Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs

Durand, Sylvain; Richard, Graziella; Bontems, François; Uzan, Marc

doi:10.1073/pnas.1119802109

Cited by 16 publications

(13 citation statements)

References 38 publications

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“…In one case the initiating ribosome competes directly with RNase J1, while in the other it competes directly with RNase Y. Our data (Figure 7B ), would suggest that the newly discovered C3 site is more frequently used than C2 to begin the destruction of hbs transcripts lacking a ribosome bound to the SD, although we cannot rule out the possibility of sequential cleavages at C2 then C3 (or indeed C1, C2 and then C3) by RNase Y complicating this interpretation, as has been proposed for RNase E in E. coli ( 30 , 31 ). Indeed, sequential cleavages might explain why cleavage at C1 appears to be stronger than C2 in the LR1comp mutant (Figure 9C ).…”

Section: Discussionmentioning

confidence: 55%

Initiating ribosomes and a 5′/3′-UTR interaction control ribonuclease action to tightly couple B. subtilis hbs mRNA stability with translation

Braun

Durand

Condon

2017

Nucleic Acids Research

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We previously showed that ribosomes initiating translation of the B. subtilis hbs mRNA at a strong Shine–Dalgarno sequence block the 5′ exoribonuclease RNase J1 from degrading into the coding sequence. Here, we identify new and previously unsuspected features of this mRNA. First, we identify RNase Y as the endoribonuclease that cleaves the highly structured 5′-UTR to give access to RNase J1. Cleavage by RNase Y at this site is modulated by a 14-bp long-range interaction between the 5′- and 3-UTRs that partially overlaps the cleavage site. In addition to this maturation/degradation pathway, we discovered a new and ultimately more important RNase Y cleavage site in the very early coding sequence, masked by the initiating ribosome. Thus, two independent pathways compete with ribosomes to tightly link hbs mRNA stability to translation initiation; in one case the initiating ribosome competes directly with RNase J1 and in the other with RNase Y. This is in contrast to prevailing models in Escherichia coli where ribosome traffic over the ORF is the main source of protection from RNases. Indeed, a second RNase Y cleavage site later in the hbs ORF plays no role in its turnover, confirming that for this mRNA at least, initiation is key.

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Section: Discussionmentioning

confidence: 55%

Initiating ribosomes and a 5′/3′-UTR interaction control ribonuclease action to tightly couple B. subtilis hbs mRNA stability with translation

Braun

Durand

Condon

2017

Nucleic Acids Research

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“…Previous examples of kinase-mediated decay of bacterial mRNAs (Durand et al, 2012) , eukaryal tRNA introns (Wu and Hopper, 2014) , and ribosomal RNA processing intermediates (Gasse et al, 2015) suggest that this mode of decay may be widespread. Coupling of RNA 5′-kinase and 5′→3′ exonucleolytic decay activities in the context of kinase-mediated decay might regulate the UPR in other organisms.…”

Section: Discussionmentioning

confidence: 99%

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response

Cherry

Peach

Hesselberth

2018

Preprint

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In the unfolded protein response (UPR), protein-folding stress in the endoplasmic reticulum (ER) activates a large transcriptional program to increase ER folding capacity. During the budding yeast UPR, the trans-ER-membrane kinase-endoribonuclease Ire1 excises an intron from the HAC1 mRNA and the exon cleavage products are ligated and translated to a transcription factor that induces hundreds of stress-response genes. HAC1 cleavage by Ire1 is thought to be the rate limiting step of its processing. Using cells with mutations in RNA repair and decay enzymes, we show that phosphorylation of two different HAC1 splicing intermediates by Trl1 RNA 5′-kinase is required for their degradation by the 5′→3′ exonuclease Xrn1 to enact opposing effects on the UPR. Kinase-mediated decay (KMD) of cleaved HAC1 3′-exon competes with its ligation to limit productive splicing and suppress the UPR, whereas KMD of the excised intron activates HAC1 translation, likely by relieving an inhibitory base-pairing interaction between the intron and 5′-untranslated region. We also found that ligated but 2′-phosphorylated HAC1 mRNA is endonucleolytically cleaved, yielding a KMD intermediate with both 5′-and 2′-phosphates at its 5′-end that inhibit 5′→3′ decay, and suggesting that Ire1 initiates the degradation of incompletely processed HAC1 s to proofread ligation or attenuate the UPR. These multiple decay events expand the scope of RNA-based regulation in the budding yeast UPR and may have implications for the control of the metazoan UPR by mRNA processing.

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“…NGD decay intermediates are degraded by Xrn1 ( 52 ). However, insofar as Xrn1 requires 5′-PO 4 substrates ( 40 ), the products of NGD that are degraded by Xrn1 could be generated by an endonuclease that creates 5′-OH RNA products that are phosphorylated by a cellular 5′-kinase activity (e.g., the tRNA ligase Trl1), promoting their decay by Xrn1— a scenario similar to 5′-kinase-mediated turnover of spliced tRNA introns by Xrn1 ( 31 ) and RegB mRNA cleavage products in bacteria ( 54 ). Thus, it is possible that many of the 5′-OH fragments we identified are products of NGD.…”

Section: Discussionmentioning

confidence: 99%

Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing

2015

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RNA cleavage by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5′-hydroxyl (5′-OH) and 2′,3′-cyclic phosphate termini. To identify 5′-OH RNA fragments produced by these cleavage events, we exploited the unique ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs with 5′-OH termini, followed by steps for library construction and analysis by massively parallel DNA sequencing. We applied the method to RNA from budding yeast and captured known 5′-OH fragments produced by tRNA Splicing Endonuclease (SEN) during processing of intron-containing pre-tRNAs and by Ire1 cleavage of HAC1 mRNA following induction of the unfolded protein response (UPR). We identified numerous novel 5′-OH fragments derived from mRNAs: some 5′-OH mRNA fragments were derived from single, localized cleavages, while others were likely produced by multiple, distributed cleavages. Many 5′-OH fragments derived from mRNAs were produced upstream of codons for highly electrostatic peptides, suggesting that the fragments may be generated by co-translational mRNA decay. Several 5′-OH RNA fragments accumulated during the induction of the UPR, some of which share a common sequence motif that may direct cleavage of these mRNAs. This method enables specific capture of 5′-OH termini and complements existing methods for identifying RNAs with 2′,3′-cyclic phosphate termini.

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Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs

Cited by 16 publications

References 38 publications

Initiating ribosomes and a 5′/3′-UTR interaction control ribonuclease action to tightly couple B. subtilis hbs mRNA stability with translation

Initiating ribosomes and a 5′/3′-UTR interaction control ribonuclease action to tightly couple B. subtilis hbs mRNA stability with translation

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response

Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing

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