Identification of the coding region for a second poly(A) polymerase in Escherichia coli.

Cao, Gong-Jie; Pogliano, Joe; Sarkar, Nirmal Kumar

doi:10.1073/pnas.93.21.11580

Cited by 35 publications

(38 citation statements)

References 34 publications

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“…In this model, both poly(A) polymerase I and PNPase are essential, explaining why removal of either enzyme leads to slower growth. Whether poly(A) polymerase II, a recently discovered enzyme (25), has any role in this process is not known.…”

Section: Discussionmentioning

confidence: 99%

Functional Overlap of tRNA Nucleotidyltransferase, Poly(A) Polymerase I, and Polynucleotide Phosphorylase

Reuven

Zhou

Deutscher

1997

Journal of Biological Chemistry

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Repair of the 3-terminal -CCA sequence of tRNA generally requires the action of the enzyme tRNA nucleotidyltransferase. However, in Escherichia coli in the absence of this enzyme, a decreased level of tRNA end repair continues. To ascertain the enzymes responsible for this residual repair, mutant strains were constructed lacking tRNA nucleotidyltransferase and other enzymes potentially involved in the process, poly(A) polymerase I and polynucleotide phosphorylase (PNPase). Strains lacking tRNA nucleotidyltransferase and either one of the other enzymes displayed decreased growth rates and increased levels of defective tRNA compared with the single cca mutant. Triple mutants lacking all three enzymes grew very slowly, had even more defective tRNA, and were devoid of activity incorporating AMP into tRNA-C-C. Overexpression of poly(A) polymerase I, but not PNPase, partially compensated for the absence of tRNA nucleotidyltransferase. These data show that poly(A) polymerase I and PNPase participate in the end repair process and are required to maintain functional tRNA levels when tRNA nucleotidyltransferase is absent.

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Section: Discussionmentioning

confidence: 99%

Functional Overlap of tRNA Nucleotidyltransferase, Poly(A) Polymerase I, and Polynucleotide Phosphorylase

Reuven

Zhou

Deutscher

1997

Journal of Biological Chemistry

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“…Poly(A) polymerases have been isolated from a number of sources, and conserved motifs are beginning to emerge (5,6,10,12,24,25,29,33,40). Comparisons of the amino acid sequences of poly(A) polymerases from the poxviruses, yeast, plants, and mammals have not provided a strong match to any of the baculovirus RNA polymerase subunits.…”

Section: Discussionmentioning

confidence: 99%

3′-End Formation of Baculovirus Late RNAs

Jin

Guarino

2000

J Virol

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Baculovirus late RNAs are transcribed by a four-subunit RNA polymerase that is virus encoded. The late viral mRNAs are capped and polyadenylated, and we have previously shown that capping is mediated by the LEF-4 subunit of baculovirus RNA polymerase. Here we report studies undertaken to determine the mechanism of 3-end formation. A globin cleavage/polyadenylation signal, which was previously shown to direct 3-end formation of viral RNAs in vivo, was cloned into a baculovirus transcription template. In vitro assays with purified baculovirus RNA polymerase revealed that 3 ends were formed not by a cleavage mechanism but rather by termination after transcription of a T-rich region of the globin sequence. Terminated RNAs were released from ternary complexes and were subsequently polyadenylated. Mutational analyses indicated that the T-rich sequence was essential for termination and polyadenylation, but the poly(A) signal and the GT-rich region of the globin polyadenylation/cleavage signal were not required. Termination was not dependent on ATP hydrolysis, indicating a slippage mechanism.mRNA 3Ј-end formation is a complicated process that requires protein-nucleic acid and protein-protein interactions. The 3Ј ends of most eukaryotic RNA polymerase II transcripts are produced by a coupled cleavage/polyadenylation reaction that requires multiple factors (reviewed in references 8, 22, and 43). The processing machinery is recruited to transcription complexes by TFIID (9) and is targeted to the phosphorylated carboxy-terminal domain (CTD) of RNA polymerase II during transcription elongation (27). Recent studies have shown that RNA polymerase II itself is an essential factor in the polyadenylation step (20).Transcription termination by RNA polymerase II occurs downstream of the cleavage site and is less well understood. Termination is defined as the process of disrupting the transcription ternary complex, in which the RNA polymerases cease their elongation function, the nascent transcripts are released, and the RNA polymerases step off from the DNA templates. Disassembly of an RNA polymerase ternary complex is mediated by termination sequences that are recognized by the RNA polymerase or by termination factors (reviewed in references 37 and 39). Failure of the elongating polymerase to stop transcription before reaching an adjacent gene can lead to a reduction in the expression of the downstream gene by destabilizing the assembly of transcription initiation factors on the adjacent promoter (3,15,16,19,31). This is especially important to the gene expression programs of compact genomes, such as yeast and viruses, which have short intergenic sequences.Baculoviruses are large double-stranded DNA viruses that have been extensively used as protein expression vectors. The genomes of several baculovirus species have been sequenced and shown to be highly compressed (1,2,14). Viral gene expression is regulated in a temporal pattern (4, 11, 30) in which immediate-and delayed-early genes are transcribed by host cell RNA polymerase II,...

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“…The major poly(A) polymerase activity of E. coli, PAPI, is encoded by the pcnB gene (28). A residual poly(A) polymerase activity detectable in E. coli pcnB mutants, called PAPII, was reported to be encoded by the f310 gene (27), but this was subsequently convincingly shown not to be the case (156), and the activity has since been attributed to PNPase (157). Thus, PNPase appears to function as both a 3Ј-to-5Ј exonuclease and, in the reverse reaction, a poly(A) polymerase.…”

Section: Polyadenylationmentioning

confidence: 99%

RNA Processing and Degradation inBacillus subtilis

Condon

2003

Microbiol Mol Biol Rev

141

134

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This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5′ end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5′ end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5′ end can have very long half-lives even if the RNA is not protected by translation

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Identification of the coding region for a second poly(A) polymerase in Escherichia coli.

Cited by 35 publications

References 34 publications

Functional Overlap of tRNA Nucleotidyltransferase, Poly(A) Polymerase I, and Polynucleotide Phosphorylase

Functional Overlap of tRNA Nucleotidyltransferase, Poly(A) Polymerase I, and Polynucleotide Phosphorylase

3′-End Formation of Baculovirus Late RNAs

RNA Processing and Degradation inBacillus subtilis

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