Correlation between genome reduction and bacterial growth

Kurokawa, Masaomi; Seno, Shigeto; Matsuda, Hideo; Ying, Bei‐Wen

doi:10.1093/dnares/dsw035

Cited by 74 publications

(144 citation statements)

References 48 publications

(51 reference statements)

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“…A correlation between the growth rate and genome reduction has been previously reported according to the manual calculation [34]. The same conclusion was drawn from the theoretical fitting suggested here, and the modified logistic model was applicable.…”

Section: Resultssupporting

confidence: 87%

“…The raw data sets of these growth curves can be found at Springer Nature Research Data Support and can be accessed online via the following URL: 10.6084/m9.figshare.5918608. The details regarding the determination of the growth data set was previously described [27, 34], and the data sets of growth in M63 and LB media were used in the present study. Evaluation of the models (goodness of fit) was assessed based on the sum of squares, which were calculated according to the following equations.…”

Section: Methodsmentioning

confidence: 99%

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A decay effect of the growth rate associated with genome reduction in Escherichia coli

et al. 2018

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BackgroundBacterial growth is an important topic in microbiology and of crucial importance to better understand living cells. Bacterial growth dynamics are quantitatively examined using various methods to determine the physical, chemical or biological features of growing populations. Due to methodological differences, the exponential growth rate, which is a parameter that is representative of growth dynamics, should be differentiated. Ignoring such differentiation in the growth analysis might overlook somehow slight but significant changes in cellular features of the growing population. Both experimental and theoretical investigations are required to address these issues.ResultsThis study experimentally verified the differentiation in growth rates attributed to different methodologies, and demonstrated that the most popular method, optical turbidity, led to the determination of a lower growth rate in comparison to the methods based on colony formation and cellular adenosine triphosphate, due to a decay effect of reading OD600 during a population increase. Accordingly, the logistic model, which is commonly applied to the high-throughput growth data reading the OD600, was revised by introducing a new parameter: the decay rate, to compensate for the lowered estimation in growth rates. An improved goodness of fit in comparison to the original model was acquired due to this revision. Applying the modified logistic model to hundreds of growth data acquired from an assortment of Escherichia coli strains carrying the reduced genomes led to an intriguing finding of a correlation between the decay rate and the genome size. The decay effect seemed to be partially attributed to the decrease in cell size accompanied by a population increase and was medium dependent.ConclusionsThe present study provides not only an improved theoretical tool for the high-throughput studies on bacterial growth dynamics linking with optical turbidity to biological meaning, but also a novel insight of the genome reduction correlated decay effect, which potentially reflects the changing cellular features during population increase. It is valuable for understanding the genome evolution and the fitness increase in microbial life.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1242-4) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 87%

Section: Methodsmentioning

confidence: 99%

A decay effect of the growth rate associated with genome reduction in Escherichia coli

et al. 2018

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“…In terms of colonization, a highly specialized population may lead to a higher rate of survival over the dispersal and also a higher rate of success in the introduction into new areas. Recent experimental observations have revealed a link between genome reduction and a growth rate decrease in bacteria (37). Similar circumstances may have occurred over the evolution of ST36, where multiple genomic deletions may lead to decreases in the growth rate of modern lineages of this clone, reducing the mutation rate because of a lower number of cell divisions.…”

Section: Discussionmentioning

confidence: 82%

Genomic Variation and Evolution ofVibrio parahaemolyticusST36 over the Course of a Transcontinental Epidemic Expansion

Martínez-Urtaza

Aerle

Abanto

et al. 2017

mBio

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Vibrio parahaemolyticus is the leading cause of seafood-related infections with illnesses undergoing a geographic expansion. In this process of expansion, the most fundamental change has been the transition from infections caused by local strains to the surge of pandemic clonal types. Pandemic clone sequence type 3 (ST3) was the only example of transcontinental spreading until 2012, when ST36 was detected outside the region where it is endemic in the U.S. Pacific Northwest causing infections along the U.S. northeast coast and Spain. Here, we used genome-wide analyses to reconstruct the evolutionary history of the V. parahaemolyticus ST36 clone over the course of its geographic expansion during the previous 25 years. The origin of this lineage was estimated to be in~1985. By 1995, a new variant emerged in the region and quickly replaced the old clone, which has not been detected since 2000. The new Pacific Northwest (PNW) lineage was responsible for the first cases associated with this clone outside the Pacific Northwest region. After several introductions into the northeast coast, the new PNW clone differentiated into a highly dynamic group that continues to cause illness on the northeast coast of the United States. Surprisingly, the strains detected in Europe in 2012 diverged from this ancestral group around 2000 and have conserved genetic features present only in the old PNW lineage. Recombination was identified as the major driver of diversification, with some preliminary observations suggesting a trend toward a more specialized lifestyle, which may represent a critical element in the expansion of epidemics under scenarios of coastal warming.IMPORTANCE Vibrio parahaemolyticus and Vibrio cholerae represent the only two instances of pandemic expansions of human pathogens originating in the marine environment. However, while the current pandemic of V. cholerae emerged more than 50 years ago, the global expansion of V. parahaemolyticus is a recent phenomenon. These modern expansions provide an exceptional opportunity to study the evolutionary process of these pathogens at first hand and gain an understanding of the mechanisms shaping the epidemic dynamics of these diseases, in particular, the emergence, dispersal, and successful introduction in new regions facilitating global spreading of infections. In this study, we used genomic analysis to examine the evolutionary divergence that has occurred over the course of the most recent transcon-

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“…This experimental evidence has pointed out one very important aspect of genome structure and function. Genome size increase is the result of horizontal gene transfer or DNA fragment retention that somehow is giving some beneicial features to recipient host, apparently an increase in itness [26]. The function of genes without evident function is still a relevant area of research since many of them provide support for itness and evolution has preserved them, therefore full genome engineering is far more complicated than previously thought.…”

Section: Genome Modiications To Understand E Colimentioning

confidence: 99%

“…The most relevant study revealed that genome size has an impact on E. coli cell growth, where it is shown that apparently dispensable sequences are needed under restrictive conditions, providing a hint of the still far future of fully functioning cells with all the desired characteristics for biotechnological applications [26]. We envision that genome reduction is a worthy efort, regardless of the method used to generate them.…”

Section: Genome Modiications To Understand E Colimentioning

confidence: 99%

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

Idalia¹,

Bernardo²

2017

≪i>Escherichia Coli

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Without a doubt, in the past 20 or so years, we have achieved the power of biology in diferent ways. In the present, we have many tools for developing novel technologies and applications for organism modiications that ultimately let us know many aspects of organisms' biology and, therefore, apply that knowledge for technological purposes. Of all the model organisms and tools for genetic modiication available, Escherichia coli stands out as a model organism and what we would like to call "molecular biologist tool box." In the present chapter, we aim to review our current knowledge regarding genetic modiications and tools for modifying E. coli to generate plasmid vectors, single and multiple gene knockouts, whole genome editing, biosensor generation and applications and synthetic gene circuits and genomes.

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Correlation between genome reduction and bacterial growth

Cited by 74 publications

References 48 publications

A decay effect of the growth rate associated with genome reduction in Escherichia coli

A decay effect of the growth rate associated with genome reduction in Escherichia coli

Genomic Variation and Evolution ofVibrio parahaemolyticusST36 over the Course of a Transcontinental Epidemic Expansion

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

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