mRNA degradation: a tale of poly(A) and multiprotein machines

Carpousis, Agamemnon J.; Vanzo, Nathalie; Raynal, Lelia C.

doi:10.1016/s0168-9525(98)01627-8

Cited by 202 publications

(148 citation statements)

References 43 publications

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“…The C terminus acts as a scaffold, necessary for protein-protein interactions with polynucleotide phosphorylase (PNPase), an RNA helicase and enolase, a complex that has been called the degradosome (Carpousis et al 1994(Carpousis et al , 1999Py et al 1994Py et al , 1996Miczak et al 1996). Deletions of portions or all of the C terminus are viable, process ribosomal RNA and tRNAs normally, but are slowed for degradation of some messages (Lopez et al 1999;Ow et al 2000; see below).…”

Section: Involvement Of the Degradosomementioning

confidence: 99%

“…The C-ter- minal domain of RNase E, not essential for its catalytic activity, acts as a scaffold for binding of polynucleotide phosphorylase (PNPase), RhlB helicase, and enolase (Carpousis et al 1994(Carpousis et al , 1999Py et al 1994Py et al , 1996Miczak et al 1996). Deletions of this C-terminal domain, although they have little or no effect on the processing of rRNA or tRNAs, significantly slow the degradation of some test substrates (untranslated mRNAs, in particular; Lopez et al 1999;Ow et al 2000;Leroy et al 2002;Ow and Kushner 2002).…”

Section: Degradosome Involvementmentioning

confidence: 99%

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Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

Massé¹,

Escorcia²,

Gottesman³

2003

Genes Dev.

656

836

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RyhB is a small antisense regulatory RNA that is repressed by the Fur repressor and negatively regulates at least six mRNAs encoding Fe-binding or Fe-storage proteins in Escherichia coli. When Fe is limiting, RyhB levels rise, and target mRNAs are rapidly degraded. RyhB is very stable when measured after treatment of cells with the transcription inhibitor rifampicin, but is unstable when overall mRNA transcription continues. We propose that RyhB turnover is coupled to and dependent on pairing with the target mRNAs. Degradation of both mRNA targets and RyhB is dependent on RNase E and is slowed in degradosome mutants. RyhB requires the RNA chaperone Hfq. In the absence of Hfq, RyhB is unstable, even when general transcription is inhibited; degradation is dependent upon RNase E. Hfq and RNase E bind similar sites on the RNA; pairing may allow loss of Hfq and access by RNase E. Two other Hfq-dependent small RNAs, DsrA and OxyS, are also stable when overall transcription is off, and unstable when it is not, suggesting that they, too, are degraded when their target mRNAs are available for pairing. Thus, this large class of regulatory RNAs share an unexpected intrinsic mechanism for shutting off their action.

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Section: Involvement Of the Degradosomementioning

confidence: 99%

Section: Degradosome Involvementmentioning

confidence: 99%

Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

Massé¹,

Escorcia²,

Gottesman³

2003

Genes Dev.

656

836

View full text Add to dashboard Cite

show abstract

“…For example, in eukaryotic cytoplasm, the poly(A) tail in conjunction with poly(A)-binding proteins increases the stability of many mRNAs (2)(3)(4)(5). On the contrary, in bacteria and chloroplasts, poly(A) tails act as mRNA destabilizing elements (6)(7)(8). In mitochondria from different organisms, polyadenylation exerts different effects on RNA stability.…”

Section: Introductionmentioning

confidence: 99%

Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3′ tails in Trypanosoma brucei mitochondria

Kao

Read

2007

Molecular and Biochemical Parasitology

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Polyadenylation plays an important role in regulating RNA stability in Trypanosoma brucei mitochondria. To date, little is known about the enzymes responsible for the addition of mRNA 3′ tails in this system. In this study, we characterize a trypanosome homolog of the human mitochondrial poly(A) polymerase, which we term kPAP2. kPAP2 is mitochondrially localized and expressed in both bloodstream and procyclic form trypanosomes. Targeted gene depletion using RNAi showed that kPAP2 is not required for T. brucei growth in either bloodstream or procyclic life stages, nor is it essential for differentiation from bloodstream to procyclic form. We also demonstrate that steady state abundance of several mitochondrial RNAs was largely unaffected upon kPAP2 downregulation. Interestingly, mRNA 3′ tail analysis of several mRNAs from both life cycle stages in uninduced kPAP2 RNAi cells demonstrated that tail length and uridine content are both regulated in a transcript-specific manner. mRNA-specific tail lengths were maintained upon kPAP2 depletion. However, the percentage of uridine residues in 3′ tails was increased, and conversely the percentage of adenosine residues was decreased, in a distinct subset of mRNAs when kPAP2 levels were downregulated. Thus, kPAP2 apparently contributes to the incorporation of adenosine residues in 3′ tails of some, but not all, mitochondrial mRNAs. Together, these data suggest that multiple nucleotidyltransferases act on mitochondrial mRNA 3′ ends, and that these enzymes are somewhat redundant and subject to complex regulation.

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“…Polyadenylation of the 39-ends of RNAs, once thought to occur exclusively in eukaryotic cells, has now been shown definitively to occur in bacterial systems as well (Carpousis et al, 1999;Rauhut & Klug, 1999;Sarkar, 1996Sarkar, , 1997. In Escherichia coli, polyadenylation targets RNAs for degradation (Carpousis et al, 1999;Régnier & Arraiano, 2000).…”

Section: Introductionmentioning

confidence: 99%

RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase

et al. 2006

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As in other bacteria, 39-tails are added post-transcriptionally to Streptomyces coelicolor RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of S. coelicolor gene SCO3896, although it bears significant sequence similarity to Escherichia coli poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that SCO2904 encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. S. coelicolor RNase PH can add poly(A) tails to a model RNA transcript in vitro. However, disruption of the RNase PH gene has no effect on RNA 39-tail length or composition in S. coelicolor; thus, RNase PH does not function as the RNA 39-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 39-tail synthesis in S. coelicolor and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of SCO3896 are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 39-tails make it indispensable in Streptomyces.

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mRNA degradation: a tale of poly(A) and multiprotein machines

Cited by 202 publications

References 43 publications

Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3′ tails in Trypanosoma brucei mitochondria

RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase

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