Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria
Bacteria produce different amounts of their proteins in response to different conditions. The ability to accurately quantitate the rates of protein synthesis across the genome is an important step toward understanding both underlying regulation and bacterial physiology at a systems level. Ribosome p...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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Elsevier
2020
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| Online Access: | https://hdl.handle.net/1721.1/125169 |
| _version_ | 1826198088284372992 |
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| author | Johnson, Grace E. Li, Gene-Wei |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Johnson, Grace E. Li, Gene-Wei |
| author_sort | Johnson, Grace E. |
| collection | MIT |
| description | Bacteria produce different amounts of their proteins in response to different conditions. The ability to accurately quantitate the rates of protein synthesis across the genome is an important step toward understanding both underlying regulation and bacterial physiology at a systems level. Ribosome profiling (deep sequencing of ribosome-protected mRNA fragments) enables accurate and high-throughput measurement of such synthesis rates. Ribosomes protect RNAs from nuclease digestion; thus, by collecting and sequencing protected footprints, one can obtain information on the position of every ribosome at the time of cell collection. Assuming ribosomes go on to translate full-length proteins, the density of ribosomes across an ORF can be used to determine protein synthesis rates. Here we outline a step-by-step protocol and discuss the steps where variability and bias may be introduced, including ways to minimize it. |
| first_indexed | 2024-09-23T10:58:40Z |
| format | Article |
| id | mit-1721.1/125169 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:58:40Z |
| publishDate | 2020 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1251692022-09-27T16:18:56Z Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria Johnson, Grace E. Li, Gene-Wei Massachusetts Institute of Technology. Department of Biology Bacteria produce different amounts of their proteins in response to different conditions. The ability to accurately quantitate the rates of protein synthesis across the genome is an important step toward understanding both underlying regulation and bacterial physiology at a systems level. Ribosome profiling (deep sequencing of ribosome-protected mRNA fragments) enables accurate and high-throughput measurement of such synthesis rates. Ribosomes protect RNAs from nuclease digestion; thus, by collecting and sequencing protected footprints, one can obtain information on the position of every ribosome at the time of cell collection. Assuming ribosomes go on to translate full-length proteins, the density of ribosomes across an ORF can be used to determine protein synthesis rates. Here we outline a step-by-step protocol and discuss the steps where variability and bias may be introduced, including ways to minimize it. 2020-05-12T12:51:33Z 2020-05-12T12:51:33Z 2018-12 2020-01-23T17:36:38Z Article http://purl.org/eprint/type/JournalArticle 1557-7988 https://hdl.handle.net/1721.1/125169 Johnson, Grace E. and Gene-Wei Li. “Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria.” Methods in enzymology 612 (2018): 225-249 © 2018 The Author(s) en 10.1016/bs.mie.2018.08.031 Methods in enzymology Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier PMC |
| spellingShingle | Johnson, Grace E. Li, Gene-Wei Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title | Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title_full | Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title_fullStr | Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title_full_unstemmed | Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title_short | Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria |
| title_sort | genome wide quantitation of protein synthesis rates in bacteria |
| url | https://hdl.handle.net/1721.1/125169 |
| work_keys_str_mv | AT johnsongracee genomewidequantitationofproteinsynthesisratesinbacteria AT ligenewei genomewidequantitationofproteinsynthesisratesinbacteria |