Genome analysis of the metabolically versatile <i>Pseudomonas umsongensis</i> GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates

Narancic, Tanja; Salvador, Manuel; Hughes, Graham M.; Beagan, Niall; Abdulmutalib, Umar; Kenny, Shane T.; Wu, Huihai; Saccomanno, Marta; Um, Jounghyun; O’Connor, Kevin E.; Jiménez, José I.

doi:10.1111/1751-7915.13712

Cited by 53 publications

(27 citation statements)

References 60 publications

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“…To this end, we evaluated a simultaneous biodegradation scheme using FAST-PETase to demonstrate that this mutant enzyme is microbe-compatible. In particular, a soil bacteria Pseudomonas putida Go19 20,21 capable of naturally utilizing TPA as a carbon and energy source and capable of producing polyhydroxyalkanoates (PHAs) was employed. Initially, we sought to combine exogenous FAST-PETase with this host to explore the possibility of simultaneous PET depolymerization and fermentation.…”

Section: Manuscript Textmentioning

confidence: 99%

Deep learning redesign of PETase for practical PET degrading applications

Diaz

Czarnecki

et al. 2021

Preprint

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Plastic waste poses an ecological challenge. While current plastic waste management largely relies on unsustainable, energy-intensive, or even hazardous physicochemical and mechanical processes, enzymatic degradation offers a green and sustainable route for plastic waste recycling. Poly(ethylene terephthalate) (PET) has been extensively used in packaging and for the manufacture of fabrics and single-used containers, accounting for 12% of global solid waste. The practical application of PET hydrolases has been hampered by their lack of robustness and the requirement for high processing temperatures. Here, we use a structure-based, deep learning algorithm to engineer an extremely robust and highly active PET hydrolase. Our best resulting mutant (FAST-PETase: Functional, Active, Stable, and Tolerant PETase) exhibits superior PET-hydrolytic activity relative to both wild-type and engineered alternatives, (including a leaf-branch compost cutinase and its mutant) and possesses enhanced thermostability and pH tolerance. We demonstrate that whole, untreated, post-consumer PET from 51 different plastic products can all be completely degraded by FAST-PETase within one week, and in as little as 24 hours at 50 C. Finally, we demonstrate two paths for closed-loop PET recycling and valorization. First, we re-synthesize virgin PET from the monomers recovered after enzymatic depolymerization. Second, we enable in situ microbially-enabled valorization using a Pseudomonas strain together with FAST-PETase to degrade PET and utilize the evolved monomers as a carbon source for growth and polyhydroxyalkanoate production. Collectively, our results demonstrate the substantial improvements enabled by deep learning and a viable route for enzymatic plastic recycling at the industrial scale.

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Section: Manuscript Textmentioning

confidence: 99%

Deep learning redesign of PETase for practical PET degrading applications

Diaz

Czarnecki

et al. 2021

Preprint

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“…The pathway for PET assimilation by Ideonella sakaiensis begins with a pair of esterases that hydrolyze the polymer to its constituent monomers, ethylene glycol and terephthalate (TPA). Ethylene glycol is a natural product that is metabolized by multiple bacteria ( 8 – 10 ). TPA resembles plant-derived aromatic compounds, but it is not widely known as a substrate for bacterial growth.…”

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confidence: 99%

“…strain E6 ( 12 , 17 ), Comamonas testosteroni T-2 ( 15 ), C. testosteroni YZW-D ( 13 ), Delftia tsuruhatensis T7 ( 20 ), Rhodococcus sp. DK17 ( 11 ), Rhodococcus jostii RHA1 ( 14 ), Pseudomonas umsongensis GO16 ( 8 ), and Acinetobacter baylyi ADP1 (TPA importer) ( 21 ). Several studies have introduced TPA catabolism into microbes for metabolic engineering applications as well ( 22 – 26 ).…”

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confidence: 99%

Biochemical and structural characterization of an aromatic ring–hydroxylating dioxygenase for terephthalic acid catabolism

Kincannon

Zahn

Clare

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Significance More than 400 million tons of plastic waste is produced each year, the overwhelming majority of which ends up in landfills. Bioconversion strategies aimed at plastics have emerged as important components of enabling a circular economy for synthetic plastics, especially those that exhibit chemically similar linkages to those found in nature, such as polyesters. The enzyme system described in this work is essential for mineralization of the xenobiotic components of poly(ethylene terephthalate) (PET) in the biosphere. Our description of its structure and substrate preferences lays the groundwork for in vivo or ex vivo engineering of this system for PET upcycling.

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“…MIL9 strain is also a promising host for all sorts of biotransformation. Most recently, the genome analysis of the closely relative strain Pseudomonas umsongensis GO16 has shown the metabolic versatility and the potential for biotransformations (Narancic et al ., 2021). Since the genome sequencing data of Pseudomonas sp.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

An efficient and regioselective biocatalytic synthesis of aromatic N‐oxides by using a soluble di‐iron monooxygenase PmlABCDEF produced in the Pseudomonas species

Petkevičius

Vaitekūnas

Gasparavičiūtė

et al. 2021

Microbial Biotechnology

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Here, we present an improved whole-cell biocatalysis system for the synthesis of heteroaromatic N-oxides based on the production of a soluble di-iron monooxygenase PmlABCDEF in Pseudomonas sp. MIL9 and Pseudomonas putida KT2440. The presented biocatalysis system performs under environmentally benign conditions, features a straightforward and inexpensive procedure and possesses a high substrate conversion and product yield. The capacity of gram-scale production was reached in the simple shake-flask cultivation. The template substrates (pyridine, pyrazine, 2aminopyrimidine) have been converted into pyridine-1-oxide, pyrazine-1-oxide and 2-aminopyrimidine-1oxide in product titres of 18.0, 19.1 and 18.3 g l -1 , respectively. To our knowledge, this is the highest reported productivity of aromatic N-oxides using biocatalysis methods. Moreover, comparing to the chemical method of aromatic N-oxides synthesis based on meta-chloroperoxybenzoic acid, the developed approach is applicable for a regioselective oxidation that is an additional advantageous option in the preparation of the anticipated N-oxides.

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Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates

Cited by 53 publications

References 60 publications

Deep learning redesign of PETase for practical PET degrading applications

Deep learning redesign of PETase for practical PET degrading applications

Biochemical and structural characterization of an aromatic ring–hydroxylating dioxygenase for terephthalic acid catabolism

An efficient and regioselective biocatalytic synthesis of aromatic N‐oxides by using a soluble di‐iron monooxygenase PmlABCDEF produced in the Pseudomonas species

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