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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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The frequency of GAAA immediately upstream and downstream of the polyadenylation signal. One thousand mRNA sequences from C. elegans and D. melanogaster were scanned in 1-nt increments using a 4-nt window. The frequency of the sequences GAAA, CAAA and TATG are presented as histograms relative to the position of the AATAAA hexanucleotide sequence.
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Figure 6: The frequency of GAAA immediately upstream and downstream of the polyadenylation signal. One thousand mRNA sequences from C. elegans and D. melanogaster were scanned in 1-nt increments using a 4-nt window. The frequency of the sequences GAAA, CAAA and TATG are presented as histograms relative to the position of the AATAAA hexanucleotide sequence.

Mentions: We also analyzed the sequences flanking polyadenylation signals to determine whether there is any apparent bias in the location of GAAA sequences. We determined the number of times the ribozyme sequence occurs within 50 or 100 nt upstream or downstream of polyadenylation signals (Table 2). This analysis did not reveal any notable positional effects. In addition, we examined 1000 sequences each from C. elegans and D. melanogaster, scanning the sequence immediately surrounding the polyadenylation signal in 1-nt increments using a 4-nt window (Figure 6). There is a marked increase in the frequency of the GAAA sequence immediately before and including the first 2 nt of the polyadenylation signal. However, the occurrence of the ribozyme sequence is no greater than CAAA. This analysis simply demonstrates the greater likelihood of a tetranucleotide sequence with three consecutive adenosines due to the polyadenylation signal.Figure 6.


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

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

The frequency of GAAA immediately upstream and downstream of the polyadenylation signal. One thousand mRNA sequences from C. elegans and D. melanogaster were scanned in 1-nt increments using a 4-nt window. The frequency of the sequences GAAA, CAAA and TATG are presented as histograms relative to the position of the AATAAA hexanucleotide sequence.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: The frequency of GAAA immediately upstream and downstream of the polyadenylation signal. One thousand mRNA sequences from C. elegans and D. melanogaster were scanned in 1-nt increments using a 4-nt window. The frequency of the sequences GAAA, CAAA and TATG are presented as histograms relative to the position of the AATAAA hexanucleotide sequence.
Mentions: We also analyzed the sequences flanking polyadenylation signals to determine whether there is any apparent bias in the location of GAAA sequences. We determined the number of times the ribozyme sequence occurs within 50 or 100 nt upstream or downstream of polyadenylation signals (Table 2). This analysis did not reveal any notable positional effects. In addition, we examined 1000 sequences each from C. elegans and D. melanogaster, scanning the sequence immediately surrounding the polyadenylation signal in 1-nt increments using a 4-nt window (Figure 6). There is a marked increase in the frequency of the GAAA sequence immediately before and including the first 2 nt of the polyadenylation signal. However, the occurrence of the ribozyme sequence is no greater than CAAA. This analysis simply demonstrates the greater likelihood of a tetranucleotide sequence with three consecutive adenosines due to the polyadenylation signal.Figure 6.

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