Identification of a Second Poly(A) Polymerase in Escherichia coli

Kalapos, Miklös Péter; Cao, Gong-Jie; Kushner, Sidney R.; Sarkar, Nirmal Kumar

doi:10.1006/bbrc.1994.1067

Cited by 36 publications

(31 citation statements)

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“…Because it is not yet possible to distinguish Class II CCA-adding enzymes from poly(A) polymerases based solely on sequence analysis (38), we included only those enzymes whose enzymatic activities had been experimentally demonstrated or could be confidently assumed. These are the H. influenzae CCAadding enzyme and poly(A) polymerase, both of which are almost identical to their experimentally characterized E. coli counterparts (21,23,39), the B. subtilis and M. leprae CCA-adding enzymes (38), and the CCA-adding enzyme from M. tuberculosis, which is almost identical to M. leprae enzyme (31). A multiple alignment of the 25-kDa core regions of these Class II enzymes, including the active site signature, is shown in Fig.…”

Section: A Phylogeny Of Eubacterial Cca- Cc- and A-adding Enzymes Amentioning

confidence: 71%

Closely Related CC- and A-adding Enzymes Collaborate to Construct and Repair the 3′-Terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans

Tomita¹,

Weiner

2002

Journal of Biological Chemistry

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The 3-terminal CCA sequence of tRNA is faithfully constructed and repaired by the CCA-adding enzyme (ATP(CTP):tRNA nucleotidyltransferase) using CTP and ATP as substrates but no nucleic acid template. Until recently, all CCA-adding enzymes from all three kingdoms appeared to be composed of a single kind of polypeptide with dual specificity for adding both CTP and ATP; however, we recently found that in Aquifex aeolicus, which lies near the deepest root of the eubacterial 16 S rRNA-based phylogenetic tree, CCA addition represents a collaboration between closely related CCadding and A-adding enzymes (Tomita, K. and Weiner, A. M. (2001) Science 294, 1334 -1336). Here we show that in Synechocystis sp. and Deinococcus radiodurans, as in A. aeolicus, CCA is added by homologous CC-and A-adding enzymes. We also find that the eubacterial CCA-, CC-, and A-adding enzymes, as well as the related eubacterial poly(A) polymerases, each fall into phylogenetically distinct groups derived from a common ancestor. Intriguingly, the Thermatoga maritima CCA-adding enzyme groups with the A-adding enzymes, suggesting that these distinct tRNA nucleotidyltransferase activities can intraconvert over evolutionary time.The 3Ј-terminal CCA sequence (positions 74 -76 in the standard cloverleaf representation) is universally present in the tRNAs of all organisms (1) and is important for many aspects of gene expression. The CCA terminus is required for the aminoacylation of tRNA (2, 3) and for translation on the ribosome where the CCA sequences of the aminoacyl-and peptidyl-tRNA pair with the large ribosomal RNA near the peptidyltransferase center (4 -6). In eubacteria, the CCA sequence is required for the efficient maturation of the 5Ј-end of tRNA by RNase P (7,8). In eukaryotes, the CCA sequence serves as an antideterminant to block 3Ј-exonuclease activity (9), and it is essential for the export of mature tRNA from the nucleus to the cytoplasm (10, 11).The CCA-adding enzyme (ATP(CTP):tRNA nucleotidyltransferase) builds and repairs the 3Ј-terminal CCA sequence of all tRNAs (12). CCA-adding activity has been identified in all three kingdoms, suggesting conservation of function and perhaps structure throughout evolution (13). CCA-adding activity is essential in some eubacteria as well as in all archaea and eukaryotes where some or all tRNA genes do not encode CCA (14). Yet, even in organisms such as Escherichia coli where all tRNA genes do encode CCA, CCA-adding activity confers a substantial selective advantage, probably by repairing tRNAs that have been subject to errant nucleolytic attack (15).The CCA-adding enzyme belongs to the nucleotidyltransferase (NTR) 1 family, a large protein superfamily that encompasses template-dependent DNA polymerases (DNA polymerase ␤) and template-independent RNA and DNA polymerases (poly(A) polymerase, terminal deoxynucleotidyltransferase, and CCA-adding enzymes) as well as metabolic regulators (GlnB uridylyltransferase, glutamine synthase adenylyltransferase) and antibiotic resistance factors (kanamycin nucleo...

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Section: A Phylogeny Of Eubacterial Cca- Cc- and A-adding Enzymes Amentioning

confidence: 71%

Closely Related CC- and A-adding Enzymes Collaborate to Construct and Repair the 3′-Terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans

Tomita¹,

Weiner

2002

Journal of Biological Chemistry

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“…In addition to the PAP I used in this work, at least one more PAP, the product of the f310 gene, has been identified in E.coli cells, and named PAP II (23). These two enzymes seem to be dispensable, since even when one of the genes is inactivated the cells are still viable (23).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, it shows significant amino acid sequence homology to tRNA nucleotidyl transferase, a CCA-adding enzyme (18)(19)(20)(21)(22). Another poly(A) polymerase enzyme, PAP II, has been identified in E.coli, but its role in RNA metabolism remains to be elucidated (23). In contrast to the mechanism in eukaryotes, E.coli polyadenylation apparently does not depend on recognition sequences and does not require a multiprotein complex for activity (2).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence

Yehudai‐Resheff

Schuster

2000

Nucleic Acids Research

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Polyadenylation of RNA molecules in bacteria and chloroplasts has been implicated as part of the RNA degradation pathway. The polyadenylation reaction is performed in Escherichia coli mainly by the enzyme poly(A) polymerase I (PAP I). In order to understand the molecular mechanism of RNA polyadenylation in bacteria, we characterized the biochemical properties of this reaction in vitro using the purified enzyme. Unlike the PAP from yeast nucleus, which is specific for ATP, E.coli PAP I can use all four nucleotide triphosphates as substrates for addition of long ribohomopolymers to RNA. PAP I displays a high binding activity to poly(U), poly(C) and poly(A) ribohomopolymers, but not to poly(G). The 3′-ends of most of the mRNA molecules in bacteria are characterized by a stem-loop structure. We show here that in vitro PAP I activity is inhibited by a stem-loop structure. A tail of two to six nucleotides located 3′ to the stem-loop structure is sufficient to overcome this inhibition. These results suggest that the stem-loop structure located in most of the mRNA 3′-ends may function as an inhibitor of polyadenylation and degradation of the corresponding RNA molecule. However, RNA 3′-ends produced by endonucleolytic cleavage by RNase E in single-strand regions of mRNA molecules may serve as efficient substrates for polyadenylation that direct these molecules for rapid exonucleolytic degradation.

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“…The major polyadenylating enzyme, designated poly(A) polymerase I (PAP I, EC 2.7.7.19), was originally identified by virtue of its role in regulating plasmid copy number, and is a product of the pcnB gene (Cao & Sarkar, 1992;He et al, 1993). Mutants of E. coli lacking PAP I still retain the ability to polyadenylate RNAs, indicating that there is at least one other polyadenylating enzyme in those cells (Kalapos et al, 1994). That enzyme does not appear to be the product of the f310 gene designated initially as PAP II, since overexpression of f310 led neither to an increase in PAP activity in the relevant cells nor to an increase in the level of RNA polyadenylation (Mohanty & Kushner, 1999a).…”

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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Identification of a Second Poly(A) Polymerase in Escherichia coli

Cited by 36 publications

References 0 publications

Closely Related CC- and A-adding Enzymes Collaborate to Construct and Repair the 3′-Terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans

Closely Related CC- and A-adding Enzymes Collaborate to Construct and Repair the 3′-Terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans

Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence

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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