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A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA.

Kolev NG, Hartland EI, Huber PW - Nucleic Acids Res. (2008)

Bottom Line: The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage.Analysis of sequences in the PolyA Cleavage Site and 3'-UTR Database (PACdb) revealed no particular bias in the frequency or distribution of the GAAA motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts.Nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.

ABSTRACT
The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs only in the presence of manganese or cadmium ions and proceeds optimally near 30 degrees C and physiological pH. The time course of cleavage in Vg1 mRNA best fits a two-step process in which both steps are first-order. In Vg1 mRNA, the ribozyme is positioned adjacent to a polyadenylation signal, but has no influence on translation of the mRNA in Xenopus oocytes. Putative GAAA ribozyme structures are also near polyadenylation sites in yeast and rat actin mRNAs. Analysis of sequences in the PolyA Cleavage Site and 3'-UTR Database (PACdb) revealed no particular bias in the frequency or distribution of the GAAA motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts. Nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mRNAs.

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Predicted base-pairing interactions between the HDE of histone mRNAs and U7 snRNAs. Selected histone mRNAs (top strand) and U7 snRNAs (bottom strand) are presented; only the region immediately flanking the Sm site (designated by a rectangle) of U7 is shown in each case. Adapted from ref. 41.
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Figure 7: Predicted base-pairing interactions between the HDE of histone mRNAs and U7 snRNAs. Selected histone mRNAs (top strand) and U7 snRNAs (bottom strand) are presented; only the region immediately flanking the Sm site (designated by a rectangle) of U7 is shown in each case. Adapted from ref. 41.

Mentions: The processing signal for histone mRNA also consists of two elements flanking the cleavage site: a conserved upstream hairpin and a purine-rich histone downstream element (HDE) (39). The 3′-end cleavage of histone mRNA requires base-pairing between the purine-rich HDE and the 5′-end of U7 snRNA (40). Dávila López and Samuelsson (41) have identified candidate U7 snRNAs genes in a greatly expanded number of organisms. In each instance, and others that we have investigated, an A/G-rich sequence in the HDE is paired with a U-rich sequence in U7 snRNA that, together, closely approximates the structure of the manganese ribozyme (Figure 7). Thus, it is plausible that this structure likewise evolved from a functional manganese ribozyme, thereby accounting for the observation that some factors are common to the 3′-end processing of both poly(A)+ and poly(A)– mRNAs.Figure 7.


A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA.

Kolev NG, Hartland EI, Huber PW - Nucleic Acids Res. (2008)

Predicted base-pairing interactions between the HDE of histone mRNAs and U7 snRNAs. Selected histone mRNAs (top strand) and U7 snRNAs (bottom strand) are presented; only the region immediately flanking the Sm site (designated by a rectangle) of U7 is shown in each case. Adapted from ref. 41.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553595&req=5

Figure 7: Predicted base-pairing interactions between the HDE of histone mRNAs and U7 snRNAs. Selected histone mRNAs (top strand) and U7 snRNAs (bottom strand) are presented; only the region immediately flanking the Sm site (designated by a rectangle) of U7 is shown in each case. Adapted from ref. 41.
Mentions: The processing signal for histone mRNA also consists of two elements flanking the cleavage site: a conserved upstream hairpin and a purine-rich histone downstream element (HDE) (39). The 3′-end cleavage of histone mRNA requires base-pairing between the purine-rich HDE and the 5′-end of U7 snRNA (40). Dávila López and Samuelsson (41) have identified candidate U7 snRNAs genes in a greatly expanded number of organisms. In each instance, and others that we have investigated, an A/G-rich sequence in the HDE is paired with a U-rich sequence in U7 snRNA that, together, closely approximates the structure of the manganese ribozyme (Figure 7). Thus, it is plausible that this structure likewise evolved from a functional manganese ribozyme, thereby accounting for the observation that some factors are common to the 3′-end processing of both poly(A)+ and poly(A)– mRNAs.Figure 7.

Bottom Line: The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage.Analysis of sequences in the PolyA Cleavage Site and 3'-UTR Database (PACdb) revealed no particular bias in the frequency or distribution of the GAAA motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts.Nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.

ABSTRACT
The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs only in the presence of manganese or cadmium ions and proceeds optimally near 30 degrees C and physiological pH. The time course of cleavage in Vg1 mRNA best fits a two-step process in which both steps are first-order. In Vg1 mRNA, the ribozyme is positioned adjacent to a polyadenylation signal, but has no influence on translation of the mRNA in Xenopus oocytes. Putative GAAA ribozyme structures are also near polyadenylation sites in yeast and rat actin mRNAs. Analysis of sequences in the PolyA Cleavage Site and 3'-UTR Database (PACdb) revealed no particular bias in the frequency or distribution of the GAAA motif that would suggest that this ribozyme is currently or was recently used for cleavage to generate processed transcripts. Nonetheless, we speculate that the complementary strands that comprise the ribozyme may account for the origin of sequence elements that direct present-day 3'-end processing of eukaryotic mRNAs.

Show MeSH
Related in: MedlinePlus