RNA-splicing endonuclease structure and function

Calvin, Kate; Li, Hong

doi:10.1007/s00018-008-7393-y

Cited by 82 publications

(95 citation statements)

References 54 publications

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“…The G-rich loop is located immediately above the putative catalytic triad and may facilitate the placement of CRISPR repeat RNA substrates. Consistent with the corresponding predicted general acid-base catalytic mechanism (proposed for the splicing endonuclease) (Calvin and Li 2008), PfCas6 does not require divalent metals and like other metal-independent nucleases cleaves on the 5Ј side of the phosphodiester bond, likely generating 5Ј hydroxyl (OH) and 2Ј, 3Ј cyclic phosphate RNA end groups (Fig. 7).…”

Section: Cas6 Generates Prokaryotic Sirnas Genes and Development 3491supporting

confidence: 81%

“…6B). We suggest that these three residues form a catalytic triad for RNA cleavage similar to that of the tRNA intron splicing endonuclease (Calvin and Li 2008). The G-rich loop is located immediately above the putative catalytic triad and may facilitate the placement of CRISPR repeat RNA substrates.…”

Section: Cas6 Generates Prokaryotic Sirnas Genes and Development 3491mentioning

confidence: 91%

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Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

Carte

Wang²,

Li³

et al. 2008

Genes Dev.

511

561

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An RNA-based gene silencing pathway that protects bacteria and archaea from viruses and other genome invaders is hypothesized to arise from guide RNAs encoded by CRISPR loci and proteins encoded by the cas genes. CRISPR loci contain multiple short invader-derived sequences separated by short repeats. The presence of virus-specific sequences within CRISPR loci of prokaryotic genomes confers resistance against corresponding viruses. The CRISPR loci are transcribed as long RNAs that must be processed to smaller guide RNAs. Here we identified Pyrococcus furiosus Cas6 as a novel endoribonuclease that cleaves CRISPR RNAs within the repeat sequences to release individual invader targeting RNAs. Cas6 interacts with a specific sequence motif in the 5 region of the CRISPR repeat element and cleaves at a defined site within the 3 region of the repeat. The 1.8 angstrom crystal structure of the enzyme reveals two ferredoxin-like folds that are also found in other RNA-binding proteins. The predicted active site of the enzyme is similar to that of tRNA splicing endonucleases, and concordantly, Cas6 activity is metal-independent. cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea.[Keywords: CRISPR; Cas; endoribonuclease; RNA processing; Dicer; RNAi] Supplemental material is available at http://www.genesdev.org.

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Section: Cas6 Generates Prokaryotic Sirnas Genes and Development 3491supporting

confidence: 81%

Section: Cas6 Generates Prokaryotic Sirnas Genes and Development 3491mentioning

confidence: 91%

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

Carte

Wang²,

Li³

et al. 2008

Genes Dev.

511

561

View full text Add to dashboard Cite

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“…Because of this independence, the intron in archaeal pre-tRNAs can be located in different positions relative to the mature domain. Several archaeal pretRNAs contain relaxed forms of the BHB motif, one being the bulge-helix-loop, consisting of a single 3-nt bulge and an internal loop separated from the bulge by a 4-bp helix (17-19).Three categories of tRNA splicing endonucleases have been described and characterized in Archaea (17,18,20) : a heterotetrameric (α 2 β 2 ) enzyme in the Crenarchaeota, a homodimeric (α 0 2 ) and homotetrameric (α 4 ) enzymes in the Euryarchaeota. Most introns located at noncanonical positions have been found in crenarchaeal genomes that encode heterotetrameric enzymes whereas a few others have been observed in the Euryarchaeota whose genomes encode homotetrameric enzymes (12).…”

mentioning

confidence: 99%

“…Three categories of tRNA splicing endonucleases have been described and characterized in Archaea (17,18,20) : a heterotetrameric (α 2 β 2 ) enzyme in the Crenarchaeota, a homodimeric (α 0 2 ) and homotetrameric (α 4 ) enzymes in the Euryarchaeota. Most introns located at noncanonical positions have been found in crenarchaeal genomes that encode heterotetrameric enzymes whereas a few others have been observed in the Euryarchaeota whose genomes encode homotetrameric enzymes (12).…”

mentioning

confidence: 99%

Evolution of introns in the archaeal world

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2011

Proc. Natl. Acad. Sci. U.S.A.

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The self-splicing group I introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions. They require RNA binding proteins to act as chaperones to correctly fold the RNA into an active intermediate structure in vivo. Pre-tRNA introns in Bacteria and in higher eukaryote plastids are typical examples of self-splicing group I introns. By contrast, two striking features characterize RNA splicing in the archaeal world. First, self-splicing group I introns cannot be found, to this date, in that kingdom. Second, the RNA splicing scenario in Archaea is uniform: All introns, whether in pre-tRNA or elsewhere, are removed by tRNA splicing endonucleases. We suggest that in Archaea, the protein recruited for splicing is the preexisting tRNA splicing endonuclease and that this enzyme, together with the ligase, takes over the task of intron removal in a more efficient fashion than the ribozyme. The extinction of group I introns in Archaea would then be a consequence of recruitment of the tRNA splicing endonuclease. We deal here with comparative genome analysis, focusing specifically on the integration of introns into genes coding for 23S rRNA molecules, and how this newly acquired intron has to be removed to regenerate a functional RNA molecule. We show that all known oligomeric structures of the endonuclease can recognize and cleave a ribosomal intron, even when the endonuclease derives from a strain lacking rRNA introns. The persistance of group I introns in mitochondria and chloroplasts would be explained by the inaccessibility of these introns to the endonuclease. molecular evolution | RNA-protein interactions I n bacterial, bacteriophage, archaeal, eukaryotic, and organelle genomes, RNAs of very different function (tRNAs, rRNAs, and mRNAs) often contain introns. The correct removal of the introns has been shown to proceed by mechanisms that fall into four classes.1. Group I self-splicing introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions involving an external guanosine-5′-triphosphate (GTP). For example, pre-tRNA introns in bacteria and in higher eukaryote plastids are self-splicing group I introns. They fold into ribozymally active tertiary structures and, in several cases, contain genes coding for maturase and reverse transcriptase (1, 2). 2. Group II self-splicing introns, and their sibling group III introns, are also autocatalytically removed, but the excision does not require free GTP, and the reaction involves the formation of an intermediate lariat (3). 3. Nuclear pre-mRNA introns in eukaryotes are removed by the spliceosome (4, 5), postulated to have evolved from the group II self-splicing introns on the basis of the formation of a lariat intermediate, and of the conserved similarities of the small nuclear ribonucleoproteins U6/U2 RNA moieties with domain V of group II ribozymes (6-11). 4. The pre-tRNA intron excision mechanism in Eukaryotes is shared with Archaea. In Eukarya, tRNA introns are small and they invariab...

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“…In outline, the 59 ends of tRNAs are processed by RNase P (Frank and Pace 1998;Xiao et al 2002), and the 39 ends are processed by RNase Z in all domains of life (Schiffer et al 2002). Introns in pre-tRNAs are removed by splicing endonucleases (Tocchini-Valentini et al 2005;Calvin and Li 2008). The archaeal endonuclease that removes tRNA introns is also involved in rRNA processing (Tang et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii

Zhang

Olsen

2009

RNA

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Messenger RNA (mRNA) processing plays important roles in gene expression in all domains of life. A number of cases of mRNA cleavage have been documented in Archaea, but available data are fragmentary. We have examined RNAs present in Methanocaldococcus (Methanococcus) jannaschii for evidence of RNA processing upstream of protein-coding genes. Of 123 regions covered by the data, 31 were found to be processed, with 30 including a cleavage site 12-16 nucleotides upstream of the corresponding translation start site. Analyses with 39-RACE (rapid amplification of cDNA ends) and 59-RACE indicate that the processing is endonucleolytic. Analyses of the sequences surrounding the processing sites for functional sites, sequence motifs, or potential RNA secondary structure elements did not reveal any recurring features except for an AUG translation start codon and (in most cases) a ribosome binding site. These properties differ from those of all previously described mRNA processing systems. Our data suggest that the processing alters the representation of various genes in the RNA pool and therefore, may play a significant role in defining the balance of proteins in the cell.

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RNA-splicing endonuclease structure and function

Cited by 82 publications

References 54 publications

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

Evolution of introns in the archaeal world

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii

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