The Metabolic Building Blocks of a Minimal Cell
Defining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, re...
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| Format: | Article |
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MDPI AG
2020-12-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/10/1/5 |
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| author | Mariana Reyes-Prieto Rosario Gil Mercè Llabrés Pere Palmer-Rodríguez Andrés Moya |
| author_facet | Mariana Reyes-Prieto Rosario Gil Mercè Llabrés Pere Palmer-Rodríguez Andrés Moya |
| author_sort | Mariana Reyes-Prieto |
| collection | DOAJ |
| description | Defining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, reproduce, and evolve to a bacterium in an ideally controlled environment. They also proposed a simplified metabolic chart capable of providing energy and basic components for a minimal living cell. For this work, we have identified the components of the minimal metabolic network based on the aforementioned studies, associated them to the KEGG database and, by applying the MetaDAG methodology, determined its Metabolic Building Blocks (MBB) and reconstructed its metabolic Directed Acyclic Graph (m-DAG). The reaction graph of this metabolic network consists of 80 compounds and 98 reactions, while its m-DAG has 36 MBBs. Additionally, we identified 12 essential reactions in the m-DAG that are critical for maintaining the connectivity of this network. In a similar manner, we reconstructed the m-DAG of JCVI-syn3.0, which is an artificially designed and manufactured viable cell whose genome arose by minimizing the one from <i>Mycoplasma mycoides</i> JCVI-syn1.0, and of “<i>Candidatus</i> Nasuia deltocephalinicola”, the bacteria with the smallest natural genome known to date. The comparison of the m-DAGs derived from a theoretical, an artificial, and a natural genome denote slightly different lifestyles, with a consistent core metabolism. The MetaDAG methodology we employ uses homogeneous descriptors and identifiers from the KEGG database, so that comparisons between bacterial strains are not only easy but also suitable for many research fields. The modeling of m-DAGs based on minimal metabolisms can be the first step for the synthesis and manipulation of minimal cells. |
| first_indexed | 2024-03-10T13:49:57Z |
| format | Article |
| id | doaj.art-fec668db519b45b7ad399963742a35f1 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T13:49:57Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-fec668db519b45b7ad399963742a35f12023-11-21T02:20:37ZengMDPI AGBiology2079-77372020-12-01101510.3390/biology10010005The Metabolic Building Blocks of a Minimal CellMariana Reyes-Prieto0Rosario Gil1Mercè Llabrés2Pere Palmer-Rodríguez3Andrés Moya4Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, SpainEvolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, SpainDepartment of Mathematics and Computer Science, University of Balearic Islands, 07122 Palma de Mallorca, SpainDepartment of Mathematics and Computer Science, University of Balearic Islands, 07122 Palma de Mallorca, SpainEvolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology, University of Valencia and Spanish Research Council, Paterna, 46980 Valencia, SpainDefining the essential gene components for a system to be considered alive is a crucial step toward the synthesis of artificial life. Fifteen years ago, Gil and coworkers proposed the core of a putative minimal bacterial genome, which would provide the capability to achieve metabolic homeostasis, reproduce, and evolve to a bacterium in an ideally controlled environment. They also proposed a simplified metabolic chart capable of providing energy and basic components for a minimal living cell. For this work, we have identified the components of the minimal metabolic network based on the aforementioned studies, associated them to the KEGG database and, by applying the MetaDAG methodology, determined its Metabolic Building Blocks (MBB) and reconstructed its metabolic Directed Acyclic Graph (m-DAG). The reaction graph of this metabolic network consists of 80 compounds and 98 reactions, while its m-DAG has 36 MBBs. Additionally, we identified 12 essential reactions in the m-DAG that are critical for maintaining the connectivity of this network. In a similar manner, we reconstructed the m-DAG of JCVI-syn3.0, which is an artificially designed and manufactured viable cell whose genome arose by minimizing the one from <i>Mycoplasma mycoides</i> JCVI-syn1.0, and of “<i>Candidatus</i> Nasuia deltocephalinicola”, the bacteria with the smallest natural genome known to date. The comparison of the m-DAGs derived from a theoretical, an artificial, and a natural genome denote slightly different lifestyles, with a consistent core metabolism. The MetaDAG methodology we employ uses homogeneous descriptors and identifiers from the KEGG database, so that comparisons between bacterial strains are not only easy but also suitable for many research fields. The modeling of m-DAGs based on minimal metabolisms can be the first step for the synthesis and manipulation of minimal cells.https://www.mdpi.com/2079-7737/10/1/5metabolic networksminimal gene set machinerydirected acyclic graphsminimal cells |
| spellingShingle | Mariana Reyes-Prieto Rosario Gil Mercè Llabrés Pere Palmer-Rodríguez Andrés Moya The Metabolic Building Blocks of a Minimal Cell Biology metabolic networks minimal gene set machinery directed acyclic graphs minimal cells |
| title | The Metabolic Building Blocks of a Minimal Cell |
| title_full | The Metabolic Building Blocks of a Minimal Cell |
| title_fullStr | The Metabolic Building Blocks of a Minimal Cell |
| title_full_unstemmed | The Metabolic Building Blocks of a Minimal Cell |
| title_short | The Metabolic Building Blocks of a Minimal Cell |
| title_sort | metabolic building blocks of a minimal cell |
| topic | metabolic networks minimal gene set machinery directed acyclic graphs minimal cells |
| url | https://www.mdpi.com/2079-7737/10/1/5 |
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