Global coordination of the mutation and growth rates across the genetic and nutritional variety in Escherichia coli

Lao, Zehui; Matsui, Yuichiro; Ijichi, Shinya; Ying, Bei‐Wen

doi:10.3389/fmicb.2022.990969

Cited by 3 publications

(4 citation statements)

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“…High-throughput growth assay demonstrated that the genome reduction commonly led to the fitness decrease ( Karcagi et al, 2016 ; Kurokawa et al, 2016 ), although it might benefit metabolic engineering ( Mizoguchi et al, 2007 ; Morimoto et al, 2008 ; Vernyik et al, 2020 ). The decreased fitness could be rapidly improved by experimental evolution ( Kawecki et al, 2012 ; Kurokawa and Ying, 2019 ), probably owing to the increased mutability of reduced genomes ( Nishimura et al, 2017 ; Lao et al, 2022 ). The evolutionary improved growth fitness was correlated to the environmental variation ( Kurokawa et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions

2023

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The genomic, environmental, and evolutionary interruptions caused the changes in bacterial growth, which were stringently associated with changes in gene expression. The growth and gene expression changes remained unclear in response to these interruptions that occurred combinative. As a pilot study, whether and how bacterial growth was affected by the individual and dual interruptions of genome reduction, environmental stress, and adaptive evolution were investigated. Growth assay showed that the presence of the environmental stressors, i.e., threonine and chloramphenicol, significantly decreased the growth rate of the wild-type Escherichia coli, whereas not that of the reduced genome. It indicated a canceling effect in bacterial growth due to the dual interruption of the genomic and environmental changes. Experimental evolution of the reduced genome released the canceling effect by improving growth fitness. Intriguingly, the transcriptome architecture maintained a homeostatic chromosomal periodicity regardless of the genomic, environmental, and evolutionary interruptions. Negative epistasis in transcriptome reorganization was commonly observed in response to the dual interruptions, which might contribute to the canceling effect. It was supported by the changes in the numbers of differentially expressed genes (DEGs) and the enriched regulons and functions. Gene network analysis newly constructed 11 gene modules, one out of which was correlated to the growth rate. Enrichment of DEGs in these modules successfully categorized them into three types, i.e., conserved, responsive, and epistatic. Taken together, homeostasis in transcriptome architecture was essential to being alive, and it might be attributed to the negative epistasis in transcriptome reorganization and the functional differentiation in gene modules. The present study directly connected bacterial growth fitness with transcriptome reorganization and provided a global view of how microorganisms responded to genomic, environmental, and evolutionary interruptions for survival from wild nature.

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Section: Introductionmentioning

confidence: 99%

Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions

2023

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“…In addition, the changes in mutation rates were coordinated with the increase in growth rates [ 37 , 38 ], revealing that the experimental evolution compensated for the genome reduction-mediated changes in growth and mutate rates. Note that such coordination might be stringently related to transcriptome reorganization.…”

Section: Genetic Requirement For Minimal Genomementioning

confidence: 99%

“…The genomic location of the mutations and the timing of the mutations fixing on the genome varied among the parallelly evolved lineages [46,47]. It indicates that the experimental evolution provides multiple trajectories for the ancestral genome to acquire The scatter plots are newly made using previously reported data [37,38]. The panels from left to right represent the nutritional richness of culture media from poor to rich.…”

Section: Evolutionary Approaches For Reduced Genomementioning

confidence: 99%

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

Aida,

Ying

2023

Biology

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

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Trends in the Use of Proper Methods for Estimating Mutation Rates in Fluctuation Experiments

Devin,

Couce

2023

Axioms

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The accurate quantification of mutation rates holds significance across diverse fields, including evolution, cancer research, and antimicrobial resistance. Eighty years ago, Luria and Delbrück demonstrated that the proper quantification of mutation rates requires one to account for the non-linear relationship between the number of mutations and the final number of mutants in a cell population. An extensive body of literature has since emerged, offering increasingly efficient methods to account for this phenomenon, with different alternatives balancing accuracy and user-friendliness for experimentalists. Nevertheless, statistically inappropriate approaches, such as using arithmetic averages of mutant frequencies as a proxy for the mutation rate, continue to be commonplace. Here, we conducted a comprehensive re-analysis of 140 publications from the last two decades, revealing general trends in the adoption of proper mutation rate estimation methods. Our findings demonstrate an upward trajectory in the utilization of best statistical practices, likely due to the wider availability of off-the-shelf computational tools. However, the usage of inappropriate statistical approaches varies substantially across specific research areas, and it is still present even in journals with the highest impact factors. These findings aim to inspire both experimentalists and theoreticians to find ways to further promote the adoption of best statistical practices for the reliable estimation of mutation rates in all fields.

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Global coordination of the mutation and growth rates across the genetic and nutritional variety in Escherichia coli

Cited by 3 publications

References 74 publications

Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions

Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions

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

Trends in the Use of Proper Methods for Estimating Mutation Rates in Fluctuation Experiments

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