial RNA degradation often begins with conversion of the 5′-terminal triphosphate to a monophosphate, creating a better substrate for subsequent ribonuclease digestion. For example, in Bacillus subtilis and related organisms, removal of the gamma and beta phosphates of primary transcripts by the RNA pyrophosphohydrolase RppH triggers rapid 5′-exonucleolytic degradation by RNase J. However, the basis for the selective targeting of a subset of cellular RNAs by this pathway has remained largely unknown. Here we report that purified B. subtilis RppH requires at least two unpaired nucleotides at the 5′ end of its RNA substrates and prefers three or more. The second of these 5′-terminal nucleotides must be G, whereas a less strict preference for a purine is evident at the third position, and A is slightly favored over G at the first position. The same sequence requirements are observed for RppH-dependent mRNA degradation in B. subtilis cells. By contrast, a parallel pathway for 5′-end-dependent RNA degradation in that species appears to involve an alternative phosphate-removing enzyme that is relatively insensitive to sequence variation at the first three positions.O f the mechanisms that control gene expression in all living organisms, mRNA degradation is among the least well understood. Within the same cell, the half-lives of distinct mRNAs can differ by up to two orders of magnitude (seconds to an hour in bacteria, minutes to more than a day in higher eukaryotes), with proportionate effects on mRNA levels (1). In addition, the lifetimes of many messages can be modulated in response to environmental signals.Although it was originally assumed that Escherichia coli could serve as a paradigm for mRNA degradation in all bacteria, it is now clear that many bacterial species use a different set of ribonucleases and distinct mechanisms to degrade mRNA. A gamma proteobacterium, E. coli generally relies on the essential endonuclease RNase E to cleave transcripts internally, generating RNA fragments that are then degraded to mononucleotides by a combination of further RNase E cleavage and 3′-exonuclease digestion (1). Remarkably, despite its crucial role in E. coli, RNase E is entirely absent from a large number of other bacteria, including many Gram-positive species and even some Gram-negative proteobacteria (2). Instead, those species generally contain one or more ribonucleases that are absent from E. coli. For example, Bacillus subtilis, Staphylococcus aureus, and Helicobacter pylori contain two such ribonucleases-RNase Y, a membraneassociated endonuclease, and RNase J, a 5′-monophosphatedependent 5′ exonuclease that is also capable of acting as an endonuclease-in addition to a number of 3′ exonucleases (2-6).Because primary transcripts in B. subtilis are protected from exonucleolytic degradation by their 5′-terminal triphosphate and 3′-terminal stem loop, it was initially believed that message degradation in that species bypasses those termini and begins with endonucleolytic cleavage, generating RNA fragments with un...

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Section: Discussionmentioning

confidence: 89%

mentioning

confidence: 99%

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

Hsieh

Richards

Liu

et al. 2013

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

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“…It has been known for some time that strong secondary structures, bound proteins and, in particular, strong ribosome binding sites the simplest explanation is that the generation of the shorter, stable ∆ermC and lac-rpsO transcripts, like those of cryIIIA and hbs, is dependent on RNase J1 5'-3' exoribonuclease activity, with an entry site provided by another enzyme, either removal of the 5' tri-phosphate group by an enzyme equivalent to the E. coli RNA pyrophosphohydrolase RppH, 24 or an endonucleolytic cleavage downstream of the 5' end (Fig. 1).…”

Section: Role Of Rnase J1/j2 In the Turnover Of Specific Rnasmentioning

confidence: 99%

What is the role of RNase J in mRNA turnover?

Condon¹

2010

RNA Biology

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T he discovery of the paralogous ribonucleases J1 and J2 has been a major advance in the study of RNA maturation and decay in Bacillus subtilis and related organisms. RNase J1 was the first bacterial enzyme shown to possess 5'-to-3' exoribonuclease activity, reversing a dogma that suggested this type of activity was unique to eukaryotic mRNA decay. RNase J1 and J2 form a complex that also has endonuclease activity and these enzymes have been shown to play a key role in the turnover and maturation of many RNAs in B. subtilis. Here, I describe recent progress in our understanding of the role of these enzymes in RNA metabolism in this organism and argue that the 5'-to-3' exoribonuclease activity may be the more important of the complex's two modes of action.

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“…In this report, we present a previously undescribed mechanism for the sequence-specific binding of single-stranded RNA by the 25 kDa subunit of CFI m . Although the Nudix domains of the eukaryotic decapping enzymes (18), bacterial 5′ pyrophophohydrolase (19), and the trypanosome mitochondrial protein MERS1 (20) act on RNA, CFI m 25 is unique among Nudix proteins in that it is capable of sequencespecific RNA binding. CFI m 25 is highly conserved throughout the eukaryotic kingdom (Fig.…”

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confidence: 99%

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Yang

Gilmartin

Doublié

2010

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

130

144

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Human Cleavage Factor Im (CFI m ) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI m 25) of the CFI m complex possesses a characteristic α/β/α Nudix fold, CFI m 25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI m 25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI m 25 is the first Nudix protein to be reported to bind RNA in a sequencespecific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap 4 A (diadenosine tetraphosphate) by CFI m 25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing.T he transcriptome complexity of higher eukaryotes requires the coordinate recognition of an array of alternative pre-mRNA processing signals in a developmental and tissue-specific manner (1, 2). The sequences that direct pre-mRNA splicing and 3′ processing are initially recognized within the nascent transcript in a process that is intimately coupled to transcription (3, 4). While the recognition of exons within the pre-mRNA is mediated by both RNA:RNA and protein:RNA interactions (5), the 3′ processing of polyadenylated mRNAs appears to rely solely on the interaction of protein factors (6) with unstructured RNA sequences (7) within the nascent transcript.Vertebrate pre-mRNA 3′ processing signals are recognized by a tripartite mechanism through which a set of short RNA sequences direct the cooperative binding of three multimeric 3′ processing factors, cleavage factor I m (CFI m ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF) (8). CPSF and CstF bind the AAUAAA hexamer and downstream GU-rich elements that flank the poly(A) site, respectively, whereas CFI m interacts with upstream sequences that may function in the regulation of alternative polyadenylation (9-11). SELEX and biochemical analyses have identified the sequence UGUAN (N ¼ A > U > G, C) as the preferred binding site of CFI m (11). In this report we have taken a structural approach to determine the mechanism of sequence-specific RNA binding by CFI m .CFI m is composed of a large subunit of 59, 68, or 72 kDa and a small subunit of 25 kDa (CFI m 25, also referred to as CPSF5 or NUDT21) (12, 13), both of which contribute to RNA binding (14). The large subunit, encoded by either of two paralogs (CPSF6 and CPSF7), contains an N-terminal RNA Recognition Motif (RRM), an internal polyproline-rich region, and a C-termina...

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The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

Cited by 382 publications

References 30 publications

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

What is the role of RNase J in mRNA turnover?

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

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The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal

Cited by 382 publications

References 30 publications

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

What is the role of RNase J in mRNA turnover?

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

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Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing