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Ribosome A and P sites revealed by length analysis of ribosome profiling data.

Martens AT, Taylor J, Hilser VJ - Nucleic Acids Res. (2015)

Bottom Line: Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths.Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations.We also show that GC-rich motifs at the 5' ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.

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The depletion of intracellular tRNAHis using 3-AT causes a sharp increase in histidines in ribosome footprints (top) compared to untreated cells (bottom). Unlike the proline enrichment, which had a clear position-specific effect, this enrichment is more evenly spread across the length of the footprints. However, a strongly conserved vertical pattern of enrichment at position 5 might indicate the A site position.
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Figure 6: The depletion of intracellular tRNAHis using 3-AT causes a sharp increase in histidines in ribosome footprints (top) compared to untreated cells (bottom). Unlike the proline enrichment, which had a clear position-specific effect, this enrichment is more evenly spread across the length of the footprints. However, a strongly conserved vertical pattern of enrichment at position 5 might indicate the A site position.

Mentions: As before, the codons were tallied at all positions and categorized by ribosome footprints of different lengths. As shown previously, we find that histidine codons are enriched after 3-AT treatment, at nearly all positions, comprising a much higher fraction of the total number of codons in ribosome footprints than from untreated cells (Figure 6). Although the effect is not limited to a single position, the enrichment at the position 5 codons downstream from the 5′ end is slightly stronger than at other positions. Despite the weak signal, this position is the likeliest candidate of the A site, for it agrees with the proline data, which set the P site 4 codons downstream the 5′ end. Aligning the footprints to the 5′ end, as before, tends to conserve vertical enrichment patterns across footprints of different lengths, again suggesting that, in yeast, the additional mRNA in longer footprints extends from the 3′ end of the ribosome.


Ribosome A and P sites revealed by length analysis of ribosome profiling data.

Martens AT, Taylor J, Hilser VJ - Nucleic Acids Res. (2015)

The depletion of intracellular tRNAHis using 3-AT causes a sharp increase in histidines in ribosome footprints (top) compared to untreated cells (bottom). Unlike the proline enrichment, which had a clear position-specific effect, this enrichment is more evenly spread across the length of the footprints. However, a strongly conserved vertical pattern of enrichment at position 5 might indicate the A site position.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402525&req=5

Figure 6: The depletion of intracellular tRNAHis using 3-AT causes a sharp increase in histidines in ribosome footprints (top) compared to untreated cells (bottom). Unlike the proline enrichment, which had a clear position-specific effect, this enrichment is more evenly spread across the length of the footprints. However, a strongly conserved vertical pattern of enrichment at position 5 might indicate the A site position.
Mentions: As before, the codons were tallied at all positions and categorized by ribosome footprints of different lengths. As shown previously, we find that histidine codons are enriched after 3-AT treatment, at nearly all positions, comprising a much higher fraction of the total number of codons in ribosome footprints than from untreated cells (Figure 6). Although the effect is not limited to a single position, the enrichment at the position 5 codons downstream from the 5′ end is slightly stronger than at other positions. Despite the weak signal, this position is the likeliest candidate of the A site, for it agrees with the proline data, which set the P site 4 codons downstream the 5′ end. Aligning the footprints to the 5′ end, as before, tends to conserve vertical enrichment patterns across footprints of different lengths, again suggesting that, in yeast, the additional mRNA in longer footprints extends from the 3′ end of the ribosome.

Bottom Line: Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths.Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations.We also show that GC-rich motifs at the 5' ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.

Show MeSH
Related in: MedlinePlus