Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products

Frontiers in Bioengineering and Biotechnology, Journal Year: 2020, Volume and Issue: 7

Published: Jan. 17, 2020

Pseudomonas putida KT2440 is a well-established chassis in industrial biotechnology. To increase the substrate spectrum, we implemented three alternative xylose utilization pathways, namely Isomerase, Weimberg, and Dahms pathways. The synthetic operons contain genes from Escherichia coli taiwanensis. For isolating pathway P. two (PP_2836 PP_4283), encoding an endogenous enzyme of Weimberg regulator for glycolaldehyde degradation, were deleted. Before after adaptive laboratory evolution, these strains characterized terms growth synthesis mono-rhamnolipids pyocyanin. engineered strain using reached highest maximal rate 0.30 h-1. After evolution lag phase was reduced significantly. titers 720 mg L-1 30 pyocyanin by evolved or Isomerase pathway, respectively. different stoichiometries pathways may allow engineering tailored valuable bioproduct synthesis.

Language: Английский

---

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

eLife, Journal Year: 2021, Volume and Issue: 10

Published: April 20, 2021

A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine taxonomic composition communities. Motivated by this challenge, investigate communities assembled pairs nutrients be predicted from those every single nutrient alone. We find that although null, naturally additive model generally predicts well family-level composition, there exist systematic deviations predictions reflect generic patterns dominance at family level. Pairs more-similar (e.g. two sugars) are on average more than dissimilar (one sugar–one organic acid). Furthermore, sugar–acid similar to sugar acid community, which may explained asymmetries benefits. Overall, our results suggest regularities interact help responses dietary changes.

Language: Английский

---

A navigation guide of synthetic biology tools for Pseudomonas putida

Biotechnology Advances, Journal Year: 2021, Volume and Issue: 49, P. 107732 - 107732

Published: March 27, 2021

Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility ability sustain difficult redox reactions operational stresses, among other attractive characteristics. A wealth genetic in silico tools have been developed enable the unravelling physiology improvement performance. However, rise this microbe as promising platform biotechnological applications has resulted diversification methods rather than standardization convergence. As consequence, multiple same purpose generated, whilst most them not embraced by scientific community, which led compartmentalization inefficient use resources. Inspired substantial increase popularity P. putida, we aim herein bring together assess all currently available (wet dry) synthetic biology specific microbe, focusing on last 5 years. We provide information principles, functionality, advantages limitations, with special focus their engineering. Additionally, compare tool portfolio those bacterial discuss future directions development. Therefore, review intended reference guide experts new 'users' chassis.

Language: Английский

---

Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida

Metabolic Engineering, Journal Year: 2021, Volume and Issue: 67, P. 373 - 386

Published: July 31, 2021

Pseudomonas putida is evolutionarily endowed with features relevant for bioproduction, especially under harsh operating conditions. The rich metabolic versatility of this species, however, comes at the price limited formation acetyl-coenzyme A (CoA) from sugar substrates. Since acetyl-CoA a key precursor number added-value products, in work we deployed an silico-guided rewiring program central carbon metabolism upgrading P. as host acetyl-CoA-dependent bioproduction. An updated kinetic model, integrating fluxomics and metabolomics datasets addition to manually-curated information enzyme mechanisms, identified targets that would lead increased levels. Based on these predictions, set plasmids based clustered regularly interspaced short palindromic repeats (CRISPR) dead CRISPR-associated protein 9 (dCas9) was constructed silence genes by CRISPR interference (CRISPRi). Dynamic reduction gene expression two (gltA, encoding citrate synthase, essential accA gene, subunit carboxylase complex) mediated 8-fold increase content rewired putida. Poly(3-hydroxybutyrate) (PHB) adopted proxy availability, synthetic pathways were engineered biopolymer accumulation. By including cell morphology extra target CRISPRi approach, fully strains programmed PHB accumulation had 5-fold titers bioreactor cultures using glucose. Thus, strategy described herein allowed rationally redirecting fluxes towards product biosynthesis-especially when deletion not option.

Language: Английский

---

Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion

Biotechnology for Biofuels and Bioproducts, Journal Year: 2022, Volume and Issue: 15(1)

Published: Feb. 7, 2022

Lignocellulose is the most abundant organic carbon polymer on earth. Its decomposition and conversion greatly impact global cycle. Furthermore, it provides feedstock for sustainable fuel other value-added products. However, continues to be underutilized, due its highly recalcitrant heterogeneric structure. Microorganisms, which have evolved versatile pathways convert lignocellulose, undoubtedly are at heart of lignocellulose conversion. Numerous studies that reported successful metabolic engineering individual strains improve biological lignin valorization. Meanwhile, bottleneck single strain modification becoming increasingly urgent in complex substrates. Alternatively, increased attention has been paid microbial consortia, as they show advantages over pure cultures, e.g., high efficiency robustness. Here, we first review recent developments communities bioconversion. emerging area synthetic ecology, an integration biology, computational opportunity bottom-up construction consortia. Then, different modes interaction their molecular mechanisms, discuss considerations how employ these interactions construct consortia via well highlight trends

Language: Английский

---

Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation

Environmental Research, Journal Year: 2022, Volume and Issue: 214, P. 114011 - 114011

Published: Aug. 17, 2022

Language: Английский

---

Microplastic Accumulation and Degradation in Environment via Biotechnological Approaches

Water, Journal Year: 2022, Volume and Issue: 14(24), P. 4053 - 4053

Published: Dec. 12, 2022

The extensive use of plastics in daily life has led to the generation huge amounts plastic waste, which causes an enormous burden on environment. More than half waste ends up landfill, and about one-fifth is managed by incineration. Only one-tenth recycled, rest, mismanaged terrestrial aquatic Here, we review how deterioration leads formation microplastics nanoplastics, are now found abundantly contaminating water bodies. It observed that increasing experimental evidence provides data presence these food items, environment, even human body. harmful effects health still need be substantiated with more precise studies. However, measures can taken reduce production improving methods used for degradation. This focuses genetic engineering, genome editing, synthetic biology, system biology approaches increase potential microorganisms degrade plastics.

Language: Английский

---

Recent progress in the synthesis of advanced biofuel and bioproducts

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 80, P. 102913 - 102913

Published: Feb. 26, 2023

Language: Английский

---

A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 3, 2023

Abstract Constraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements media uptake fluxes performed. We show how hybrid neural-mechanistic can serve as an architecture machine learning providing a way improve predictions. illustrate our with growth rate Escherichia coli and Pseudomonas putida grown gene knocked-out mutants. Our systematically outperform constraint-based require training set sizes orders magnitude smaller than classical methods. approach opens doorway enhancing modeling: instead constraining mechanistic additional experimental measurements, grasp power while fulfilling constrains, thus saving time resources typical systems biology or biological engineering projects.

Language: Английский

---

Synthetic biology tools for environmental protection

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 68, P. 108239 - 108239

Published: Aug. 22, 2023

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, immediate beneficial impact environment came reducing our oil dependency. However, is starting play a more direct role environmental protection. Toxic released by industries agriculture endanger environment, disrupting ecosystem balance biodiversity loss. This review highlights that can help protection providing remediation systems capable sensing responding specific pollutants. Remediation strategies based genetically engineered microbes plants are discussed. Further, an overview computational facilitate design application tools presented.

Language: Английский

---