Catalytically critical nucleotide in domain 5 of a group II intron.

Peebles, Craig L.; Zhang, Mincheng; Perlman, Philip S.; Franzen, James S.

doi:10.1073/pnas.92.10.4422

Cited by 86 publications

(101 citation statements)

References 13 publications

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“…The catalytic core of the spliceosome consists of a highly structured RNA network formed between U2, U6, and U5 snRNAs and the sites of chemistry in the pre-mRNA (Parker et al 1987;Wu and Manley 1989;Newman and Norman 1992;Kandels-Lewis and Seraphin 1993;Lesser and Guthrie 1993;Sontheimer and Steitz 1993). Mechanistic and structural similarities between the spliceosomal snRNAs and Group II autocatalytic introns strongly support the hypothesis that spliceosomal snRNA sequences are central to the catalysis of pre-mRNA splicing (Moore and Sharp 1993;Padgett et al 1994;Boulanger et al 1995;Peebles et al 1995;Sigel et al 2000;Villa et al 2002;Hilliker and Staley 2004). In particular an RNA complex between U2 and U6 snRNAs is believed to play a critical role in the catalytic core of the spliceosome, acting as a scaffold to juxtapose the reactive 5¢SS and BP sequences and to position a bound metal ion that is essential for splicing catalysis (Madhani and Guthrie 1992;Sun and Manley 1995;Yean et al 2000;Huppler et al 2002;Sashital et al 2004).…”

Section: Introductionmentioning

confidence: 72%

Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome

Turner¹,

Norman²,

Churcher³

et al. 2006

RNA

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Current models of the core of the spliceosome include a network of RNA-RNA interactions involving the pre-mRNA and the U2, U5, and U6 snRNAs. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor. However, the sequence of Prp8 is almost entirely novel, and it offers few clues to the molecular basis of Prp8-RNA interactions. We have used an innovative transposon-based strategy to establish that catalytic core RNAs make multiple contacts in the central region of Prp8, underscoring the intimate relationship between this protein and the catalytic center of the spliceosome. Our analysis of RNA interactions identifies a discrete, highly conserved region of Prp8 as a prime candidate for the role of cofactor for the spliceosome's RNA core.

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Section: Introductionmentioning

confidence: 72%

Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome

Turner¹,

Norman²,

Churcher³

et al. 2006

RNA

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“…Indeed, U814 is adjacent to the AGC ''triad'' of D5, which is among the most conserved and catalytically important regions of the intron (Chanfreau and Jacquier 1994;Boulanger et al 1995;Peebles et al 1995;Konforti et al 1998a), and which resembles a similar triad within the spliceosomal U6 snRNA (Madhani and Guthrie 1992;Hilliker and Staley 2004). The conservation and mutational sensitivity of the AGC triad has long led to the expectation that it is a central component of the intron active site.…”

Section: G1: a Novel Role In The First Step Of Splicingmentioning

confidence: 99%

“…Many studies have demonstrated the central importance of nucleotides in D5 (Chanfreau and Jacquier 1994;Peebles et al 1995;Abramovitz et al 1996;Boudvillain et al 2000). A remaining mystery, however, is the role of functionalities in the essential 2-nucleotide (nt) bulge that separates the upper and lower stems of the D5 hairpin.…”

Section: Introductionmentioning

confidence: 99%

Three essential and conserved regions of the group II intron are proximal to the 5′-splice site

Lencastre¹,

Pyle²

2007

RNA

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Despite the central role of group II introns in eukaryotic gene expression and their importance as biophysical and evolutionary model systems, group II intron tertiary structure is not well understood. In order to characterize the architectural organization of intron ai5g, we incorporated the photoreactive nucleotides s 4 U and s 6 dG at specific locations within the intron core and monitored the formation of cross-links in folded complexes. The resulting data reveal the locations for many of the most conserved, catalytically important regions of the intron (i.e., the J2/3 linker region, the IC1(i-ii) bulge in domain 1, the bulge of D5, and the 59-splice site), showing that all of these elements are closely colocalized. In addition, we show by nucleotide analog interference mapping (NAIM) that a specific functional group in J2/3 plays a role in first-step catalysis, which is consistent with its apparent proximity to other first-step components. These results extend our understanding of active-site architecture during the first step of group II intron self-splicing and they provide a structural basis for spliceosomal comparison.

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“…Domains 5 and 6 (and 1) of yeast group II introns have been shown to be essential for splicing (Jarrell et al, 1988% Boulanger et al, 1995Peebles et al, 1995) and evidence has been obtained supporting the view that an edit in domain 6 of the Oenothera c/d intron is necessary for intron excission (Borner et al, 1995). We generated cDNAs from primers antisense to the exon downstream from each maize nadl intron.…”

Section: Translation Initiation Of Mat-r Transcripts (Alsomentioning

confidence: 73%

The plant mitochondrial mat-r gene/nad1 gene complex

Wolstenhome¹

1996

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Abstract' s.We have completed sequencing segments of the maize mitochondrial (ret) DNA that contains all five of the exons (A-E) of the gene (nadl) for subunit I of the respiratory chain NADH dehydrogenase. Analysis of these sequences indicates that exons B and C are joined by a continuous group 11intron, but the remaining exons are associated with partial group H introns and are encoded at widely separated locations in the maize mtDNA molecule. Production of mature nadl gene transcripts is postulated to involve both cis-splicing of the b/c intron and trans-splicing of each of the other three introns. In the partial We intron upstream from exon E is encoded a gene (mat-r) for a protein related to fungal maturases. From comparison of the maize split d/e intron, and the soybean continuous d/e intron it was found that the location at which the maize dle intron underwent rearrangement is marked by a repeated 8 nt sequence on each intron half. Interestingly, there is a 9 or 10 nt repeat on each of the two halves of the a/b and c/d introns. We have shown that mature transcripts of the maize nadl gene contain 23 edited (CŨ ) nucleotides and that transcripts of maize and soybean mat-r genes contain 15 and 14 C~U edits, respectively. The majority of edits in nadl transcripts result in amino acid replacements that increase similarity between the maize NAD1 protein and NAD1 proteins of other plant species and of animal species. Edits in mat-r transcripts result in an increase in amino acid similarity of the maize and soybean MAT-R proteins to each other, and of each of these proteins to fungal and bryophyte maturases.We found that the intron between exons b and c is not edited. Edits in other introns are rare and have so far been detected only in domain 6 regions. Unspliced transcripts of exon C and of exon E are partially edited, confirming that editing can precede both cis-and trans-splicing.From data obtained using PCR and sequencing we have shown that transcripts containing all possible exon combinations exist in maize mitochondria. This supports the view that splicing of maize nadl exons can occur in any order, Wd that mans-splicing of exons can occur in advance of cis-splicing of exons B and C. Also, we obtained evidence that the relative rates of splicing are greater for B+C and C+D exons, than for A+B and D+E exons.Attempts made to induce cis-splicing in vitro of the B and C exons by excision of the continuous intron between them have been unsuccessful.Comparisons of nadl, nad2 and nad5 intron sequences have been made to gain information on intron interrelationships. DISCLAIMERPortions of this document may be illegible in electronic image products.Images are produced from the best available original document. * .A pseudo-mat-r gene was detected (using degenerate primers and PCR reactions), sequenced, and mapped on the maize (normal) mtDNA molecule. : 7-10-92 to 7-9-96 Objectives of the Proposed WorkThe major objective for the work outline at the time of the original application was to learn about the structur...

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Catalytically critical nucleotide in domain 5 of a group II intron.

Cited by 86 publications

References 13 publications

Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome

Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome

Three essential and conserved regions of the group II intron are proximal to the 5′-splice site

The plant mitochondrial mat-r gene/nad1 gene complex

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