POLYADENYLATION OF mRNA IN PROKARYOTES

Sarkar, Nirmal Kumar

doi:10.1146/annurev.biochem.66.1.173

Cited by 207 publications

(182 citation statements)

References 105 publications

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“…Using swap experiments between CCA-adding enzymes and the N and C termini of the class II Escherichia coli poly(A) polymerase (23,24), Betat et al (25) identified a region between residues 219 and 245 in the CCA-adding enzyme that determined whether the chimeric enzymes behaved as a CCA-adding enzyme or a poly(A) polymerase. The ability of this region to confer CCA-adding activity on the N terminus of poly(A) polymerase is most surprising and is consistent with the notion that scrunching, counting, and the nucleotide specificity switch in class II CCA-adding enzymes may be localized, intrinsic characteristics of the NTR active site; however, we hesitate to interpret the results of Betat et al (25) structurally because no structure has been determined for E. coli poly(A) polymerase; the helix M regions of the E. coli poly(A) polymerase and CCA-adding enzymes exhibit little if any homology; and helix M appears to be remote from the tRNA acceptor stem in the cocrystal structure of the A. aeolicus A-adding enzyme (21).…”

Section: Resultsmentioning

confidence: 99%

Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases

Cho

Verlinde

Weiner

2007

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

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CCA-adding enzymes build and repair the 3 -terminal CCA sequence of tRNA. These unusual RNA polymerases use either a ribonucleoprotein template (class I) or pure protein template (class II) to form mock base pairs with the Watson-Crick edges of incoming CTP and ATP. Guided by the class II Bacillus stearothermophilus CCA-adding enzyme structure, we introduced mutations designed to reverse the polarity of hydrogen bonds between the nucleobases and protein template. We were able to transform the CCA-adding enzyme into a (U,G)-adding enzyme that incorporates UTP and GTP instead of CTP and ATP; we transformed the related Aquifex aeolicus CC-and A-adding enzymes into UU-and G-adding enzymes and Escherichia coli poly(A) polymerase into a poly(G) polymerase; and we transformed the B. stearothermophilus CCAadding enzyme into a poly(C,A) polymerase by mutations in helix J that appear, based on the apoenzyme structure, to sterically limit addition to CCA. We also transformed the B. stearothermophilus CCA-adding enzyme into a dCdCdA-adding enzyme by mutating an arginine that interacts with the incoming ribose 2 hydroxyl. Most importantly, we found that mutations in helix J can affect the specificity of the nucleotide binding site some 20 Å away, suggesting that the specificity of both class I and II enzymes may be dictated by an intricate network of hydrogen bonds involving the protein, incoming nucleotide, and 3 end of the tRNA. Collaboration between RNA and protein in the form of a ribonucleoprotein template may help to explain the evolutionary diversity of the nucleotidyltransferase family.nucleotidyltransferase ͉ tRNA T he CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase (NTR)] builds and repairs tRNA by adding the nucleotide sequence CCA to the 3Ј terminus of immature or damaged tRNA (1). Although this unusual RNA polymerase has no nucleic acid template, it constructs the CCA sequence one nucleotide at a time using CTP and ATP as substrates (1). All CCA-adding enzymes and poly(A) polymerases belong to the NTR superfamily, which can be divided into two distinct classes according to sequence motifs in the catalytic domain (2-6). The class I and class II CCA-adding enzymes exhibit little if any homology outside the NTR domain (6). Class I NTRs include archaeal CCA-adding enzymes, eukaryotic poly(A) polymerases, and probably eukaryotic terminal uridylyltransferases (7, 8); class II NTRs include eukaryotic and eubacterial CCAadding enzymes as well as eubacterial poly(A) polymerases (6).We found previously that a single NTR motif adds all three nucleotides (9, 10), that tRNA does not rotate or translocate along the enzyme during addition of C75 and A76 (11), and that a single active subunit in these dimeric or tetrameric enzymes can carry out all three steps of CCA addition (9). We therefore proposed that the growing 3Ј end of tRNA refolds progressively to reposition the new 3Ј hydroxyl identically relative to the single active site (10,12). This prediction was confirmed by cocrystal structures of the class I archaeal...

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Section: Resultsmentioning

confidence: 99%

Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases

Cho

Verlinde

Weiner

2007

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

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“…In E. coli, polyadenylation of mRNAs, which is primarily carried out by E. coli Poly(A) polymerase (PAP I), instead seems to have a role in the degradation of mRNA (31). Some years ago, it was noticed that the degradation of mRNA or mRNA fragments by exonucleases is reduced when PAP I is absent in the cell (32,33).…”

Section: Cofactors In Rna Degradationmentioning

confidence: 99%

Degradation of mRNA in Escherichia coli

Jain

2002

IUBMB Life

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SummaryDegradation of messenger RNAs (mRNAs) is a universal process that occurs in every cell and has important implications for nucleotide metabolism and gene expression. One organism in which mRNA degradation has been thoroughly studied is the bacterium Escherichia coli (E. coli). In this review I describe what is presently known about the different processes involved in the conversion of mRNAs from high molecular weight species to mononucleotides in E. coli. The ribonucleases and accessory factors involved in mRNA degradation, and features on mRNAs that make them resistant or sensitive to degradation will also be described. At the conclusion of this review, some of the anticipated directions of future research on this topic will be discussed.

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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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POLYADENYLATION OF mRNA IN PROKARYOTES

Cited by 207 publications

References 105 publications

Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases

Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases

Degradation of mRNA in Escherichia coli

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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