An Ultra-Sensitive
            <i>Comamonas thiooxidans</i>
            Biosensor for the Rapid Detection of Enzymatic Polyethylene Terephthalate (PET) Degradation

Dierkes, Robert F.; Wypych, Alan; Pérez-García, Pablo; Danso, Dominik; Chow, Jennifer; Streit, Wolfgang R.

doi:10.1128/aem.01603-22

Cited by 15 publications

(9 citation statements)

References 52 publications

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“…5 A). While Comamonas is commonly recognized as capable of degrading TPA (Dierkes Robert et al 2022 ; Hosaka et al 2013 ), the utilization of EG and BHET has not been characterized before. This means that CNB-1-based whole-cell biocatalyst can completely mineralize the PET microplastics, rather than merely degrading it into smaller molecules.…”

Section: Resultsmentioning

confidence: 99%

“…Comamonadaceae is a dominant species in the activated sludge system, comprising more than 2% of the total abundance of sludge microorganisms (Wu et al 2019 ; Zhang et al 2020a ). Additionally, studies have reported that Comamonas can degrade terephthalic acid (TPA) and ethylene glycol (EG), which are the main products of PET depolymerization (Aksu et al 2021 ; Dierkes Robert et al 2022 ; Hosaka et al 2013 ; Ma et al 2009 ). The objective of this study is to create a whole-cell biocatalyst for the degradation of PET microplastics.…”

Section: Introductionmentioning

confidence: 99%

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Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation

Cao,

Xia,

et al. 2023

Bioresour. Bioprocess.

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The escalating crisis of polyethylene terephthalate (PET) microplastic contamination in biological wastewater treatment systems is a pressing environmental concern. These microplastics inevitably accumulate in sewage sludge due to the absence of effective removal technologies. Addressing this urgent issue, this study introduces a novel approach using DuraPETase, a potent enzyme with enhanced PET hydrolytic activity at ambient temperatures. Remarkably, this enzyme was successfully secreted from Comamonas testosteroni CNB-1, a dominant species in the active sludge. The secreted DuraPETase showed significant hydrolytic activity toward p-NPB and PET nanoplastics. Furthermore, the CNB-1 derived whole-cell biocatalyst was able to depolymerize PET microplastics under ambient temperature, achieving a degradation efficiency of 9% within 7 days. The CNB-1-based whole biocatalysts were also capable of utilizing PET degradation intermediates, such as terephthalic acid (TPA) and ethylene glycol (EG), and bis(2-hydroxyethyl)-TPA (BHET), for growth. This indicates that it can completely mineralize PET, as opposed to merely breaking it down into smaller molecules. This research highlights the potential of activated sludge as a potent source for insitu microplastic removal. Graphical Abstract

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation

Cao,

Xia,

et al. 2023

Bioresour. Bioprocess.

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“…The species of the genus Comamonas are commonly found in a variety of environmental samples and are among the common bacteria in soil [5,6], food waste compost [7], wetlands [8] and wastewater treatment systems [9,10]. In addition, the genus Comamonas has a broad metabolic capacity to degrade various organic and inorganic substrates, including amino acids, aromatic compounds, carboxylic acids, heavy metals and steroids [11][12][13]. Moreover, several studies have extensively described the roles of Comamonas species in the processes of wastewater bioaugmentation and bioremediation [14,15].…”

Section: Introductionmentioning

confidence: 99%

Comamonas resistens sp. nov. and Pseudomonas triclosanedens sp. nov., two members of the phylum Pseudomonadota isolated from the wastewater treatment system of a pharmaceutical factory

Yin,

Han,

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Five strains of two novel species were isolated from the wastewater treatment systems of a pharmaceutical factory located in Zhejiang province, PR China. Strains ZM22T and Y6 were identified as belonging to a potential novel species of the genus Comamonas , whereas strains ZM23T, ZM24 and ZM25 were identified as belonging to a novel species of the genus Pseudomonas . These strains were characterized by polyphasic approaches including 16S rRNA gene analysis, multi-locus sequence analysis, average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH), physiological and biochemical tests, as well as chemotaxonomic analysis. Genome-based phylogenetic analysis further confirmed that strains ZM22T and Y6 form a distinct clade closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T. Strains ZM23T, ZM24 and ZM25 were grouped as a separate clade closely related to Pseudomonas nitroreducens DSM 14399T and Pseudomonas nicosulfuronedens LAM1902T. The orthoANI and isDDH results indicated that strains ZM22T and Y6 belong to the same species. In addition, genomic DNA fingerprinting demonstrated that these strains do not originate from a single clone. The same results were observed for strains ZM23T, ZM24 and ZM25. Strains ZM22T and Y6 were resistant to multiple antibiotics, whereas strains ZM23T, ZM24 and ZM25 were able to degrade an emerging pollutant, triclosan. The phylogenetic, physiological and biochemical characteristics, as well as chemotaxonomy, allowed these strains to be distinguished from their genus, and we therefore propose the names Comamonas resistens sp. nov. (type strain ZM22=MCCC 1K08496T=KCTC 82561T) and Pseudomonas triclosanedens sp. nov. (type strain ZM23T=MCCC 1K08497T=JCM 36056T), respectively.

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“…Among emerging applications of genetically encoded biosensors, these tools are expected to play a significant role in advancing and supporting the biological synthesis and degradation of plastics, contributing to achieving greater waste circularity 27–29 . For example, to support the transition away from petrochemical-based to renewable feedstocks, biosensors have been applied to facilitate metabolic engineering efforts to produce drop-in monomer precursors and/or for bio-based plastic production 4,30,31 .…”

Section: Introductionmentioning

confidence: 99%

“…For example, to support the transition away from petrochemical-based to renewable feedstocks, biosensors have been applied to facilitate metabolic engineering efforts to produce drop-in monomer precursors and/or for bio-based plastic production 4,30,31 . Additionally, biosensors can be highly powerful screening tools to discovery and optimize novel enzymes for the efficient breakdown of plastics 27,28 . Here, we applied DoE as a design framework to achieve customised performance of activator-based biosensors.…”

Section: Introductionmentioning

confidence: 99%

Tuning the performance of a TphR-based terephthalate biosensor with a design of experiments approach

Gonzalez,

Chacón,

Butterfield

et al. 2024

Preprint

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Transcription factor-based biosensors are genetic tools that aim to predictability link the presence of a specific input stimuli to a tailored gene expression output. The performance characteristics of a biosensor fundamentally determines its potential applications. However, current methods to engineer and optimise tailored biosensor responses are highly nonintuitive, and struggle to investigate multidimensional sequence/design space efficiently. In this study we employ a design of experiments (DoE) approach to build a framework for efficiently engineering activator-based biosensors with tailored performances, and we apply the framework for the development of biosensors for the polyethylene terephthalate (PET) plastic degradation monomer terephthalate (TPA). We simultaneously engineer the core promoter and operator regions of the responsive promoter, and by employing a dual refactoring approach, we were able to explore an enhanced biosensor design space and assign their causative performance effects. The approach employed here serves as a foundational framework for engineering transcriptional biosensors and enabled development of tailored biosensors with enhanced dynamic range and diverse signal output, sensitivity, and steepness. We further demonstrate its applicability on the development of tailored biosensors for primary screening of PET hydrolases and enzyme condition screening, demonstrating the potential of statistical modelling in optimizing biosensors for tailored industrial and environmental applications.Abstract FigureGraphical Abstract. Employment of a DoE framework for fine-tuning biosensor performance.HighlightsBioinformatic mining of allosteric transcription factors to produce TPA biosensorsEfficient sampling of complex sequence-function relationships of genetic circuitsModelling to learn and optimise biosensor genetic circuitsApplication of biosensors for primary and secondary enzyme screening applications

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An Ultra-Sensitive Comamonas thiooxidans Biosensor for the Rapid Detection of Enzymatic Polyethylene Terephthalate (PET) Degradation

Abstract: Plastics and microplastics accumulate in all ecological niches. The construction of more sensitive biosensors allows to monitor and screen potential PET degradation in natural environments and industrial samples.

Cited by 15 publications

References 52 publications

Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation

Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation

Comamonas resistens sp. nov. and Pseudomonas triclosanedens sp. nov., two members of the phylum Pseudomonadota isolated from the wastewater treatment system of a pharmaceutical factory

Tuning the performance of a TphR-based terephthalate biosensor with a design of experiments approach

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