Exoribonuclease superfamilies: structural analysis and phylogenetic distribution

Zuo, Y.; Deutscher, Murray P.

doi:10.1093/nar/29.5.1017

Cited by 458 publications

(509 citation statements)

References 54 publications

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“…The amino acid sequences of PNPases from bacteria, as well as from the nuclear genomes of plants and mammals, display a high level of homology and feature similar structures comprised of five motifs (Figures 1 and 2) [12,[24][25][26][27][28]. The protein is composed of two domains that are related to the RNase PH enzyme.…”

Section: Similar Structure Of the Rnase Ph Pnpase And Exosome Complexesmentioning

confidence: 99%

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

2007

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The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation machine which exonucleolytically degrades RNA from 3¢ to 5¢. In prokaryotes and in eukaryotic organelles, a trimeric complex of PNPase forms a circular doughnutshaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome. In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that is responsible for 3¢ to 5¢ exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase.

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Section: Similar Structure Of the Rnase Ph Pnpase And Exosome Complexesmentioning

confidence: 99%

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

2007

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“…Endonucleolytic cleavage of mRNAs generates mRNA fragments with new 3 and 5 ends that can serve as substrates for exo-ribonucleases. E. coli does not contain any 5 to 3 exonucleases, but contains at least eight 3 to 5 exonucleases (20). Two of these, PNPase and RNase II, have a role in the processing of RNA fragments generated by endonucleolytic cleavage (Fig.…”

Section: Initiation Of 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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“…However, the biochemical and physiological functions of CAF1 proteins are not clearly established. CAF1 proteins belong to the DEDDh subgroup of the DEDD family of nucleases, which requires three aspartates (D), a glutamate (E), and a nearby histidine for activity (DEDDh) [17,18]. Although the yeast CAF1 shows deadenylase activity in vitro [17,19], the role of this activity in vivo is unclear.…”

Section: Introductionmentioning

confidence: 99%

The Arabidopsis homologs of CCR4-associated factor 1 show mRNA deadenylation activity and play a role in plant defence responses

Liang

Liu

et al. 2008

Cell Res

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Messenger RNA (mRNA) turnover in eukaryotic cells begins with shortening of the poly (A) tail at the 3′ end, a process called deadenylation. In yeast, the deadenylation reaction is predominantly mediated by CCR4 and CCR4-associated factor 1 (CAF1), two components of the well-characterised protein complex named CCR4-NOT. We report here that AtCAF1a and AtCAF1b, putative Arabidopsis homologs of the yeast CAF1 gene, partially complement the growth defect of the yeast caf1 mutant in the presence of caffeine or at high temperatures. The expression of AtCAF1a and AtCAF1b is induced by multiple stress-related hormones and stimuli. Both AtCAF1a and AtCAF1b show deadenylation activity in vitro and point mutations in the predicted active sites disrupt this activity. T-DNA insertion mutants disrupting the expression of AtCAF1a and/or AtCAF1b are defective in deadenylation of stress-related mRNAs, indicating that the two AtCAF1 proteins are involved in regulated mRNA deadenylation in vivo. Interestingly, the single and double mutants of AtCAF1a and AtCAF1b show reduced expression of pathogenesis-related (PR) genes PR1 and PR2 and are more susceptible to Pseudomonas syringae pv tomato DC3000 (Pst DC3000) infection, whereas transgenic plants over-expressing AtCAF1a show elevated expression of PR1 and PR2 and increased resistance to the same pathogen. Our results suggest roles of the AtCAF1 proteins in regulated mRNA deadenylation and defence responses to pathogen infections.

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Exoribonuclease superfamilies: structural analysis and phylogenetic distribution

Cited by 458 publications

References 54 publications

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

Degradation of mRNA in Escherichia coli

The Arabidopsis homologs of CCR4-associated factor 1 show mRNA deadenylation activity and play a role in plant defence responses

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