Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling
The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2016-02-01
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| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124715015296 |
| _version_ | 1818914148234297344 |
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| author | Fuad Mohammad Christopher J. Woolstenhulme Rachel Green Allen R. Buskirk |
| author_facet | Fuad Mohammad Christopher J. Woolstenhulme Rachel Green Allen R. Buskirk |
| author_sort | Fuad Mohammad |
| collection | DOAJ |
| description | The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling. |
| first_indexed | 2024-12-19T23:41:46Z |
| format | Article |
| id | doaj.art-223274cd3c7547c0867397ade3c3d301 |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-19T23:41:46Z |
| publishDate | 2016-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-223274cd3c7547c0867397ade3c3d3012022-12-21T20:01:24ZengElsevierCell Reports2211-12472016-02-0114468669410.1016/j.celrep.2015.12.073Clarifying the Translational Pausing Landscape in Bacteria by Ribosome ProfilingFuad Mohammad0Christopher J. Woolstenhulme1Rachel Green2Allen R. Buskirk3Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USADepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USADepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USADepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USAThe rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling.http://www.sciencedirect.com/science/article/pii/S2211124715015296 |
| spellingShingle | Fuad Mohammad Christopher J. Woolstenhulme Rachel Green Allen R. Buskirk Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling Cell Reports |
| title | Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling |
| title_full | Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling |
| title_fullStr | Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling |
| title_full_unstemmed | Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling |
| title_short | Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling |
| title_sort | clarifying the translational pausing landscape in bacteria by ribosome profiling |
| url | http://www.sciencedirect.com/science/article/pii/S2211124715015296 |
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