Experimental Microbial Evolution of Extremophiles

Blum, Paul H.; Rudrappa, Deepak; Singh, Raghuveer; McCarthy, Samuel; Pavlik, Benjamin J.

doi:10.1007/978-3-319-13521-2_22

Cited by 7 publications

(3 citation statements)

References 103 publications

(114 reference statements)

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“…This adaptive potential of microorganisms is increasingly explored in biotechnology by adaptive laboratory evolution (ALE) experiments (Blum et al, 2016 ). ALE can be utilized to improve production strains by increasing their tolerance to the metabolic product (Hu et al, 2016 ; Lennen, 2016 ), by activating latent pathways (Wang et al, 2016 ) or by enabling the utilization of non-native substrates (Lee and Palsson, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

et al. 2017

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Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution. However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes are simpler to implement and therefore allow higher throughput. The specific regimen of adaptive evolution may have a profound impact on the adapted cell state. Indeed, substantial effects of the selection regime on the resulting geno- and phenotypes have been reported in the literature. In this study we compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different selection regimens result in subtle genotypic and phenotypic differences key adaptations appear independently of the selection regime.

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Section: Introductionmentioning

confidence: 99%

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

et al. 2017

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“…Many attempts have been made by researchers to develop methods to stimulate the production of new chemical molecules (Mutka et al 2006;Gottelt et al 2010;Scherlach et al2010;Laureti 2011;Baltz et al 2011;Garbeva et al 2011). One of these methods includes adaptive laboratory evolution that has been successfully used to augment the production of antimicrobial molecules (Goers et al 2014;Charusanti et al 2012;Stergiopoulos et al 2013;Blum et al, 2016;Chunxiao et al 2018). The adaptive laboratory evolution is a phenomenon in which a parent strain is serially passed against a certain selection pressure for few generations to promote adaptation to a new prevailing niche.…”

Section: Introductionmentioning

confidence: 99%

Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency inStreptomyces

Harwani¹,

Begani²,

Barupal³

et al. 2021

Preprint

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In the present study, adaptive laboratory evolution was used to stimulate antibiotic production in a weak antibiotic-producing Streptomyces strain JB140. The seven different competition experiments utilized three serial passages (three cycles of adaptation-selection of 15 days each) of a weak antibiotic-producing Streptomyces strain (wild-type) against one (biculture) or two (triculture) or three (quadriculture) target pathogens. This resulted in the evolution of a weak antibiotic-producing strain into the seven unique mutant phenotypes that acquired the ability to constitutively exhibit increased antimicrobial activity against bacterial pathogens. The mutant not only effectively inhibited the growth of the tested pathogens but also observed to produce antimicrobial against multidrug-resistant (MDR) E. coli. Intriguingly, the highest antimicrobial activity was registered with the Streptomyces mutants that were adaptively evolved against the three pathogens (quadriculture competition). In contrast to the adaptively evolved mutants, a weak antimicrobial activity was detected in the un-evolved, wild-type Streptomyces. To get molecular evidence of evolution, RAPD profiles of the wild-type Streptomyces and its evolved mutants were compared that revealed significant polymorphism among them. These results demonstrated that competition-based adaptive laboratory evolution method can constitute a platform for evolutionary engineering to select improved phenotypes (mutants) with increased production of antibiotics against targeted pathogens.

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“…For example, increased production of l -serine in E. coli was achieved through ALE in cultures with increasing amount of l -serine [36]. Elsewhere, hydrogen induced stress has been used to develop strains overproducing hydrogen in Thermotoga maritima [37–39]. Strain mutagenesis methods and environmental conditions provided for mutating cells and enriching mutants are two major factors affecting ALE efficiency and effectiveness.…”

Section: Introductionmentioning

confidence: 99%

GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli

Wang

Sun

et al. 2019

Microb Cell Fact

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Background Late-stage fermentation broth contains high concentrations of target chemicals. Additionally, it contains various cellular metabolites which have leaked from lysed cells, which would exert multifactorial stress to industrial hyperproducers and perturb both cellular metabolism and product formation. Although adaptive laboratory evolution (ALE) has been wildly used to improve stress tolerance of microbial cell factories, single-factor stress condition (i.e. target product or sodium chloride at a high concentration) is currently provided. In order to enhance bacterial stress tolerance to actual industrial production conditions, ALE in late-stage fermentation broth is desired. Genome replication engineering assisted continuous evolution (GREACE) employs mutants of the proofreading element of DNA polymerase complex (DnaQ) to facilitate mutagenesis. Application of GREACE coupled-with selection under stress conditions is expected to accelerate the ALE process. Results In this study, GREACE was first modified by expressing a DnaQ mutant KR5-2 using an arabinose inducible promoter on a temperature-sensitive plasmid, which resulted in timed mutagenesis introduction. Using this method, tolerance of a lysine hyperproducer E. coli MU-1 was improved by enriching mutants in a lysine endpoint fermentation broth. Afterwards, the KR5-2 expressing plasmid was cured to stabilize acquired genotypes. By subsequent fermentation evaluation, a mutant RS3 with significantly improved lysine production capacity was selected. The final titer, yield and total amount of lysine produced by RS3 in a 5-L batch fermentation reached 155.0 ± 1.4 g/L, 0.59 ± 0.02 g lysine/g glucose, and 605.6 ± 23.5 g, with improvements of 14.8%, 9.3%, and 16.7%, respectively. Further metabolomics and genomics analyses, coupled with molecular biology studies revealed that mutations SpeB A302V , AtpB S165N and SecY M145V mainly contributed both to improved cell integrity under stress conditions and enhanced metabolic flux into lysine synthesis. Conclusions Our present study indicates that improving a lysine hyperproducer by GREACE-assisted ALE in its stressful living environment is efficient and effective. Accordingly, this is a promising method for improving other valuable chemical hyperproducers. Electronic supplementary material The online version of this article (10.1186/s12934-019-1153-6) contains supplementary material, which is available to authorized users.

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Experimental Microbial Evolution of Extremophiles

Cited by 7 publications

References 103 publications

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

Adaptive laboratory evolution triggers pathogen-dependent broad-spectrum antimicrobial potency inStreptomyces

GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli

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