Customized valorization of waste streams by Pseudomonas putida: State-of-the-art, challenges, and future trends

Aza-BODIPY-based logic gate chemosensors and their applications

Dimethylaniline-substituted aza-BODIPY dyes (DA, DM, DP) were designed and synthesized aiming for ion detection. The Zn2+ recognition ability was found in all compounds and the binding mechanism was possibly via dimethylaniline sites linked to the aza-BODIPY core. Upon Zn2+ addition, the new absorption band and the color change occurred due to the altered charge transfer of the adducts. The custom-made colorimeter was successfully integrated into the dye's application, demonstrating a good linear relationship between resistance values and Zn2+ concentration. The chromophore test strips were fabricated and exhibited distinct color changes upon aqueous Zn2+ exposure. The compound DA also exhibits logical behavior with DA-Zn2+-Cu2+ system. In terms of environmental hazards, the compounds exhibited no adverse effect on Pseudomonas putida at the concentration level of 0.2 mg/mL. These findings indicated that all synthesized aza-BODIPYs might be suitable for chemosensor probes for Zn2+ detection with possibly low environmental risk.

Enhancing Pseudomonas cell growth for the production of medium-chain-length polyhydroxyalkanoates from Antarctic krill shell waste

Antarctic krill shell waste (AKSW), a byproduct of Antarctic krill processing, has substantial quantity but low utilization. Utilizing microbial-based cell factories, with Pseudomonas putida as a promising candidate, offers an ecofriendly and sustainable approach to producing valuable bioproducts from renewable sources. However, the high fluoride content in AKSW impedes the cell growth of P. putida. This study aims to investigate the transcriptional response of P. putida to fluoride stress from AKSW and subsequently conduct genetic modification of the strain based on insights gained from transcriptomic analysis. Notably, the engineered strain KT+16840+03100 exhibited a remarkable 33.7-fold increase in cell growth, capable of fermenting AKSW for medium-chain-length-polyhydroxyalkanoates (mcl-PHA) biosynthesis, achieving a 40.3-fold increase in mcl-PHA yield compared to the control strain. This research advances our understanding of how P. putida responds to fluoride stress from AKSW and provides engineered strains that serve as excellent platforms for producing mcl-PHA through AKSW.

A comprehensive review on enzymatic biodegradation of polyethylene terephthalate

Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.

Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 19: Suitability of taxonomic units notified to EFSA until September 2023

The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. The QPS approach is based on an assessment of published data for each taxonomic unit (TU), with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a TU are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 71 microorganisms notified to EFSA between April and September 2023 (30 as feed additives, 22 as food enzymes or additives, 7 as novel foods and 12 from plant protection products [PPP]), 61 were not evaluated because: 26 were filamentous fungi, 1 was Enterococcus faecium, 5 were Escherichia coli, 1 was a bacteriophage (all excluded from the QPS evaluation) and 28 were TUs that already have a QPS status. The other 10 notifications belonged to 9 TUs which were evaluated for a possible QPS status: Ensifer adhaerens and Heyndrickxia faecalis did not get the QPS recommendation due to the limited body of knowledge about their occurrence in the food and/or feed chains and Burkholderia ubonensis also due to its ability to generate biologically active compounds with antimicrobial activity; Klebsiella pneumoniae, Serratia marcescens and Pseudomonas putida due to safety concerns. K. pneumoniae is excluded from future QPS evaluations. Chlamydomonas reinhardtii is recommended for QPS status with the qualification 'for production purposes only'; Clostridium tyrobutyricum is recommended for QPS status with the qualification 'absence of genetic determinants for toxigenic activity'; Candida oleophila has been added as a synonym of Yarrowia lipolytica. The Panel clarifies the extension of the QPS status for genetically modified strains.

Co-production of 2,5-dihydroxymethylfuran and furfuralcohol from sugarcane bagasse via chemobiocatalytic approach in a sustainable system

2,5-Dihydroxymethylfuran and furfuryl alcohol serve as versatile building-blocks in pharmaceuticals, polymers, and value-added intermediates. To develop an efficient and sustainable method for their production from biomass, a combined approach using deep eutectic solvent Citric acid:Betaine (CTA:BT) for bagasse catalysis and recombinant E. coli SCFD23 for bioreduction of bagasse-derived 5-hydroxymethylfurfural and furfural was devised. Bagasse was effectively transformed into 5-hydroxymethylfurfural (48 mM) and furfural (14 mM) in CTA:BT (8 wt%)-water at 170 °C for 30 min. Bioreduction of 5-hydroxymethylfurfural and furfural by SCFD23 cell co-expressing formate dehydrogenase and NAD(P)H-dependent aldehyde reductase (SsCR) yielded 2,5-dihydroxymethylfuran (90.0 % yield) and furfuryl alcohol (99.0 % yield) in 6 h, using biomass-derived formic acid, xylose and glucose as co-substrates. Molecular docking confirmed the stable binding and reductase activity of SsCR with the biomass-derived 5-hydroxymethylfurfural and furfural. An efficient and eco-friendly chemobiological approach was applied for co-production of 2,5-dihydroxymethylfuran and furfuryl alcohol from biomass in one-pot two-step reaction.

Coupling chemistry and biology for the synthesis of advanced bioproducts

Chemical and biological syntheses can both lead to a myriad of compounds. Biology enables us to harness the metabolism of microbial cell factories to produce key target molecules from renewable biomass-derived substrates. Although bio-based feedstocks are sustainably sourced and more benign than the rapidly depleting fossil fuels that chemical processes have historically relied on, limiting pathways solely to biological reactions may not equate to a greener process overall. In fact, bioreactors rely on substantial quantities of water and can be inefficient since organisms typically operate around ambient conditions and are sensitive to perturbations in their environment. Hybridizing biosynthetic pathways with green chemistry can instead be a more potent strategy to reduce our net manufacturing footprint. Emerging chemistries have demonstrated considerable success in performing complex transformations on biological feedstocks without significant solvent use. Many of these transformations would be too slow to perform enzymatically or infeasible altogether. Here, we put forth the concept that by carefully considering the merits and drawbacks of synthetic biology and chemistry as well as one's own use case, there exist many opportunities for coupling the two. Merging these syntheses can unlock a wider suite of functional group transformations, thereby enabling future manufacturing processes to sustainably access a larger space of valuable, platform chemicals.

Engineering microbial division of labor for plastic upcycling

Plastic pollution is rapidly increasing worldwide, causing adverse impacts on the environment, wildlife and human health. One tempting solution to this crisis is upcycling plastics into products with engineered microorganisms; however, this remains challenging due to complexity in conversion. Here we present a synthetic microbial consortium that efficiently degrades polyethylene terephthalate hydrolysate and subsequently produces desired chemicals through division of labor. The consortium involves two Pseudomonas putida strains, specializing in terephthalic acid and ethylene glycol utilization respectively, to achieve complete substrate assimilation. Compared with its monoculture counterpart, the consortium exhibits reduced catabolic crosstalk and faster deconstruction, particularly when substrate concentrations are high or crude hydrolysate is used. It also outperforms monoculture when polyhydroxyalkanoates serves as a target product and confers flexible tuning through population modulation for cis-cis muconate synthesis. This work demonstrates engineered consortia as a promising, effective platform that may facilitate polymer upcycling and environmental sustainability.

Sugarcane wastes as microbial feedstocks: A review of the biorefinery framework from resource recovery to production of value-added products

Sugarcane industry is a major agricultural sector capable of producing sugars with byproducts including straw, bagasse, and molasses. Sugarcane byproducts are no longer wastes since they can be converted into carbon-rich resources for biorefinery if pretreatment of these is well established. Considerable efforts have been devoted to effective pretreatment techniques for each sugarcane byproduct to supply feedstocks in microbial fermentation to produce value-added fuels, chemicals, and polymers. These value-added chains, which start with low-value industrial wastes and end with high-value products, can make sugarcane-based biorefinery a more viable option for the modern chemical industry. In this review, recent advances in sugarcane valorization techniques are presented, ranging from sugarcane processing, pretreatment, and microbial production of value-added products. Three lucrative products, ethanol, 2,3-butanediol, and polyhydroxyalkanoates, whose production from sugarcane wastes has been widely researched, are being explored. Future studies and development in sugarcane waste biorefinery are discussed to overcome the challenges remaining.