Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium
Abstract Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half‐lives, proteins, and protein half‐lives with ribosome densities and derived the...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2023-10-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.202211301 |
| _version_ | 1797279796042924032 |
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| author | Marc Weber Adrià Sogues Eva Yus Raul Burgos Carolina Gallo Sira Martínez Maria Lluch‐Senar Luis Serrano |
| author_facet | Marc Weber Adrià Sogues Eva Yus Raul Burgos Carolina Gallo Sira Martínez Maria Lluch‐Senar Luis Serrano |
| author_sort | Marc Weber |
| collection | DOAJ |
| description | Abstract Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half‐lives, proteins, and protein half‐lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160‐fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100‐fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn. |
| first_indexed | 2024-03-07T16:31:14Z |
| format | Article |
| id | doaj.art-164836aea25b4702bde2577501844e10 |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-03-07T16:31:14Z |
| publishDate | 2023-10-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-164836aea25b4702bde2577501844e102024-03-03T10:16:04ZengSpringer NatureMolecular Systems Biology1744-42922023-10-011910n/an/a10.15252/msb.202211301Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacteriumMarc Weber0Adrià Sogues1Eva Yus2Raul Burgos3Carolina Gallo4Sira Martínez5Maria Lluch‐Senar6Luis Serrano7Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainAbstract Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half‐lives, proteins, and protein half‐lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160‐fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100‐fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.https://doi.org/10.15252/msb.202211301data integrationMycoplasma pneumoniaeprotein synthesisribosome profilingtranslation efficiency |
| spellingShingle | Marc Weber Adrià Sogues Eva Yus Raul Burgos Carolina Gallo Sira Martínez Maria Lluch‐Senar Luis Serrano Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium Molecular Systems Biology data integration Mycoplasma pneumoniae protein synthesis ribosome profiling translation efficiency |
| title | Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium |
| title_full | Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium |
| title_fullStr | Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium |
| title_full_unstemmed | Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium |
| title_short | Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium |
| title_sort | comprehensive quantitative modeling of translation efficiency in a genome reduced bacterium |
| topic | data integration Mycoplasma pneumoniae protein synthesis ribosome profiling translation efficiency |
| url | https://doi.org/10.15252/msb.202211301 |
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