Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.8 (polynucleotide phosphorylase)
723 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Plant mitochondrial genomes are extraordinarily large and complex compared to their animal counterparts, due to the presence of large noncoding regions. Multiple promoters are common for plant mitochondrial genes, and transcription exhibits little or no modulation. Mature functional RNAs are produced through various posttranscriptional processes, and control of RNA stability has a major impact on RNA abundance. This control involves polyadenylation which targets RNA for degradation by polynucleotide phosphorylase (PNPase). Here, we have analyzed polyadenylated RNA fragments from Arabidopsis plants down-regulated for PNPase (PNP- plants). Because of their polyadenylated status and the accumulation of the corresponding RNA in PNP- versus wild-type plants, these sequences represent mitochondrial RNA degradation tags. Analysis of these tags revealed that PNPase is involved in degrading rRNA and tRNA maturation by-products but also RNA transcribed from regions that are in some cases highly expressed although lacking known functional genes. Some of these transcripts, such as RNA containing chimeric open reading frames created by recombination or antisense RNA transcribed on the opposite strand of a known gene, may present potential detrimental effects to mitochondrial function. Taken together, our data show that the relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and PNPase.
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PMID:Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase. 1653 27

Adaptation of Escherichia coli at low temperature implicates a drastic reprogramming of gene expression patterns. Mechanisms operating downstream of transcription initiation, such as control of transcription termination, mRNA stability and translatability, play a major role in controlling gene expression in the cold acclimation phase. It was previously shown that Rho-dependent transcription termination within pnp, the gene encoding polynucleotide phosphorylase (PNPase), was suppressed in pnp nonsense mutants, whereas it was restored by complementation with wild type allele. Using a tRNA gene as a reporter and the strong Rho-dependent transcription terminator t ( imm ) of bacteriophage P4 as a tester, here we show that specific sites in the 5'-untranslated region of pnp mRNA are required for PNPase-sensitive cold-induced suppression of Rho-dependent transcription termination. We suggest that suppression of Rho-dependent transcription termination within pnp and its restoration by PNPase is an autogenous regulatory circuit that modulates pnp expression during cold acclimation.
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PMID:Autogenous regulation of Escherichia coli polynucleotide phosphorylase during cold acclimation by transcription termination and antitermination. 1738 64

The first step in the current model for the processing and maturation of mono- and polycistronic tRNA precursors in Escherichia coli involves initial cleavages by RNase E 1-3 nt downstream of each chromosomally encoded CCA determinant. Subsequently, each mature 5' terminus is generated by single RNase P cleavage, while the 3' terminus undergoes exonucleolytic processing by a combination of 3' --> 5' exonucleases. Here we describe for the first time a previously unidentified pathway for the maturation of tRNAs in polycistronic operons (valV valW and leuQ leuP leuV) where the processing of the primary transcripts is independent of RNase E. Rather, RNase P cleavages separate the individual tRNA precursors with the concomitant formation of their mature 5' termini. Furthermore, both polynucleotide phosphorylase (PNPase) and RNase II are required for the removal of the 3' Rho-dependent terminator sequences. Our data indicate that RNase P substrate recognition is more complex than previously envisioned.
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PMID:Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. 1798 36

Transfer-messenger RNA (tmRNA, 10Sa RNA, ssrA) is bacterial RNA having both tRNA and mRNA properties and playing an essential role in recycling of 70S ribosomes that are stalled on defective mRNA. The trans-translational system is thought to play a crucial role in bacterial survival under adverse conditions. Streptomycetes are Gram-positive soil bacteria exposed to various physical and chemical stresses that activate specialized responses such as synthesis of antibiotics and morphological differentiation. Comparative sequence analysis of ssrA genes of streptomycetes revealed the most significant differences in the central parts of tag-reading frames, in the stop codons and in the 15-34 nucleotide sequences following stop codons. A major challenge in understanding the interactions that control the function of tmRNA is the definition of protein interactions. Proteins from various phases of development of Streptomyces aureofaciens associated with tmRNA were analyzed. Using affinity chromatography on tmRNA-Sepharose and photo cross-linking experiments with [(32)P]labeled tmRNA seven proteins, the beta and beta'-subunits of DNA dependent RNA polymerase, polyribonucleotide nucleotidyltransferase (PNPase), ribosomal protein SS1, ATP-binding cassette transporters, elongation factor Tu, and SmpB were identified among the proteins associated with tmRNA of S. aureofaciens. We examined the functional role of ribosomal protein SS1 in a defined in vitro trans-translation system. Our data show that the protein SS1 that structurally differs from S1 of Escherichia coli is required for translation of the tmRNA tag-reading frame.
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PMID:SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation. 1830 77

Polyadenylation in animal mitochondria is very unique. Unlike other systems, polyadenylation is needed to generate UAA stop codons that are not encoded in mitochondrial (mt) DNA. In some cases, polyadenylation is required for the mt tRNA maturation by editing of its 3' termini. Furthermore, recent studies on human mt poly(A) polymerase (PAP) and PNPase provide new insights and questions for the regulatory mechanism and functional role of polyadenylation in human mitochondria.
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PMID:Polyadenylation in mammalian mitochondria: insights from recent studies. 1831 63

RNA degradation is a major process controlling RNA levels and plays a central role in cell metabolism. From the labile messenger RNA to the more stable noncoding RNAs (mostly rRNA and tRNA, but also the expanding class of small regulatory RNAs) all molecules are eventually degraded. Elimination of superfluous transcripts includes RNAs whose expression is no longer required, but also the removal of defective RNAs. Consequently, RNA degradation is an inherent step in RNA quality control mechanisms. Furthermore, it contributes to the recycling of the nucleotide pool in the cell. Escherichia coli has eight 3'-5' exoribonucleases, which are involved in multiple RNA metabolic pathways. However, only four exoribonucleases appear to accomplish all RNA degradative activities: polynucleotide phosphorylase (PNPase), ribonuclease II (RNase II), RNase R, and oligoribonuclease. Here, we summarize the available information on the role of bacterial 3'-5' exoribonucleases in the degradation of different substrates, highlighting the most recent data that have contributed to the understanding of the diverse modes of operation of these degradative enzymes.
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PMID:The role of 3'-5' exoribonucleases in RNA degradation. 1921 73

The polyadenylation-stimulated RNA degradation pathway takes place in plant and algal organelles, yet the identities of the enzymes that catalyze the addition of the tails remain to be clarified. In a search for the enzymes responsible for adding poly(A) tails in Chlamydomonas and Arabidopsis organelles, reverse genetic and biochemical approaches were employed. The involvement of candidate enzymes including members of the nucleotidyltransferase (Ntr) family and polynucleotide phosphorylase (PNPase) was examined. For several of the analyzed nuclear-encoded proteins, mitochondrial localization was established and possible dual targeting to mitochondria and chloroplasts could be predicted. We found that certain members of the Ntr family, when expressed in bacteria, displayed poly(A) polymerase (PAP) activity and partially complemented an Escherichia coli strain lacking the endogenous PAP1 enzyme. Other Ntr proteins appeared to be specific for tRNA maturation. When the expression of PNPase was down-regulated by RNAi in Chlamydomonas, very few poly(A) tails were detected in chloroplasts for the atpB transcript, suggesting that this enzyme may be solely responsible for chloroplast polyadenylation activity in this species. Depletion of PNPase did not affect the number or sequence of mitochondrial mRNA poly(A) tails, where unexpectedly we found, in addition to polyadenylation, poly(U)-rich tails. Together, our results identify several Ntr-PAPs and PNPase in organelle polyadenylation, and reveal novel poly(U)-rich sequences in Chlamydomonas mitochondria.
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PMID:Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. 1930 54

The Gram-negative anaerobic pathogen Dichelobacter nodosus is the principal causative agent of footrot in sheep. The intA, intB and intC elements are mobile genetic elements which integrate into two tRNA genes downstream from csrA (formerly glpA) and pnpA in the D. nodosus chromosome. CsrA homologues act as global repressors of virulence in several bacterial pathogens, as does polynucleotide phosphorylase, the product of pnpA. We have proposed a model in which virulence in D. nodosus is controlled in part by the integration of genetic elements downstream from csrA and pnpA, altering the expression of these putative global regulators of virulence. We describe here a novel integrated genetic element, the intD element, which is 32kb in size and contains an integrase gene, intD, several genes related to genes on other integrated elements of D. nodosus, a type IV secretion system and a putative mobilisation region, suggesting that the intD element has a role in the transfer of other genetic elements. Most of the D. nodosus strains examined which contained the intD gene were benign, with intD integrated next to pnpA, supporting our previous observation that virulent strains of D. nodosus have the intA element next to pnpA.
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PMID:The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype. 1932 4

Here we report a unique processing pathway in Escherichia coli for tRNA(Leu5) in which the exoribonuclease polynucleotide phosphorylase (PNPase) removes the Rho-independent transcription terminator from the leuX transcript without requiring the RhlB RNA helicase. Our data demonstrate for the first time that PNPase can efficiently degrade an RNA substrate containing secondary structures in vivo. Furthermore, RNase P, an endoribonuclease that normally generates the mature 5'-ends of tRNAs, removes the leuX terminator inefficiently independent of PNPase activity. RNase P cleaves 4-7 nt downstream of the CCA determinant generating a substrate for RNase II, which removes an additional 3-4 nt. Subsequently, RNase T completes the 3' maturation process by removing the remaining 1-3 nt downstream of the CCA determinant. RNase E, G and Z are not involved in terminator removal. These results provide further evidence that the E. coli tRNA processing machinery is far more diverse than previously envisioned.
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PMID:Processing of the Escherichia coli leuX tRNA transcript, encoding tRNA(Leu5), requires either the 3'-->5' exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. 1990 95

Polyadenylation is a universal post-transcriptional modification involved in degradation and quality control of bacterial RNAs. In Escherichia coli, it is admitted that any accessible RNA 3' end can be tagged by a poly(A) tail for decay. However, we do not have yet an overall view of the population of polyadenylated molecules. The sampling of polyadenylated RNAs presented here demonstrates that rRNA fragments and tRNA precursors originating from the internal spacer regions of the rrn operons, in particular, rrnB are abundant poly(A) polymerase targets. Focused analysis showed that Glu tRNA precursors originating from the rrnB and rrnG transcripts exhibit long 3' trailers that are primarily removed by PNPase and to a lesser extent by RNase II and poly(A) polymerase. Moreover, 3' trimming by exoribonucleases precedes 5' end maturation by RNase P. Interestingly, characterization of RNA fragments that accumulate in a PNPase deficient strain showed that Glu tRNA precursors still harbouring the 5' leader can be degraded by a 3' to 5' quality control pathway involving poly(A) polymerase. This demonstrates that the surveillance of tRNA maturation described for a defective tRNA also applies to a wild-type tRNA.
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PMID:Search for poly(A) polymerase targets in E. coli reveals its implication in surveillance of Glu tRNA processing and degradation of stable RNAs. 2214 50


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