The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.
Previous studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongati...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC5786338?pdf=render |
| _version_ | 1818693533490479104 |
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| author | Khanh Dao Duc Yun S Song |
| author_facet | Khanh Dao Duc Yun S Song |
| author_sort | Khanh Dao Duc |
| collection | DOAJ |
| description | Previous studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel. |
| first_indexed | 2024-12-17T13:15:12Z |
| format | Article |
| id | doaj.art-fe92e74a3e6a480ebbd197a9047abdde |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-17T13:15:12Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-fe92e74a3e6a480ebbd197a9047abdde2022-12-21T21:47:01ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042018-01-01141e100716610.1371/journal.pgen.1007166The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.Khanh Dao DucYun S SongPrevious studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel.http://europepmc.org/articles/PMC5786338?pdf=render |
| spellingShingle | Khanh Dao Duc Yun S Song The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. PLoS Genetics |
| title | The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. |
| title_full | The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. |
| title_fullStr | The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. |
| title_full_unstemmed | The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. |
| title_short | The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. |
| title_sort | impact of ribosomal interference codon usage and exit tunnel interactions on translation elongation rate variation |
| url | http://europepmc.org/articles/PMC5786338?pdf=render |
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