Metabolic engineering of Yarrowia lipolytica for poly(ethylene terephthalate) degradation

Freshwater plastisphere: a review on biodiversity, risks, and biodegradation potential with implications for the aquatic ecosystem health

The plastisphere, a unique microbial biofilm community colonizing plastic debris and microplastics (MPs) in aquatic environments, has attracted increasing attention owing to its ecological and public health implications. This review consolidates current state of knowledge on freshwater plastisphere, focussing on its biodiversity, community assembly, and interactions with environmental factors. Current biomolecular approaches revealed a variety of prokaryotic and eukaryotic taxa associated with plastic surfaces. Despite their ecological importance, the presence of potentially pathogenic bacteria and mobile genetic elements (i.e., antibiotic resistance genes) raises concerns for ecosystem and human health. However, the extent of these risks and their implications remain unclear. Advanced sequencing technologies are promising for elucidating the functions of plastisphere, particularly in plastic biodegradation processes. Overall, this review emphasizes the need for comprehensive studies to understand plastisphere dynamics in freshwater and to support effective management strategies to mitigate the impact of plastic pollution on freshwater resources.

Commercialization potential of PET (polyethylene terephthalate) recycled nanomaterials: A review on validation parameters

Polyethylene Terephthalate (PET) is a polymer which is considered as one of the major contaminants to the environment. The PET waste materials can be recycled to produce value-added products. PET can be converted to nanoparticles, nanofibers, nanocomposites, and nano coatings. To extend the applications of PET nanomaterials, understanding its commercialization potential is important. In addition, knowledge about the factors affecting recycling of PET based nanomaterials is essential. The presented review is focused on understanding the PET commercialization aspects, keeping in mind market analysis, growth drivers, regulatory affairs, safety considerations, issues associated with scale-up, manufacturing challenges, economic viability, and cost-effectiveness. In addition, the paper elaborates the challenges associated with the use of PET based nanomaterials. These challenges include PET contamination to water, soil, sediments, and human exposure to PET nanomaterials. Moreover, the paper discusses in detail about the factors affecting PET recycling, commercialization, and circular economy with specific emphasis on life cycle assessment (LCA) of PET recycled nanomaterials.

Optimizing concentration and interaction mechanism of Demodesmus sp. and Achromobacter pulmonis sp. consortium to evaluate their potential for dibutyl phthalate removal from synthetic wastewater

A green approach of Desmodesmus sp. to Achromobacter pulmonis (1:1) coculture ratios was optimized to improve the removal efficiency of dibutyl phthalate (DBP) from simulated wastewater. High DBP resistance bacterial strains and microalgae was optimized from plastic contaminated water and acclimation process respectively. The influence of various factors on DBP removal performance was comprehensively investigated. Highest DBP removal 93 % was recorded, when the ratios algae-bacteria 1:1, with sodium acetate, pH-6, shaking speed-120 rpm and lighting periods L:D-12:12. Enough nutrient (TN/TP/TOC) availability and higher protein-108 mg/L and sugar-40 mg/L were observed in presences of 50 mg/L DBP. The degradation and sorption were calculated 81,12; 27,39 & 43,12 % in algae-bacteria, only algae and only bacteria system respectively. The degradation kinetics t1/2 3.74,22.15,12.86 days were evaluated, confirming that algae-bacteria effectively degrade the DBP. This outcome leading to promote a green sustainable approach to remove the emerging contamination from wastewater.

Microbial colonization patterns and biodegradation of petrochemical and biodegradable plastics in lake waters: insights from a field experiment

Introduction

Once dispersed in water, plastic materials become promptly colonized by biofilm-forming microorganisms, commonly known as plastisphere.

Methods

By combining DNA sequencing and Confocal Laser Scanning Microscopy (CLSM), we investigated the plastisphere colonization patterns following exposure to natural lake waters (up to 77 days) of either petrochemical or biodegradable plastic materials (low density polyethylene - LDPE, polyethylene terephthalate - PET, polylactic acid - PLA, and the starch-based MaterBi® - Mb) in comparison to planktonic community composition. Chemical composition, water wettability, and morphology of plastic surfaces were evaluated, through Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM), and static contact angle analysis, to assess the possible effects of microbial colonization and biodegradation activity.

Results and Discussion

The phylogenetic composition of plastisphere and planktonic communities was notably different. Pioneering microbial colonisers, likely selected from lake waters, were found associated with all plastic materials, along with a core of more than 30 abundant bacterial families associated with all polymers. The different plastic materials, either derived from petrochemical hydrocarbons (i.e., LDPE and PET) or biodegradable (PLA and Mb), were used by opportunistic aquatic microorganisms as adhesion surfaces rather than carbon sources. The Mb-associated microorganisms (i.e. mostly members of the family Burkholderiaceae) were likely able to degrade the starch residues on the polymer surfaces, although the Mb matrix maintained its original chemical structure and morphology. Overall, our findings provide insights into the complex interactions between aquatic microorganisms and plastic materials found in lake waters, highlighting the importance of understanding the plastisphere dynamics to better manage the fate of plastic debris in the environment.

Mutation in yl-HOG1 represses the filament-to-yeast transition in the dimorphic yeast Yarrowia lipolytica

BACKGROUND

Yarrowia lipolytica is a dimorphic fungus, which switches from yeast to filament form in response to environmental conditions. For industrial purposes it is important to lock cells in the yeast or filamentous form depending on the fermentation process. yl-Hog1 kinase is a key component of the HOG signaling pathway, responsible for activating the osmotic stress response. Additionally, deletion of yl-Hog1 leads to increased filamentation in Yarrowia lipolytica, but causes significant sensitivity to osmotic stress induced by a high concentration of a carbon source.

RESULTS

In this study, we tested the effect of point mutations on the function of yl-Hog1 protein kinase. The targets of modification were the phosphorylation sites (T171A-Y173A) and the active center (K49R). Introduction of the variant HOG1-49 into the hog1∆ strain partially improved growth under osmotic stress, but did not recover the yeast-like shape of the cells. The HOG1-171/173 variant was not functional, and its introduction further weakened the growth of hog1∆ strains in hyperosmotic conditions. To verify a genetic modification in filament form, we developed a new system based on green fluorescent protein (GFP) for easier screening of proper mutants.

CONCLUSIONS

These results provide new insights into the functions of yl-Hog1 protein in dimorphic transition and constitute a good starting point for further genetic modification of Y. lipolytica in filament form.

Repurposing of waste PET by microbial biotransformation to functionalized materials for additive manufacturing

Plastic waste is an outstanding environmental thread. Poly(ethylene terephthalate) (PET) is one of the most abundantly produced single-use plastics worldwide, but its recycling rates are low. In parallel, additive manufacturing is a rapidly evolving technology with wide-ranging applications. Thus, there is a need for a broad spectrum of polymers to meet the demands of this growing industry and address post-use waste materials. This perspective article highlights the potential of designing microbial cell factories to upcycle PET into functionalized chemical building blocks for additive manufacturing. We present the leveraging of PET hydrolyzing enzymes and rewiring the bacterial C2 and aromatic catabolic pathways to obtain high-value chemicals and polymers. Since PET mechanical recycling back to original materials is cost-prohibitive, the biochemical technology is a viable alternative to upcycle PET into novel 3D printing materials, such as replacements for acrylonitrile butadiene styrene. The presented hybrid chemo-bio approaches potentially enable the manufacturing of environmentally friendly degradable or higher-value high-performance polymers and composites and their reuse for a circular economy.

ONE-SENTENCE SUMMARY

Biotransformation of waste PET to high-value platform chemicals for additive manufacturing.

Development of a yeast whole-cell biocatalyst for MHET conversion into terephthalic acid and ethylene glycol

BACKGROUND

Over the 70 years since the introduction of plastic into everyday items, plastic waste has become an increasing problem. With over 360 million tonnes of plastics produced every year, solutions for plastic recycling and plastic waste reduction are sorely needed. Recently, multiple enzymes capable of degrading PET (polyethylene terephthalate) plastic have been identified and engineered. In particular, the enzymes PETase and MHETase from Ideonella sakaiensis depolymerize PET into the two building blocks used for its synthesis, ethylene glycol (EG) and terephthalic acid (TPA). Importantly, EG and TPA can be re-used for PET synthesis allowing complete and sustainable PET recycling.

RESULTS

In this study we used Saccharomyces cerevisiae, a species utilized widely in bioindustrial fermentation processes, as a platform to develop a whole-cell catalyst expressing the MHETase enzyme, which converts monohydroxyethyl terephthalate (MHET) into TPA and EG. We assessed six expression architectures and identified those resulting in efficient MHETase expression on the yeast cell surface. We show that the MHETase whole-cell catalyst has activity comparable to recombinant MHETase purified from Escherichia coli. Finally, we demonstrate that surface displayed MHETase is active across a range of pHs, temperatures, and for at least 12 days at room temperature.

CONCLUSIONS

We demonstrate the feasibility of using S. cerevisiae as a platform for the expression and surface display of PET degrading enzymes and predict that the whole-cell catalyst will be a viable alternative to protein purification-based approaches for plastic degradation.

Production of PETase by engineered Yarrowia lipolytica for efficient poly(ethylene terephthalate) biodegradation

There has been a growing interest in poly(ethylene terephthalate) PET degradation studies in the last few years due to its widespread use and large-scale plastic waste accumulation in the environment. One of the most promising enzymatic methods in the context of PET degradation is the use of PETase from Ideonella sakaiensis, which has been reported to be an efficient enzyme for hydrolysing ester bonds in PET. In our study, we expressed a codon-optimized PETase gene in the yeast Yarrowia lipolytica. The obtained strain was tested for its ability to degrade PET directly in culture, and a screening of different supplements that might raise the level of PET hydrolysis was performed. We also carried out long-term cultures with PET film, the surface of which was examined by scanning electron microscopy. The efficiency of PET degradation was tested based on the concentration of degradation products released, and the results showed that supplementation of the culture with olive oil resulted in 66 % higher release of terephthalic acid into the medium compared to the mutant culture without supplementation. The results indicate the possibility of ethylene glycol uptake by both strains, and, additionally, the PETase produced by the newly engineered strain hydrolyses MHET. The structure of the PET film after culture with the modified strain, meanwhile, had numerous surface defects, cracks, and deformations.

Advanced insights on removal of antibiotics by microalgae-bacteria consortia: A state-of-the-art review and emerging prospects

Antibiotics abuse has triggered a growing environmental problem, posing a major threat to both ecosystem and human health. Unfortunately, there are still several shortcomings to current antibiotics removal technologies. Microalgae-bacteria consortia have been shown to be a promising antibiotics treatment technology owing to advantages of high antibiotics removal efficiency, low operational cost, and carbon emission reduction. This review aims to introduce the removal mechanisms, influencing factors, and future research perspectives for using microalgae-bacteria consortia to remove antibiotics. The interaction mechanisms between microalgae and bacteria are comprehensively revealed, and their exclusive advantages have been summarized in a "Trilogy" strategy, including "reinforced physical contact", "upgraded substance utilization along with antibiotics degradation", and "robust biological regulation". What's more, the relationship between different interaction mechanisms is emphatically analyzed. The important influencing factors, including concentration and classes of antibiotics, environmental conditions, and operational parameters, of antibiotics removal were also assessed. Three innovative treatment systems (microalgae-bacteria fuel cells (MBFCs), microalgae-bacteria membrane photobioreactors (MB-MPBRs), and microalgae-bacteria granular sludge (MBGS)) along with three advanced techniques (metabolic engineering, machine learning, and molecular docking and dynamics) are then introduced. In addition, concrete implementing schemes of the above advanced techniques are also provided. Finally, the current challenges and future research directions in using microalgae-bacteria consortia to remove antibiotics have been summarized. Overall, this review addresses the current state of microalgae-bacteria consortia for antibiotics treatment and provides corresponding recommendations for enhancing antibiotics removal efficiency.

New roles for Yarrowia lipolytica in molecules synthesis and biocontrol

Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend its bioproduction ability related to the synthesis of new value-added molecules relevant to human food and disease treatment. New synthetic tools have been reported and new enzymes with biotechnological importance are recovered. Additionally, metabolic events occurring during substrate utilization and recombinant protein production have been elucidated. Its contributions as feed and in controlling disease in the food industry have also been provided. Likewise, the recent abilities of Yarrowia lipolytica in the bioconversion of food waste into single-cell protein have been reported. These aforementioned events made the novelty of this review compared to the existing ones on this oleaginous yeast. KEY POINTS: • The production of biolipids by the heterotrophic yeast Yarrowia lipolytica is examined. • A Summary of information concerning new value-added molecules has been highlighted. • Special focus on the importance of Yarrowia lipolytica in regulating the immune system has been provided.

Cation–π and hydrophobic interaction controlled PET recognition in double mutated cutinase – identification of a novel binding subsite for better catalytic activity

Accelerated hydrolysis of polyethylene terephthalate (PET) by enzymatic surface modification of various hydrolases, which would not degrade the building blocks of PET in order to retain the quality of recycled PET, is a promising research area. Many studies have been reported to identify mutations of different hydrolases that can improve PET degradation. Recently, the mutation of glycine and phenyl alanine with alanine in cutinase was found to improve the activity of PET degradation 6-fold. Yet, a deep insight into the overall structural basis as well as the explicit role played by the amino acid residues for PET degradation is still elusive, which is nevertheless important for comparative analyses, structure–function relations and rational optimization of the degradation process. Our molecular dynamics simulations coupled with quantum mechanical study demonstrate that mutations of anchor residue phenyl alanine to alanine at the PET binding cleft of cutinase unveiled a distal yet novel binding subsite, which alters the nature of dispersive interaction for PET recognition and binding. The phenyl alanine engages in π–π interaction with the phenyl ring of PET (−8.5 kcal mol⁻¹), which on one side helps in PET recognition, but on the other side restricts PET to attain fully extended conformations over the entire binding cleft. The loss of π–π interaction due to mutation of phenyl alanine to alanine is not only compensated by the favourable cation–π and hydrophobic interactions from the arginine residues (−17.1 kcal mol⁻¹) found in the newly discovered subsite, but also favours the fully extended PET conformation. This subsequently impacts the overall increased catalytic activity of mutated cutinase.

Molecular recognition and binding of PET on cutinase controlled by switching between π–π and cation–π interactions.