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A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF - J. Biol. Chem. (2015)

Bottom Line: The frameshift is the sensor and effector in an autoregulatory circuit.When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general.A conserved RNA secondary structure 3' of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting.

View Article: PubMed Central - PubMed

Affiliation: From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

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Related in: MedlinePlus

Conservation of antizyme mRNA sequences from Basidiomycota, and their encoded products.A, an alignment of 35 ORF1 antizyme mRNA sequences was used to generate the nucleotide and amino acid logos shown here. Of these sequences, 34 belong to Agaricomycetes, and 1 belongs to Dacrymycetes (supplemental Sequence List S1). Starting from the 3′ end of the nucleotide logo indicated are the ORF1 stop codon, the shift site, the sequence of module A, and the conserved peptide encoding region. Other conserved features more distal to the shift site, such as a conserved dipeptide and a conserved 5′ stem loop, are also indicated. The gaps in the logos indicate that each nucleotide or amino acid residue occurs with equal probability at the corresponding position. B, alignment of 54 Basidiomycotal antizyme mRNA sequences 3′ of the shift site. The region shown here contains the conserved 3′ RNA structure. The nucleotide variations in loop 2 are highlighted in green. The correct reading frame is indicated in the first sequence of the alignment. The absolutely conserved four nucleotide sequence abutting stem 1 are shown in magenta. Completely conserved nucleotides are indicated by an asterisk below the alignment. The four sequences of the Tremellomycetes class that lack the potential RNA structure were left uncolored and were not taken into account when analyzing the alignment. The underlined names are of the sequences used for the alignments in Fig. 2A. The scheme of the phylogenetic tree was adapted from the work of Floudas et al. (41) and is not intended to indicate precise evolutionary distances and scales. P.taeda* refers to an EST derived from a Pinus taeda library that is an Agaricomycetes contaminant of unknown identity. Dacryop.** stands for Dacryopinax sp. C, the predicted secondary structure of the putative RNA stimulator, inferred from the alignment, featuring the C. cinerea mRNA sequence; the coloring corresponds to that of the alignment.
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Figure 2: Conservation of antizyme mRNA sequences from Basidiomycota, and their encoded products.A, an alignment of 35 ORF1 antizyme mRNA sequences was used to generate the nucleotide and amino acid logos shown here. Of these sequences, 34 belong to Agaricomycetes, and 1 belongs to Dacrymycetes (supplemental Sequence List S1). Starting from the 3′ end of the nucleotide logo indicated are the ORF1 stop codon, the shift site, the sequence of module A, and the conserved peptide encoding region. Other conserved features more distal to the shift site, such as a conserved dipeptide and a conserved 5′ stem loop, are also indicated. The gaps in the logos indicate that each nucleotide or amino acid residue occurs with equal probability at the corresponding position. B, alignment of 54 Basidiomycotal antizyme mRNA sequences 3′ of the shift site. The region shown here contains the conserved 3′ RNA structure. The nucleotide variations in loop 2 are highlighted in green. The correct reading frame is indicated in the first sequence of the alignment. The absolutely conserved four nucleotide sequence abutting stem 1 are shown in magenta. Completely conserved nucleotides are indicated by an asterisk below the alignment. The four sequences of the Tremellomycetes class that lack the potential RNA structure were left uncolored and were not taken into account when analyzing the alignment. The underlined names are of the sequences used for the alignments in Fig. 2A. The scheme of the phylogenetic tree was adapted from the work of Floudas et al. (41) and is not intended to indicate precise evolutionary distances and scales. P.taeda* refers to an EST derived from a Pinus taeda library that is an Agaricomycetes contaminant of unknown identity. Dacryop.** stands for Dacryopinax sp. C, the predicted secondary structure of the putative RNA stimulator, inferred from the alignment, featuring the C. cinerea mRNA sequence; the coloring corresponds to that of the alignment.

Mentions: The putative stimulatory element 3′ of the frameshift site is a potential RNA secondary structure starting 19 nucleotides downstream of the frameshift site. The structure consists of two directly adjacent stem loops, suggesting that they may co-axially stack on each other (Fig. 2, B and C). Its position relative to the frameshift site suggests that it would be just outside the ribosome mRNA tunnel during the frameshift event (36). With the exception of two recently described cases (37, 38), this is different from the other previously described stimulatory structures that are located closer to the frameshift site and presumed to act from within the mRNA entrance tunnel at the mRNA unwinding site (23).


A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF - J. Biol. Chem. (2015)

Conservation of antizyme mRNA sequences from Basidiomycota, and their encoded products.A, an alignment of 35 ORF1 antizyme mRNA sequences was used to generate the nucleotide and amino acid logos shown here. Of these sequences, 34 belong to Agaricomycetes, and 1 belongs to Dacrymycetes (supplemental Sequence List S1). Starting from the 3′ end of the nucleotide logo indicated are the ORF1 stop codon, the shift site, the sequence of module A, and the conserved peptide encoding region. Other conserved features more distal to the shift site, such as a conserved dipeptide and a conserved 5′ stem loop, are also indicated. The gaps in the logos indicate that each nucleotide or amino acid residue occurs with equal probability at the corresponding position. B, alignment of 54 Basidiomycotal antizyme mRNA sequences 3′ of the shift site. The region shown here contains the conserved 3′ RNA structure. The nucleotide variations in loop 2 are highlighted in green. The correct reading frame is indicated in the first sequence of the alignment. The absolutely conserved four nucleotide sequence abutting stem 1 are shown in magenta. Completely conserved nucleotides are indicated by an asterisk below the alignment. The four sequences of the Tremellomycetes class that lack the potential RNA structure were left uncolored and were not taken into account when analyzing the alignment. The underlined names are of the sequences used for the alignments in Fig. 2A. The scheme of the phylogenetic tree was adapted from the work of Floudas et al. (41) and is not intended to indicate precise evolutionary distances and scales. P.taeda* refers to an EST derived from a Pinus taeda library that is an Agaricomycetes contaminant of unknown identity. Dacryop.** stands for Dacryopinax sp. C, the predicted secondary structure of the putative RNA stimulator, inferred from the alignment, featuring the C. cinerea mRNA sequence; the coloring corresponds to that of the alignment.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4505036&req=5

Figure 2: Conservation of antizyme mRNA sequences from Basidiomycota, and their encoded products.A, an alignment of 35 ORF1 antizyme mRNA sequences was used to generate the nucleotide and amino acid logos shown here. Of these sequences, 34 belong to Agaricomycetes, and 1 belongs to Dacrymycetes (supplemental Sequence List S1). Starting from the 3′ end of the nucleotide logo indicated are the ORF1 stop codon, the shift site, the sequence of module A, and the conserved peptide encoding region. Other conserved features more distal to the shift site, such as a conserved dipeptide and a conserved 5′ stem loop, are also indicated. The gaps in the logos indicate that each nucleotide or amino acid residue occurs with equal probability at the corresponding position. B, alignment of 54 Basidiomycotal antizyme mRNA sequences 3′ of the shift site. The region shown here contains the conserved 3′ RNA structure. The nucleotide variations in loop 2 are highlighted in green. The correct reading frame is indicated in the first sequence of the alignment. The absolutely conserved four nucleotide sequence abutting stem 1 are shown in magenta. Completely conserved nucleotides are indicated by an asterisk below the alignment. The four sequences of the Tremellomycetes class that lack the potential RNA structure were left uncolored and were not taken into account when analyzing the alignment. The underlined names are of the sequences used for the alignments in Fig. 2A. The scheme of the phylogenetic tree was adapted from the work of Floudas et al. (41) and is not intended to indicate precise evolutionary distances and scales. P.taeda* refers to an EST derived from a Pinus taeda library that is an Agaricomycetes contaminant of unknown identity. Dacryop.** stands for Dacryopinax sp. C, the predicted secondary structure of the putative RNA stimulator, inferred from the alignment, featuring the C. cinerea mRNA sequence; the coloring corresponds to that of the alignment.
Mentions: The putative stimulatory element 3′ of the frameshift site is a potential RNA secondary structure starting 19 nucleotides downstream of the frameshift site. The structure consists of two directly adjacent stem loops, suggesting that they may co-axially stack on each other (Fig. 2, B and C). Its position relative to the frameshift site suggests that it would be just outside the ribosome mRNA tunnel during the frameshift event (36). With the exception of two recently described cases (37, 38), this is different from the other previously described stimulatory structures that are located closer to the frameshift site and presumed to act from within the mRNA entrance tunnel at the mRNA unwinding site (23).

Bottom Line: The frameshift is the sensor and effector in an autoregulatory circuit.When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general.A conserved RNA secondary structure 3' of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting.

View Article: PubMed Central - PubMed

Affiliation: From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

Show MeSH
Related in: MedlinePlus