Microbial adaptive evolution

Shi, Aiqin; Feng, Fan; Broach, James R.

doi:10.1093/jimb/kuab076

Cited by 32 publications

(16 citation statements)

References 94 publications

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“…Strains AMA_NO and AMA166, isolated post- and pre-COVID pandemic, were used to study changes at the genomic level to identify gene acquisition that could indicate patterns of adaptative genomic evolution [ 54 , 55 ]. The source of the AMA_NO strain was a patient with COVID-19.…”

Section: Resultsmentioning

confidence: 99%

Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic

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et al. 2023

Biology

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Background: After the emergence of COVID-19, numerous cases of A. baumannii/SARS-CoV-2 co-infection were reported. Whether the co-infecting A. baumannii strains have distinctive characteristics remains unknown. Methods and Results: A. baumannii AMA_NO was isolated in 2021 from a patient with COVID-19. AMA166 was isolated from a mini-BAL used on a patient with pneumonia in 2016. Both genomes were similar, but they possessed 337 (AMA_NO) and 93 (AMA166) unique genes that were associated with biofilm formation, flagellar assembly, antibiotic resistance, secretion systems, and other functions. The antibiotic resistance genes were found within mobile genetic elements. While both strains harbored the carbapenemase-coding gene blaOXA-23, only the strain AMA_NO carried blaNDM-1. Representative functions coded for by virulence genes are the synthesis of the outer core of lipooligosaccharide (OCL5), biosynthesis and export of the capsular polysaccharide (KL2 cluster), high-efficiency iron uptake systems (acinetobactin and baumannoferrin), adherence, and quorum sensing. A comparative phylogenetic analysis including 239 additional sequence type (ST) 2 representative genomes showed high similarity to A. baumannii ABBL141. Since the degree of similarity that was observed between A. baumannii AMA_NO and AMA166 is higher than that found among other ST2 strains, we propose that they derive from a unique background based on core-genome phylogeny and comparative genome analysis. Conclusions: Acquisition or shedding of specific genes could increase the ability of A. baumannii to infect patients with COVID-19.

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Section: Resultsmentioning

confidence: 99%

Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic

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et al. 2023

Biology

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“…Fitness and productivity of a producing organism can be improved by several means, including rational metabolic engineering, adaptive laboratory evolution (ALE) (24,25), the use of reduced and minimal genomes (26, 27), and the improvement of fermentation conditions (28). Metabolic engineering of E. coli strains optimising L-cysteine production, targets the overexpression of speci c bottleneck genes (Fig.…”

Section: Introductionmentioning

confidence: 99%

Metabolic stress constrains fermentative production of L-cysteine in Escherichia coli by accelerating transposition through mobile genetic elements in synthetic plasmid constructs

Heieck

Arnold

Brück

2022

Preprint

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Background L-cysteine is an essential chemical building block in the pharmaceutical-, cosmetic-, food and agricultural sector. Conventionally, L-cysteine production relies on the conversion of keratinous biomass mediated by hydrochloric acid. Today, fermentative production based on recombinant E. coli, where L-cysteine production is streamlined and facilitated by synthetic plasmid constructs, is an alternative process at industrial scale. However, space-time yields and process stability are still to be optimised for improved economic viability. We simulate an industrial fermentation process with Escherichia coli harbouring various L-cysteine production plasmid constructs. Results In a comparative experimental design, theE. coli K12 production strain W3110 and the reduced genome strain MDS42, almost free of insertion sequences, were used as hosts. Data indcates that W3110 populations acquire growth fitness at the expense of L-cysteine productivity within 60 generations, while production in MDS42 populations remains stable. For the first time, the negative impact of predominantly insertion sequence family 3 and 5 transposases on L-cysteine production is reported, by combining differential transcriptome analysis with NGS based deep plasmid sequencing. Furthermore, metabolic clustering of differentially expressed genes supports the hypothesis, that metabolic stress induces rapid propagation of plasmid rearrangements, leading to reduced L-cysteine yields in evolving populations over industrial fermentation time scales. Conclusion The results of this study implicate how selective deletion of insertion sequence families could be a new route for improving industrial L-cysteine or even general amino acid production using recombinant E. coli hosts. Instead of using minimal genome strains, a selective deletion of certain IS families could offer the benefits of adaptive laboratory evolution (ALE) while maintaining enhanced L-cysteine production stability.

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“…In nature, bacteria are the most abundant organisms on earth and have developed diverse metabolic functions during evolution. , Thereinto, some bacteria are found with the ability to metabolize lactate, which makes them credible candidates for remolding TME. − In fact, the therapeutic properties of bacteria have been confirmed by consuming “metabolic wastes” produced by tumor cells into immune activating substances to provoke a potent antitumor immunity. , Moreover, bacteria ( Veillonella atypica , Eubacterium hallii , Shewanella oneidensis MR-1, etc.) could metabolize lactate in the complicated physiological environment, which provide a God-given opportunity to enhance the antineoplastic therapeutic effects.…”

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“…21 In nature, bacteria are the most abundant organisms on earth and have developed diverse metabolic functions during evolution. 22,23 Thereinto, some bacteria are found with the ability to metabolize lactate, which makes them credible candidates for remolding TME. 24−26 In fact, the therapeutic properties of bacteria have been confirmed by consuming "metabolic wastes" produced by tumor cells into immune activating substances to provoke a potent antitumor immunity.…”

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confidence: 99%

An Engineered Bacterium-Based Lactate Bioconsumer for Regulating Immunosuppressive Tumor Microenvironment to Potentiate Antitumor Immunity

Zhang,

Jin,

Luo

et al. 2023

ACS Materials Lett.

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In this study, a bacterium-based lactate bioconsumer (designated Bac@ RFH) was elaborately engineered for persistent lactate consumption to potentiate antitumor immunotherapy. Specifically, Shewanella oneidensis MR-1 was surfacemodified with RFH nanoparticles (R848-loaded Fe-TCPP metal−organic framework nanoparticles coated with hyaluronic acid) via covalent borate ester bonds to prepare Bac@RFH bioconsumer, which could specifically target and colonize in tumors to efficiently metabolize intratumoral lactate and concurrently trigger the reduction of the Fe 3+ moieties of RFH through bacteria-mediated electron transfer, resulting in the decomposition of RFH to release Fe 2+ and R848. Moreover, the overexpressed H 2 O 2 in the tumor microenvironment (TME) was catalyzed by the Fe 2+ -driven Fenton reaction to produce cytotoxic ROS, which elicited immunogenic cell death of tumor cells, resulting in DCs maturation and effector T cells activation to eliminate tumors. With the combination of R848-mediated immune activation, Bac@RFH could significantly reshape the immunosuppressive TME for boosting antitumor immunity, such as reducing the recruitment of Tregs and MDSCs as well as promoting the M2-to-M1 polarization of tumor-associated macrophages. In addition, the synergy of Bac@RFH and αPD-1 could evoke robust immune responses to suppress tumor growth and achieve a tumor suppression rate over 90%, which represents a smart strategy to potentiate antitumor immunotherapy via bacterium-based metabolic regulation.

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Microbial adaptive evolution

Cited by 32 publications

References 94 publications

Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic

Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic

Metabolic stress constrains fermentative production of L-cysteine in Escherichia coli by accelerating transposition through mobile genetic elements in synthetic plasmid constructs

An Engineered Bacterium-Based Lactate Bioconsumer for Regulating Immunosuppressive Tumor Microenvironment to Potentiate Antitumor Immunity

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