Poly(A) RNA in Escherichia coli: nucleotide sequence at the junction of the lpp transcript and the polyadenylate moiety.

Cao, Gong-Jie; Sarkar, Nirmal Kumar

doi:10.1073/pnas.89.16.7546

Cited by 52 publications

(35 citation statements)

References 23 publications

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“…By contrast, when PAP I was overexpressed in a PNPase-deficient strain, tails consisted of homopolymer sequences (Mohanty & Kushner, 2000). lpp displayed only homopolymer tails when clones were isolated from strains deficient in the exoribonucleases PNPase and RNase II (Cao & Sarkar, 1992).…”

Section: Sequence Analysis Of Poly(a) Tails Suggests Pnpase Is the Prmentioning

confidence: 99%

“…Endonucleolytic cleavage is followed by polyadenylation and digestion of poly(A) tails by exonucleases such as RNase II and polynucleotide phosphorylase (PNPase) (Steege, 2000). Poly(A) polymerase I (PAP I) is the enzyme primarily responsible for addition of poly(A) tails (Cao & Sarkar, 1992). Surprisingly, PNPase has been shown to function also as a poly(A) polymerase in E. coli, synthesizing poly(A) tails that are heteropolymers and accounting for the residual polyadenylation activity seen in PAP I-deficient strains (Mohanty & Kushner, 2000).…”

Section: Introductionmentioning

confidence: 99%

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cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor

Bralley

Jones

2002

Microbiology

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In Escherichia coli the poly(A) tails of messenger and rRNAs are a major determinant of RNA stability. These tails are formed primarily by poly(A) polymerase I (PAP I) in wild-type strains or by polynucleotide phosphorylase (PNPase) in PAP I-deficient strains. In Streptomyces coelicolor it has been shown that mycelial RNAs display biochemical characteristics consistent with the presence of poly(A) tails. To confirm the occurrence of polyadenylation, rRNA and mRNA transcripts from S. coelicolor were isolated by oligo(dT)-dependent RT-PCR followed by cDNA cloning. One of the clones obtained was polyadenylated at a site corresponding to the mature 3' terminus of 16S rRNA, while two 23S rRNA cDNA clones were polyadenylated at precursor processing sites. Other clones identified polyadenylation sites internal to the coding regions of both 16S and 23S rRNAs, and redD and actII-orf4 mRNAs. While most rRNA cDNA clones displayed adenosine homopolymer tails, the poly(A) tails of three rRNAs and all the redD and actII-orf4 clones consisted of a variety of heteropolymers. These results suggest that the enzyme primarily responsible for polyadenylation in S. coelicolor is PNPase rather than a PAP I homologue.

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Section: Sequence Analysis Of Poly(a) Tails Suggests Pnpase Is the Prmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor

Bralley

Jones

2002

Microbiology

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“…The lpp terminator (Fig. 1B) was selected because the lpp mRNA is relatively stable and polyadenylation has been reported in vivo (6,27). The native lpp terminator was used to replace the large stemloop of the malE-malF RNA, and the resulting mRNA (lppstem) and its polyadenylated derivative were used as substrates for the degradosome and for His-tagged PNPase.…”

Section: Fig 4 Purified C-terminally His-tagged Pnpase Is Activementioning

confidence: 99%

“…Nevertheless, only recently was polyadenylation considered to have a role in determining mRNA stability in bacteria. Two poly(A) polymerases have been cloned and characterized from Escherichia coli (6,7), and several mRNAs have been shown to possess poly(A) tails (6, 8 -12). Post-transcriptional addition of a poly(A) tail at the 3Ј-end of mRNA has been shown to destabilize certain RNA molecules (13,14).…”

mentioning

confidence: 99%

Polyadenylation Promotes Degradation of 3′-Structured RNA by theEscherichia coli mRNA Degradosome in Vitro

Blum

Carpousis

Higgins

1999

Journal of Biological Chemistry

102

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Polyadenylation contributes to the destabilization of bacterial mRNA. We have investigated the role of polyadenylation in the degradation of RNA by the purified Escherichia coli degradosome in vitro. RNA molecules with 3-ends incorporated into a stable stem-loop structure could not readily be degraded by purified polynucleotide phosphorylase or by the degradosome, even though the degradosome contains active RhlB helicase which normally facilitates degradation of structured RNA. The exoribonucleolytic activity of the degradosome was due to polynucleotide phosphorylase, rather than the recently reported exonucleolytic activity exhibited by a purified fragment of RNase E (Huang, H., Liao, J., and Cohen, S. N. (1998) Nature 391, 99 -102). Addition of a 3-poly(A) tail stimulated degradation by the degradosome. As few as 5 adenosine residues were sufficient to achieve this stimulation, and generic sequences were equally effective. The data show that the degradosome requires a single-stranded "toehold" 3 to a secondary structure to recognize and degrade the RNA molecule efficiently; polyadenylation can provide this single-stranded 3-end. Significantly, oligo(G) and oligo(U) tails were unable to stimulate degradation; for oligo(G), at least, this is probably due to the formation of a G quartet structure which makes the 3-end inaccessible. The inaccessibility of 3-oligo(U) sequences is likely to have a role in stabilization of RNA molecules generated by Rho-independent terminators.

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“…We employed lpp mRNA and bacteriophage λ oop RNA as model transcripts. Both transcripts were previously demonstrated to be specifically polyadenylated by PAP I (Cao & Sarkar, 1992b;O'Hara et al, 1995;Wróbel et al, 1998;Mohanty & Kushner, 1999a), and polyadenylation of lpp and oop RNAs leads to a significant decrease in their stability in E. coli cells (O'Hara et al, 1995;Szalewska-Pal / asz et al, 1998;Mohanty & Kushner, 1999a). …”

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confidence: 99%

Growth‐rate dependent RNA polyadenylation in Escherichia coli

Jasiecki

Węgrzyn

2003

EMBO Reports

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RNA polyadenylation occurs not only in eukaryotes but also in bacteria. In prokaryotes, polyadenylated RNA molecules are usually degraded more efficiently than non-modified transcripts. Here we demonstrate that two transcripts, which were shown previously to be substrates for poly(A) polymerase I (PAP I), Escherichia coli lpp messenger RNA and bacteriophage λ oop RNA, are polyadenylated more efficiently in slowly growing bacteria than in rapidly growing bacteria. Intracellular levels of PAP I varied in inverse proportion to bacterial growth rate. Moreover, transcription from a promoter for the pcnB gene (encoding PAP I) was shown to be more efficient under conditions of low bacterial growth rates. We conclude that efficiency of RNA polyadenylation in E. coli is higher in slowly growing bacteria because of more efficient expression of the pcnB gene. This may allow regulation of the stability of certain transcripts (those subjected to PAP I-dependent polyadenylation) in response to various growth conditions. EMBO reports 4, 172-177 (2003) doi:10.1038/sj.embor.embor733 INTRODUCTIONDespite the fact that bacterial poly(A) polymerase was described 40 years ago (August et al., 1962), specific polyadenylation at the 3′ end of RNA was for a long time believed to be unique to eukaryotic messenger RNAs. Studies of the last ten years, initiated by the discovery of the structural gene for poly(A) polymerase I (PAP I) in Escherichia coli (Cao & Sarkar, 1992a), clearly demonstrated that prokaryotic RNAs are also polyadenylated.Two poly(A) polymerases, PAP I and PAP II, were discovered in E. coli. PAP I, which is responsible for over 90% of poly(A) polymerase activity in E. coli cells (O'Hara et al., 1995;Mohanty & Kushner, 1999a), is encoded by the pcnB gene (Cao & Sarkar, 1992a), but the gene encoding PAP II is still unknown (Mohanty & Kushner, 1999b). One could speculate that polynucleotide phosphorylase (PNPase) functions as an exonuclease and also as a poly(A) polymerase, which could account for the activity of PAP II. Various RNA molecules are polyadenylated with different efficiency, and it appears that the susceptibility of certain RNAs to polyadenylation depends on the presence of single-stranded segments at either the 5′ or the 3′ end and monophosphorylation at an unpaired 5′ terminus (Feng & Cohen, 2000;Yehudai-Resheff & Schuster, 2000).There are many reports indicating that bacterial RNA polyadenylation leads to decreased stability of transcripts (O'Hara et al., 1995;Xu & Cohen, 1995;Szalewska-Pal / asz et al., 1998;Blum et al., 1999). Results of other experiments showed either stabilization of specific transcripts, or a lack of effect on the halflives of other mRNAs after enhanced polyadenylation (Mohanty & Kushner, 1999a). However, transcripts stabilized or unaffected by polyadenylation are very rare, and it is therefore generally accepted that this process may regulate gene expression by promoting RNA degradation (for reviews see Sarkar, 1996;Carpousis et al., 1999;Rauhut & Klug, 1999;Regnier & Arraiano, 2000;...

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Poly(A) RNA in Escherichia coli: nucleotide sequence at the junction of the lpp transcript and the polyadenylate moiety.

Cited by 52 publications

References 23 publications

cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor

cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor

Polyadenylation Promotes Degradation of 3′-Structured RNA by theEscherichia coli mRNA Degradosome in Vitro

Growth‐rate dependent RNA polyadenylation in Escherichia coli

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