Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5′–3′ Exo/Endoribonuclease RNase J

Dorléans, Audrey; Sierra-Gallay, I. Li de la; Piton, Jérémie; Zig, Léna; Gilet, Laetitia; Putzer, Harald; Condon, Ciarán

doi:10.1016/j.str.2011.06.018

Cited by 68 publications

(92 citation statements)

References 32 publications

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“…The first binding site obviously is the 59 phosphate-binding pocket while the second site of attachment is thought to be a path of positively charged residues at the surface of the b-CASP domain. In accordance with the biochemical data, the 5th residue would be the first to exit the catalytic channel and bind to the positively charged residues (47).…”

Section: Protein Structure and Catalytic Mechanismsupporting

confidence: 79%

“…This does not exclude the fact that RNase J does act as an endonuclease in vivo, but could simply reflect the fact that the few substrates tested so far are not present in the optimal conformation, or that we are missing an additional factor required for cleavage. However, new crystallographic data, discussed further on, provide a rational insight into why the endonucleolytic activity of RNase J might be restricted in vivo (47,48). In the archea, recently identified RNase J orthologs have a strong 59 exonucleolytic activity but no significant endonuclease activity (31,32).…”

Section: Endonucleolytic Cleavage Specificitymentioning

confidence: 99%

“…New information on how RNase J functions, comes from two recent studies that show the RNase J structure in an open conformation: one describes the structure of T. thermophilus RNase J bound to a short 4-nucleotide RNA (47); the other that of B. subtilis RNase J1 in the apo-form including a model for the enzyme/RNA complex (48). In the open structures, the angle between the b-lactamase and b-CASP domains is widened to create a channel for the RNA.…”

Section: Protein Structure and Catalytic Mechanismmentioning

confidence: 99%

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mRNA degradation and maturation in prokaryotes: the global players

Laalami

Putzer

2011

BioMolecular Concepts

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The degradation of messenger RNA is of universal importance for controlling gene expression. It directly affects protein synthesis by modulating the amount of mRNA available for translation. Regulation of mRNA decay provides an efficient means to produce just the proteins needed and to rapidly alter patterns of protein synthesis. In bacteria, the half-lives of individual mRNAs can differ by as much as two orders of magnitude, ranging from seconds to an hour. Most of what we know today about the diverse mechanisms of mRNA decay and maturation in prokaryotes comes from studies of the two model organisms Escherichia coli and Bacillus subtilis. Their evolutionary distance provided a large picture of potential pathways and enzymes involved in mRNA turnover. Among them are three ribonucleases, two of which have been discovered only recently, which have a truly general role in the initiating events of mRNA degradation: RNase E, RNase J and RNase Y. Their enzymatic characteristics probably determine the strategies of mRNA metabolism in the organism in which they are present. These ribonucleases are coded, alone or in various combinations, in all prokaryotic genomes, thus reflecting how mRNA turnover has been adapted to different ecological niches throughout evolution.

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Section: Protein Structure and Catalytic Mechanismsupporting

confidence: 79%

Section: Endonucleolytic Cleavage Specificitymentioning

confidence: 99%

Section: Protein Structure and Catalytic Mechanismmentioning

confidence: 99%

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mRNA degradation and maturation in prokaryotes: the global players

Laalami

Putzer

2011

BioMolecular Concepts

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“…Purified RNase J appears to require at least 9-10 unpaired nucleotides at the 5′ end for maximum 5′-exonuclease activity and 4-5 unpaired nucleotides for exonucleolytic processivity (4,14), more than the number needed for phosphate removal by RppH. Therefore, the length requirements of RNase J are likely to predominate even Fig.…”

Section: Discussionmentioning

confidence: 99%

“…though phosphate removal by RppH often appears to be rate determining [as judged from the low steady-state ratio of the monophosphorylated to triphosphorylated forms of transcripts targeted by RppH (7)]. Conversely, whereas RppH has strict sequence requirements, the 5′-exonuclease activity of RNase J exhibits little if any sequence dependence (14), as would be expected for an enzyme that must rapidly degrade a great variety of decay intermediates to mononucleotides. Consequently, the specificity of RppH-dependent mRNA degradation in B. subtilis should be defined by the length requirements of RNase J and the sequence requirements of RppH.…”

Section: Discussionmentioning

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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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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“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria

Zhang

Hess

Zhang

2022

mLife

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RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA‐turnover‐related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.

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Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5′–3′ Exo/Endoribonuclease RNase J

Cited by 68 publications

References 32 publications

mRNA degradation and maturation in prokaryotes: the global players

mRNA degradation and maturation in prokaryotes: the global players

Specificity of RppH-dependent RNA degradation in Bacillus subtilis

“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria

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