A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes

Bonocora, Richard P.; Shub, David A.

doi:10.1046/j.1365-2958.2001.02318.x

Cited by 3 publications

(6 citation statements)

References 19 publications

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“…As reported, 26 two specific I-BmoI-DNA complexes are observed; an upper complex (UC) that corresponds to interactions of full-length I-BmoI with substrate ( Figure 2(a), lanes 2, 3, 6, 7, 10 and 11), and a lower complex (LC) that corresponds to interactions of proteolyzed fragments of I-BmoI that retain DNA-binding activity (Figure 2(a), lanes 2-4, 6-8, and [10][11][12]. To demonstrate that the UC has catalytic activity, we supplemented binding reactions with 10 mM MgCl 2 to induce cleavage, and analyzed the reactions by native gel electrophoresis to detect double-strand cleavage by I-BmoI.…”

Section: Characterization Of I-bmoi-dna Complexesmentioning

confidence: 99%

“…In addition, a recently characterized homing endonuclease possesses a PE-(D/E)-XK motif characteristic of restriction enzymes. 11,12 Interestingly, the GIY-YIG domain (also termed the Uri domain) is found in a number of unrelated enzymes including type II restriction enzymes, 13,14 the UvrC nucleotide excision repair protein, [15][16][17] and reverse transcriptases of some retrotransposons. 18 Among the homing endonuclease families, the GIY-YIG enzymes are the least understood, particularly with respect to the mechanism of double-strand cleavage.…”

Section: Introductionmentioning

confidence: 99%

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Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI

Carter

Friedrich

Kleinstiver

et al. 2007

Journal of Molecular Biology

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Section: Characterization Of I-bmoi-dna Complexesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI

Carter

Friedrich

Kleinstiver

et al. 2007

Journal of Molecular Biology

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“…This single intron belongs to self-splicing group I harboring an open reading frame encoding specific DNA endonuclease (28). Because the degradation of spliced introns is very fast, and no polyadenylation of intron sequences has been analyzed yet, with the exception of one chloroplast intron that was characterized recently (29) to harbor a short poly(A) tail, we looked for polyadenylation of this transcript.…”

Section: Rna Polyadenylation In Synechocystis-mentioning

confidence: 99%

RNA Polyadenylation and Degradation in Cyanobacteria Are Similar to the Chloroplast but Different from Escherichia coli

Rott

Zipor

Portnoy

et al. 2003

Journal of Biological Chemistry

124

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The mechanism of RNA degradation in Escherichia coli involves endonucleolytic cleavage, polyadenylation of the cleavage product by poly(A) polymerase, and exonucleolytic degradation by the exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase II. The poly(A) tails are homogenous, containing only adenosines in most of the growth conditions. In the chloroplast, however, the same enzyme, PNPase, polyadenylates and degrades the RNA molecule; there is no equivalent for the E. coli poly(A) polymerase enzyme. Because cyanobacteria is a prokaryote believed to be related to the evolutionary ancestor of the chloroplast, we asked whether the molecular mechanism of RNA polyadenylation in the Synechocystis PCC6803 cyanobacteria is similar to that in E. coli or the chloroplast. We found that RNA polyadenylation in Synechocystis is similar to that in the chloroplast but different from E. coli. No poly(A) polymerase enzyme exists, and polyadenylation is performed by PNPase, resulting in heterogeneous poly(A)-rich tails. These heterogeneous tails were found in the amino acid coding region, the 5 and 3 untranslated regions of mRNAs, as well as in rRNA and the single intron located at the tRNA fmet . Furthermore, unlike E. coli, the inactivation of PNPase or RNase II genes caused lethality. Together, our results show that the RNA polyadenylation and degradation mechanisms in cyanobacteria and chloroplast are very similar to each other but different from E. coli.The molecular mechanism of RNA degradation in prokaryotes and organelles includes a series of sequential steps. The degradation starts with the initial endonucleolytic cleavage carried out primarily by the endoribonuclease E (RNase E). The cleavage products are then polyadenylated at their 3Ј ends by the poly(A) polymerase (PAP) 1 enzyme in Escherichia coli and the polynucleotide phosphorylase (PNPase) in the chloroplast. The polyadenylated molecules are then rapidly degraded exonucleolytically by PNPase and ribonuclease II (RNase II) (1-3). Finally, the remaining short oligoribonucleotides are degraded by the oligoribonuclease enzyme (4). Although the inhibition of polyadenylation in the chloroplast inhibited exonucleolytic degradation, implying that this is the only mechanism in the RNA degradation process, two RNA degradation mechanisms, a polyadenylation-dependent and a polyadenylation-independent one, were suggested to take place in E. coli (5, 6). Polyadenylation in E. coli is carried out primarily by PAP (7). Also in this bacterium, the RNase E enzyme, part of the PNPase population, an RNA helicase, some RNA molecules, and the glycolytic enzyme enolase are associated in a high molecular weight complex called a degradosome (8).In the chloroplast, the photosynthetic organelle of the plant cell is believed to have an evolutionary prokaryotic origin; many characteristics of the gene expression system resemble those of bacteria. When the RNA degradation mechanism was analyzed in the chloroplast, it was found to be very similar to that of E. coli (1-3). However...

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“…Similarly, the LAGLIDADG fold has only been found in HEs. I-SspI is unique in that it supports the PD-(D/E)-XK fold, but recognizes a long site: 23 bp, of which the central 17 bp show particularly high specificity [95,97,99]. This target site is pseudopalindromic and encompasses the entire anticodon stem and loop of the tRNA fMet gene.…”

Section: The Pd-(d/e)xk Familymentioning

confidence: 99%

“…The first member of this family to be identified was I-Ssp6803I, or I-SspI for simplicity. It was the first example of a chromosomally encoded group I intron endonuclease in bacteria [95]. I-SspI is encoded by a selfsplicing intron in the tRNA fMet gene of Synechocystis PCC6803 [95,96].…”

Section: The Pd-(d/e)xk Familymentioning

confidence: 99%

Homing endonucleases: from basics to therapeutic applications

Marcaida

Muñoz

Blanco

et al. 2009

Cell. Mol. Life Sci.

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Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.

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A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes

Abstract: SummaryOpen reading frames (ORFs) are frequently inserted into group I self-splicing introns. These ORFs encode either maturases that are required for splicing of the intron or DNA endonucleases that promote intron mobility. A self-splicing intron in the tRNA fMet gene of

Cited by 3 publications

References 19 publications

Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI

Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI

RNA Polyadenylation and Degradation in Cyanobacteria Are Similar to the Chloroplast but Different from Escherichia coli

Homing endonucleases: from basics to therapeutic applications

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