Efforts to Minimise the Bacterial Genome as a Free-Living Growing System

Biology, Год журнала: 2023, Номер 12(9), С. 1170 - 1170

Опубликована: Авг. 25, 2023

Exploring the minimal genetic requirements for cells to maintain free living is an exciting topic in biology. Multiple approaches are employed address question of genome. In addition constructing synthetic genome test tube, reducing size wild-type a practical approach obtaining essential genomic sequence cells. The well-studied Escherichia coli has been used as model organism reduction owing its fast growth and easy manipulation. Extensive studies have reported how reduce bacterial collections disturbed strains acquired, which were sufficiently reviewed previously. However, common issue decrease caused by disturbance remains largely unaddressed. This mini-review discusses considerable efforts made improve fitness, was decreased due reduction. proposal perspective clarified further accumulated deletion minimise terms reduction, experimental evolution, medium optimization, machine learning.

Язык: Английский

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Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

Computational and Structural Biotechnology Journal, Год журнала: 2023, Номер 21, С. 2654 - 2663

Опубликована: Янв. 1, 2023

The composition of medium components is crucial for achieving the best performance synthetic construction in genetically engineered cells. Which and how determine performance, e.g., productivity, remain poorly investigated. To address questions, a comparative survey with two Escherichia coli strains was performed. As case study, carried pathways producing aromatic compounds 4-aminophenylalanine (4APhe) or tyrosine (Tyr), common upstream but differentiated downstream metabolism. Bacterial growth compound production were examined hundreds combinations that comprised 48 pure chemicals. resultant data sets linking to bacterial subjected machine learning improved production. Intriguingly, primary determining 4PheA Tyr differentiated, which initial resource (glucose) pathway inducer (IPTG) construction, respectively. Fine-tuning component significantly increased yields 4APhe Tyr, indicating single could be construction. Transcriptome analysis observed local global changes gene expression respectively, revealing divergent metabolic strategies foreign native metabolites. study demonstrated ML-assisted optimization provide novel point view on make meet designed working principle achieve expected biological function.Graphical abstract

Язык: Английский

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Experimental evolution for the recovery of growth loss due to genome reduction

eLife, Год журнала: 2024, Номер 13

Опубликована: Май 1, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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A data-driven approach for cell culture medium optimization

Biochemical Engineering Journal, Год журнала: 2024, Номер unknown, С. 109591 - 109591

Опубликована: Ноя. 1, 2024

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Reviewer #3 (Public Review): Diversity for commonality in the evolutionary changes of the reduced genome to regain the growth fitness

Опубликована: Янв. 23, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1,000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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eLife assessment: Diversity for commonality in the evolutionary changes of the reduced genome to regain the growth fitness

Опубликована: Янв. 23, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1,000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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Experimental evolution for the recovery of growth loss due to genome reduction

eLife, Год журнала: 2024, Номер 13

Опубликована: Янв. 23, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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Reviewer #1 (Public Review): Diversity for commonality in the evolutionary changes of the reduced genome to regain the growth fitness

Опубликована: Янв. 23, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1,000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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Reviewer #2 (Public Review): Diversity for commonality in the evolutionary changes of the reduced genome to regain the growth fitness

Опубликована: Янв. 23, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1,000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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Experimental evolution for the recovery of growth loss due to genome reduction

Опубликована: Апрель 19, 2024

As the genome encodes information crucial for cell growth, a sizeable genomic deficiency often causes significant decrease in growth fitness. Whether and how decreased fitness caused by reduction could be compensated evolution was investigated here. Experimental with an Escherichia coli strain carrying reduced conducted multiple lineages approximately 1,000 generations. The rate, which largely declined due to reduction, considerably recovered, associated improved capacity. Genome mutations accumulated during were significantly varied across evolutionary randomly localized on genome. Transcriptome reorganization showed common direction conserved chromosomal periodicity, regardless of highly diversified gene categories, regulons, pathways enriched differentially expressed genes. transcriptome evolution, found dissimilar those must have followed divergent mechanisms individual lineages. Gene network reconstruction successfully identified three modules functionally differentiated, responsible changes fitness, mutation, expression, respectively. diversity approaches homeostatic architecture as if compensation like all roads leading Rome.

Язык: Английский

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