The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes
The current theoretical proposals of minimal genomes have not attempted to outline the essential machinery for proper translation in cells. Here, we present a proposal of a minimal translation machinery based on (1) a comparative analysis of bacterial genomes of insects’ endosymbionts using a machin...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.858983/full |
| _version_ | 1811279339785814016 |
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| author | María José Garzón Mariana Reyes-Prieto Mariana Reyes-Prieto Rosario Gil Rosario Gil |
| author_facet | María José Garzón Mariana Reyes-Prieto Mariana Reyes-Prieto Rosario Gil Rosario Gil |
| author_sort | María José Garzón |
| collection | DOAJ |
| description | The current theoretical proposals of minimal genomes have not attempted to outline the essential machinery for proper translation in cells. Here, we present a proposal of a minimal translation machinery based on (1) a comparative analysis of bacterial genomes of insects’ endosymbionts using a machine learning classification algorithm, (2) the empiric genomic information obtained from Mycoplasma mycoides JCVI-syn3.0 the first minimal bacterial genome obtained by design and synthesis, and (3) a detailed functional analysis of the candidate genes based on essentiality according to the DEG database (Escherichia coli and Bacillus subtilis) and the literature. This proposed minimal translational machinery is composed by 142 genes which must be present in any synthetic prokaryotic cell designed for biotechnological purposes, 76.8% of which are shared with JCVI-syn3.0. Eight additional genes were manually included in the proposal for a proper and efficient translation. |
| first_indexed | 2024-04-13T00:52:53Z |
| format | Article |
| id | doaj.art-11f6c8e586c743f4bb0a6e4a97f69d50 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-13T00:52:53Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-11f6c8e586c743f4bb0a6e4a97f69d502022-12-22T03:09:50ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-04-011310.3389/fmicb.2022.858983858983The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced GenomesMaría José Garzón0Mariana Reyes-Prieto1Mariana Reyes-Prieto2Rosario Gil3Rosario Gil4Departament de Genètica, Universitat de València, Burjassot, SpainInstitute for Integrative Systems Biology, Universitat de València–Consejo Superior de Investigaciones Científicas, Paterna, SpainSequencing and Bioinformatics Service, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community, Valencia, SpainDepartament de Genètica, Universitat de València, Burjassot, SpainInstitute for Integrative Systems Biology, Universitat de València–Consejo Superior de Investigaciones Científicas, Paterna, SpainThe current theoretical proposals of minimal genomes have not attempted to outline the essential machinery for proper translation in cells. Here, we present a proposal of a minimal translation machinery based on (1) a comparative analysis of bacterial genomes of insects’ endosymbionts using a machine learning classification algorithm, (2) the empiric genomic information obtained from Mycoplasma mycoides JCVI-syn3.0 the first minimal bacterial genome obtained by design and synthesis, and (3) a detailed functional analysis of the candidate genes based on essentiality according to the DEG database (Escherichia coli and Bacillus subtilis) and the literature. This proposed minimal translational machinery is composed by 142 genes which must be present in any synthetic prokaryotic cell designed for biotechnological purposes, 76.8% of which are shared with JCVI-syn3.0. Eight additional genes were manually included in the proposal for a proper and efficient translation.https://www.frontiersin.org/articles/10.3389/fmicb.2022.858983/fulltranslation machineryminimal genomeendosymbiontsJCVI-sync3.0cosymbionts |
| spellingShingle | María José Garzón Mariana Reyes-Prieto Mariana Reyes-Prieto Rosario Gil Rosario Gil The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes Frontiers in Microbiology translation machinery minimal genome endosymbionts JCVI-sync3.0 cosymbionts |
| title | The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes |
| title_full | The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes |
| title_fullStr | The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes |
| title_full_unstemmed | The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes |
| title_short | The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes |
| title_sort | minimal translation machinery what we can learn from naturally and experimentally reduced genomes |
| topic | translation machinery minimal genome endosymbionts JCVI-sync3.0 cosymbionts |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.858983/full |
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