Primordial mimicry induces morphological change in Escherichia coli

Lü, Hui; Aida, Honoka; Kurokawa, Masaomi; Chen, Feng; Xia, Yang; Xu, Jian; Li, Kai; Ying, Bei‐Wen; Yomo, Tetsuya

doi:10.1038/s42003-021-02954-w

Cited by 12 publications

(13 citation statements)

References 81 publications

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“…Both systematic single-gene knockout ( Baba et al, 2006 ; Joyce et al, 2006 ) and genome reduction ( Kato and Hashimoto, 2007 ; Mizoguchi et al, 2008 ; Karcagi et al, 2016 ) were intensively reported. The genome-reduced strains were successfully applied to studies on metabolic engineering ( Lee et al, 2009 ), experimental evolution ( Choe et al, 2019 ), growth prediction ( Ashino et al, 2019 ), origin of life ( Lu et al, 2022 ), and so on. Whether and how genome reduction contributes to growth dynamics have been intensively studied in liquid media ( Karcagi et al, 2016 ; Kurokawa et al, 2016 ), which has led to valuable insights into adaptive evolution and niche expansion ( Nishimura et al, 2017 ; Choe et al, 2019 ; Kurokawa et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

2022

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Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.

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Section: Introductionmentioning

confidence: 99%

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

2022

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“…The E. coli cell populations were analyzed using an Amnis™ ImageStream™X imaging flow cytometer installed with INSPIRE acquisition software (Luminex, Austin, TX, USA), as described in our previous study [ 23 ]. Green fluorescence was induced with a 200 mW 488 nm laser, and the emission was detected with a 505–560 nm filter in Channel 2.…”

Section: Methodsmentioning

confidence: 99%

“…To ensure enough cell number for SEM analysis, bacteria at the late exponential phase were collected by centrifugation (Eppendorf centrifuge 5453, Hamburg, Germany) at 5000× g at 4 °C for 10 min, followed by two washings with M63 minimal medium, and fixed in 2.5% ( v/v ) glutaraldehyde at 4 °C. All of the procedures including dehydration, embedding, sectioning, and staining were performed according to our previous protocols [ 23 ]. The bacteria cells were then visualized using a scanning electron microscope (Hitachi S-4800, Tokyo, Japan) at an accelerating voltage of 3 kV.…”

Section: Methodsmentioning

confidence: 99%

“…Salmonella cells double the average length of swarmer cells and the number of flagella per cell during swarming, resulting in a significant increase in motor power [ 19 ]. Such morphological plasticity in bacteria indicates that bacterial morphology has a high potential for directed adaption in the laboratory under specific experimental conditions, such as Lenski’s long-term laboratory evolution [ 20 , 21 , 22 ] and our previous study where E. coli was adapted in an oleic acid vesicle (OAV)-rich medium [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

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Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution

Tian

Wang

Liu

et al. 2023

IJMS

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Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.

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“…One out of 13 mutators failed to grow in the minimal medium, as the genetic construction was performed with the rich medium. Note that the gene circuit sequence was previously used in various studies ( Ying et al, 2014 , 2015 , 2017 ; Ishizawa et al, 2015 ; Kishimoto et al, 2015 ; Shibai et al, 2017 ; Lu et al, 2022 ), and no experimental bias was observed.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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Fitness and mutability are the primary traits of living organisms for adaptation and evolution. However, their quantitative linkage remained largely deficient. Whether there is any general relationship between the two features and how genetic and environmental variables influence them remained unclear and were addressed here. The mutation and growth rates of an assortment of Escherichia coli strain collections, including the wild-type strains and the genetically disturbed strains of either reduced genomes or deletion of the genes involved in the DNA replication fidelity, were evaluated in various media. The contribution of media to the mutation and growth rates was differentiated depending on the types of genetic disturbance. Nevertheless, the negative correlation between the mutation and growth rates was observed across the genotypes and was common in all media. It indicated the comprehensive association of the correlated mutation and growth rates with the genetic and medium variation. Multiple linear regression and support vector machine successfully predicted the mutation and growth rates and the categories of genotypes and media, respectively. Taken together, the study provided a quantitative dataset linking the mutation and growth rates, genotype, and medium and presented a simple and successful example of predicting bacterial growth and mutability by data-driven approaches.

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Primordial mimicry induces morphological change in Escherichia coli

Cited by 12 publications

References 81 publications

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution

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

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