Reconstructing organisms in silico: genome-scale models and their emerging applications

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(12), P. 731 - 743

Published: Sept. 21, 2020

Language: Английский

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Towards bio-upcycling of polyethylene terephthalate

Metabolic Engineering, Journal Year: 2021, Volume and Issue: 66, P. 167 - 178

Published: April 19, 2021

Over 359 million tons of plastics were produced worldwide in 2018, with significant growth expected the near future, resulting global challenge end-of-life management. The recent identification enzymes that degrade previously considered non-biodegradable opens up opportunities to steer plastic recycling industry into realm biotechnology. Here, sequential conversion post-consumer polyethylene terephthalate (PET) two types bioplastics is presented: a medium chain-length polyhydroxyalkanoate (PHA) and novel bio-based poly(amide urethane) (bio-PU). PET films are hydrolyzed by thermostable polyester hydrolase yielding highly pure ethylene glycol. obtained hydrolysate used directly as feedstock for terephthalate-degrading Pseudomonas umsongensis GO16, also evolved efficiently metabolize glycol, produce PHA. strain further modified secrete hydroxyalkanoyloxy-alkanoates (HAAs), which monomers chemo-catalytic synthesis bio-PU. In short, value-chain upcycling shown circumvents costly purification monomers, adding technological flexibility management plastics.

Language: Английский

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Industrial biotechnology of Pseudomonas putida: advances and prospects

Applied Microbiology and Biotechnology, Journal Year: 2020, Volume and Issue: 104(18), P. 7745 - 7766

Published: Aug. 13, 2020

Abstract Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity traced to its remarkably versatile metabolism, adapted withstand physicochemical stress, and the capacity thrive harsh environments. Owing these characteristics, there growing interest this microbe for industrial use, corresponding research has made rapid progress recent years. Hereby, strong drivers are exploitation of cheap renewable feedstocks waste streams produce value-added chemicals steady genetic strain engineering systems biology understanding bacterium. Here, we summarize advances prospects engineering, synthetic biology, applications P. as cell factory. Key points • global Novel tools enable system-wide streamlined genomic engineering. Applications range from bioeconomy biosynthetic drugs.

Language: Английский

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Designing Microbial Cell Factories for the Production of Chemicals

JACS Au, Journal Year: 2022, Volume and Issue: 2(8), P. 1781 - 1799

Published: Aug. 4, 2022

The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined produce interests renewable carbon sources. for the can be defined into three categories with reference microbial host selected engineering: native-existing pathways, nonnative-existing and nonnative-created pathways. Recent trends in leveraging discovering designing de novo (as pathways) discussed this Perspective. We highlight key approaches successful case studies that exemplify these concepts. Once designed constructed factory, systems metabolic engineering strategies used improve performance strain meet industrial standards. In second part Perspective, current design tools eye toward future. Finally, we survey future challenges need addressed advance chemicals.

Language: Английский

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Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1751 - 1766

Published: Jan. 11, 2021

Abstract As a frequent inhabitant of sites polluted with toxic chemicals, the soil bacterium and plant-root colonizer Pseudomonas putida can tolerate high levels endogenous exogenous oxidative stress. Yet, ultimate reason such phenotypic property remains largely unknown. To shed light on this question, metabolic network-wide routes for NADPH generation—the currency that fuels redox-stress quenching mechanisms—were inspected when P. KT2440 was challenged sub-lethal H2O2 dose as proxy conditions. 13C-tracer experiments, metabolomics, flux analysis, together assessment physiological parameters measurement enzymatic activities, revealed substantial reconfiguration in environments. In particular, periplasmic glucose processing rerouted to cytoplasmic oxidation, cyclic operation pentose phosphate pathway led significant NADPH-forming fluxes, exceeding biosynthetic demands by ~50%. The resulting surplus, turn, fueled glutathione system reduction. These properties not only account tolerance environmental insults—some which end up formation reactive oxygen species—but they also highlight value bacterial host platform bioremediation engineering.

Language: Английский

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Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

New Biotechnology, Journal Year: 2023, Volume and Issue: 74, P. 1 - 15

Published: Jan. 31, 2023

Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into design-build-test-learn cycle (DBTLc) will shift metabolic paradigm from almost artisanal labor towards a fully automated workflow. Here, we provide perspective on how DBTLc could be harnessed to construct next-generation bacterial factories fast, high-throughput fashion. Innovative toolsets approaches that pushed boundaries each segment are reviewed this end. We also present most recent efforts automation DBTLc, which heralds autonomous pipeline biology near future.

Language: Английский

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Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: May 19, 2020

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged a serious threat pollution. Bioremediation is key to eliminate persistent contaminants from environment. The traditional bioremediation processes showed limitations, therefore, it necessary discover new technologies for best results. Here, in this review, we have provided an outlook on alternative strategies via synthetic biology, including exploring prerequisites analysis research data developing biological models microbial bioremediation. Moreover, cell coordination community, signaling, quorum sensing are engineered enhanced also described along promising gene editing tools obtaining host target sequences responsible degradation compounds. genetic circuit two-component regulatory system (TCRS) based biosensors detection briefly explained. These developments expected increase efficiency

Language: Английский

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Functional attractors in microbial community assembly

Cell Systems, Journal Year: 2021, Volume and Issue: 13(1), P. 29 - 42.e7

Published: Oct. 16, 2021

Language: Английский

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Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates

Biotechnology Journal, Journal Year: 2020, Volume and Issue: 16(3)

Published: Oct. 21, 2020

Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil-derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers play a critical role central metabolism producer bacteria, as they act dynamic reservoirs carbon and reducing equivalents. PHAs continue to attract industrial attention starting point toward renewable, biodegradable, biocompatible, versatile thermoplastic elastomeric materials. Pseudomonas species have been known for long efficient biopolymer producers, especially medium-chain-length PHAs. The surge synthetic biology metabolic engineering approaches recent years offers possibility exploiting untapped potential cell factories tailored In this article, an overview regulatory circuits rule PHA accumulation putida is provided, leading biosynthesis novel (e.g., including nonbiological chemical elements their structures) discussed. disrupt existing future market segments closer realization than ever before. review concluded by pinpointing challenges currently hinder wide adoption bio-based PHAs, strategies programmable polymer from alternative substrates engineered P. strains proposed.

Language: Английский

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Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Oct. 23, 2020

Abstract High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due trade-offs between carbon use for growth production. To these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions elimination couple metabolite production strongly with growth. We compute MCS solution-sets a non-native product indigoidine, sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. implement total of genes knockdowns using multiplex-CRISPRi. MCS-based shifts from stationary exponential phase. 25.6 g/L, 0.22 g/l/h, ~50% maximum theoretical (0.33 g indigoidine/g glucose). These phenotypes maintained batch fed-batch mode, across scales (100-ml shake flasks, 250-ml ambr®, 2-L bioreactors).

Language: Английский

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