Engineered polymer nanoparticles as artificial chaperones facilitating the selective refolding of denatured enzymes

Molecular chaperones assist in protein refolding by selectively binding to proteins in their nonnative states. Despite progress in creating artificial chaperones, these designs often have a limited range of substrates they can work with. In this paper, we present molecularly imprinted flexible polymer nanoparticles (nanoMIPs) designed as customizable biomimetic chaperones. We used model proteins such as cytochrome c, laccase, and lipase to screen polymeric monomers and identify the most effective formulations, offering tunable charge and hydrophobic properties. Utilizing a dispersed phase imprinting approach, we employed magnetic beads modified with destabilized whole-protein as solid-phase templates. This process involves medium exchange facilitated by magnetic pulldowns, resulting in the synthesis of nanoMIPs featuring imprinted sites that effectively mimic chaperone cavities. These nanoMIPs were able to selectively refold denatured enzymes, achieving up to 86.7% recovery of their activity, significantly outperforming control samples. Mechanistic studies confirmed that nanoMIPs preferentially bind denatured rather than native enzymes, mimicking natural chaperone interactions. Multifaceted analyses support the functionality of nanoMIPs, which emulate the protective roles of chaperones by selectively engaging with denatured proteins to inhibit aggregation and facilitate refolding. This approach shows promise for widespread use in protein recovery within biocatalysis and biomedicine.

From sustainable feedstocks to microbial foods

Climate change-induced alterations in weather patterns, such as frequent and severe heatwaves, cold waves, droughts, floods, heavy rain and storms, are reducing crop yields and agricultural productivity. At the same time, greenhouse gases arising from food production and supply account for almost 30% of anthropogenic emissions. This vicious circle is producing a global food crisis. Sustainable food resources and production systems are needed now, and microbial foods are one possible solution. In this Perspective, we highlight the most promising technologies, and carbon and energy sources, for microbial food production.

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

BACKGROUND

Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development.

RESULTS

Here we report the development of a computational workflow that predicts metabolite-gene-pathway sets. Metabolite-gene-pathway sets present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate metabolite-gene-pathway sets. A GEM is a computational model that predicts reaction fluxes at a genome scale and can be constructed in a cell-specific manner by using omics data. The computational workflow is first validated by comparing the resulting metabolite-gene pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from acute myeloid leukemia and renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the metabolite-gene-pathway sets predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting metabolite-gene-pathway sets is also discussed.

CONCLUSIONS

Validation of the metabolite-gene-pathway set-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting metabolite-gene-pathway sets will help identify novel oncometabolites and also suggest cancer treatment strategies.

Metabolic engineering and fermentation of microorganisms for carotenoids production

Carotenoids are natural pigments that exhibit a wide range of red, orange, and yellow colors and are extensively used in the food, nutraceuticals, cosmetics, and aquaculture industries. While advances in systems metabolic engineering have established a foundation for constructing carotenoid-producing microbial cell factories at a laboratory scale, translating these technologies to industrial scales remains a big challenge. Moreover, there is a need to devise cost-effective methods for downstream processing and purification of carotenoids. In this review, we discuss recent strategies in metabolic engineering, such as metabolic flux optimization, enzyme assembly, and storage capacity engineering, aimed at constructing high-performance carotenoid-producing microbial strains. We also review recent approaches for cost-effective downstream processing and purification of carotenoids.

Observing growth and interfacial dynamics of nanocrystalline ice in thin amorphous ice films

Ice crystals at low temperatures exhibit structural polymorphs including hexagonal ice, cubic ice, or a hetero-crystalline mixture of the two phases. Despite the significant implications of structure-dependent roles of ice, mechanisms behind the growths of each polymorph have been difficult to access quantitatively. Using in-situ cryo-electron microscopy and computational ice-dynamics simulations, we directly observe crystalline ice growth in an amorphous ice film of nanoscale thickness, which exhibits three-dimensional ice nucleation and subsequent two-dimensional ice growth. We reveal that nanoscale ice crystals exhibit polymorph-dependent growth kinetics, while hetero-crystalline ice exhibits anisotropic growth, with accelerated growth occurring at the prismatic planes. Fast-growing facets are associated with low-density interfaces that possess higher surface energy, driving tetrahedral ordering of interfacial H2O molecules and accelerating ice growth. These findings, based on nanoscale observations, improve our understanding on early stages of ice formation and mechanistic roles of the ice interface.

Complete microbial synthesis of crocetin and crocins from glycerol in Escherichia coli

BACKGROUND

Crocin, a glycosylated apocarotenoid pigment predominantly found in saffron, has garnered significant interest in the field of biotechnology for its bioactive properties. Traditional production of crocins and their aglycone, crocetin, typically involves extraction from crocin-producing plants. This study aimed to develop an alternative biosynthetic method for these compounds by engineering the metabolic pathways of zeaxanthin, crocetin, and crocin in Escherichia coli strains.

RESULTS

Employing a series of genetic modifications and the strategic overexpression of key enzymes, we successfully established a complete microbial pathway for synthesizing crocetin and four glycosylated derivatives of crocetin, utilizing glycerol as the primary carbon source. The overexpression of zeaxanthin cleavage dioxygenase and a novel variant of crocetin dialdehyde dehydrogenase resulted in a notable yield of crocetin (34.77 ± 1.03 mg/L). Further optimization involved the overexpression of new types of crocetin and crocin-2 glycosyltransferases, facilitating the production of crocin-1 (6.29 ± 0.19 mg/L), crocin-2 (5.29 ± 0.24 mg/L), crocin-3 (1.48 ± 0.10 mg/L), and crocin-4 (2.72 ± 0.13 mg/L).

CONCLUSIONS

This investigation introduces a pioneering and integrated microbial synthesis method for generating crocin and its derivatives, employing glycerol as a sustainable carbon feedstock. The substantial yields achieved highlight the commercial potential of microbial-derived crocins as an eco-friendly alternative to plant extraction methods. The development of these microbial processes not only broadens the scope for crocin production but also suggests significant implications for the exploitation of bioengineered compounds in pharmaceutical and food industries.

A community effort in SARS-CoV-2 drug discovery

The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.

Recent advances in systems metabolic engineering

Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Furthermore, we highlight recent trends in systems metabolic engineering, which involve the application of multiple tools discussed in this review. Finally, the paper addresses the challenges and perspectives of transitioning academic-level metabolic engineering studies to commercial-scale production.

Superior anodic electro-fermentation by enhancing capacity for extracellular electron transfer

Anodic electro-fermentation (AEF), where an anode replaces the terminal electron acceptor, shows great promise. Recently a Lactococcus lactis strain blocked in NAD+ regeneration was demonstrated to use ferricyanide as an alternative electron acceptor to support fast growth, but the need for high concentrations of this non-regenerated electron acceptor limits practical applications. To address this, growth of this L. lactis strain, and an adaptively evolved (ALE) mutant with enhanced ferricyanide respiration capacity were investigated using an anode as electron acceptor in a bioelectrochemical system (BES) setup. Both strains grew well, however, the ALE mutant significantly faster. The ALE mutant almost exclusively generated 2,3-butanediol, whereas its parent strain mainly produced acetoin. The ALE mutant interacted efficiently with the anode, achieving a record high current density of 0.81 ± 0.05 mA/cm2. It is surprising that a Lactic Acid Bacterium, with fermentative metabolism, interacts so well with an anode, which demonstrates the potential of AEF.

Sustainable production and degradation of plastics using microbes

Plastics are indispensable in everyday life and industry, but the environmental impact of plastic waste on ecosystems and human health is a huge concern. Microbial biotechnology offers sustainable routes to plastic production and waste management. Bacteria and fungi can produce plastics, as well as their constituent monomers, from renewable biomass, such as crops, agricultural residues, wood and organic waste. Bacteria and fungi can also degrade plastics. We review state-of-the-art microbial technologies for sustainable production and degradation of bio-based plastics and highlight the potential contributions of microorganisms to a circular economy for plastics.

Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes

In metabolic engineering, predicting gene overexpression targets remains challenging because both endogenous and heterologous genes in a large metabolic space can be candidates, in contrast to gene knockout targets that are confined to endogenous genes. We report the development of iBridge that identifies positive and negative metabolites exerting positive and negative impacts on product formation, respectively, based on the sum of covariances of their outgoing (consuming) reaction fluxes for a target chemical. Then, "bridge" reactions converting negative metabolites to positive metabolites are identified as overexpression targets, while the opposites as downregulation targets. Using iBridge, overexpression and downregulation targets are suggested for the production of 298 chemicals and validated for 36 chemicals experimentally demonstrated in previous studies. Finally, iBridge is employed to engineer Escherichia coli strains capable of producing 10.3 g/L of D-panthenol, a compound not previously produced, as well as putrescine and 4-hydroxyphenyllactate at enhanced titers, 63.7 and 8.3 g/L, respectively.

Functional annotation of enzyme-encoding genes using deep learning with transformer layers

Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the Enzyme Commission (EC) number. Consequently, the ability to predict EC numbers could substantially reduce the number of un-annotated genes. Here we present a deep learning model, DeepECtransformer, which utilizes transformer layers as a neural network architecture to predict EC numbers. Using the extensively studied Escherichia coli K-12 MG1655 genome, DeepECtransformer predicted EC numbers for 464 un-annotated genes. We experimentally validated the enzymatic activities predicted for three proteins (YgfF, YciO, and YjdM). Further examination of the neural network's reasoning process revealed that the trained neural network relies on functional motifs of enzymes to predict EC numbers. Thus, DeepECtransformer is a method that facilitates the functional annotation of uncharacterized genes.

Deep learning for metabolic pathway design

The establishment of a bio-based circular economy is imperative in tackling the climate crisis and advancing sustainable development. In this realm, the creation of microbial cell factories is central to generating a variety of chemicals and materials. The design of metabolic pathways is crucial in shaping these microbial cell factories, especially when it comes to producing chemicals with yet-to-be-discovered biosynthetic routes. To aid in navigating the complexities of chemical and metabolic domains, computer-supported tools for metabolic pathway design have emerged. In this paper, we evaluate how digital strategies can be employed for pathway prediction and enzyme discovery. Additionally, we touch upon the recent strides made in using deep learning techniques for metabolic pathway prediction. These computational tools and strategies streamline the design of metabolic pathways, facilitating the development of microbial cell factories. Leveraging the capabilities of deep learning in metabolic pathway design is profoundly promising, potentially hastening the advent of a bio-based circular economy.

Enhanced production of difficult-to-express proteins through knocking down rnpA gene expression

Escherichia coli has been employed as a workhorse for the efficient production of recombinant proteins. However, some proteins were found to be difficult to produce in E. coli. The stability of mRNA has been considered as one of the important factors affecting recombinant protein production. Here we report a generally applicable and simple strategy for enhancing mRNA stability, and consequently improving recombinant protein production in E. coli. RNase P, a ribozyme comprising an RNA subunit (RnpB) and a protein subunit (RnpA), is involved in tRNA maturation. Based on the finding that purified RnpA can digest rRNA and mRNA in vitro, it was reasoned that knocking down the level of RnpA might enhance recombinant protein production. For this, the synthetic small regulatory RNA-based knockdown system was applied to reduce the expression level of RnpA. The developed RnpA knockdown system allowed successful overexpression of 23 different recombinant proteins of various origins and sizes, including Cas9 protein, antibody fragment, and spider silk protein. Notably, a 284.9-kDa ultra-high molecular weight, highly repetitive glycine-rich spider silk protein, which is one of the most difficult proteins to produce, could be produced to 1.38 g L-1 , about two-fold higher than the highest value previously achieved, by a fed-batch culture of recombinant E. coli strain employing the RnpA knockdown system. The RnpA-knockdown strategy reported here will be generally useful for the production of recombinant proteins including those that have been difficult to produce.

Beneficial Role of Multi-Disciplinary Treatment for Anaplastic Thyroid Cancer with Initial Distant Metastasis

PURPOSE/OBJECTIVE(S)

Anaplastic thyroid cancer (ATC) is a rare, highly aggressive tumor, with median survival around 5 months. Approximately half of the ATC patients presents with distant metastases at diagnosis, showing even more devastating prognosis, yet no outcome analysis had been reported. In this study, we aim to evaluate the clinical outcome of M1 ATC patients, and to define the group of patients who would benefit from local treatment based on multi-disciplinary approach.

MATERIALS/METHODS

A total of 133 histology-confirmed ATC patients underwent protocol-based multidisciplinary treatment including surgery and chemoradiotherapy (CRT) between May 2016 and January 2022. Patients received intensity-modulated radiotherapy of 30 fractions concurrently with paclitaxel on days 1, 8 and 15 every 4 weeks, and lenvatinib was added upon progression. After 18 fractions of CRT, interim response analysis using modified RECIST was conducted for adaptive treatment planning. We reviewed 58 patients with distant metastasis at diagnosis (stage IVC). Overall survival (OS) and progression-free survival (PFS) were measured from the day of diagnosis.

RESULTS

Most common metastatic site was lung (91.4%), followed by bone (31.0%) and brain (5.2%). Lenvatinib was added for 35 patients after any sign of progression. Fourteen patients received upfront surgery (16 debulking and 5 total) followed by adjuvant CRT in 16 patients. Thirty-one patients received upfront CRT with 2 patients receiving total resection after sufficient down-staging. Six (10%) patients could not complete radiotherapy but continued receiving systemic treatment. The median follow-up was 5.9 months. The median and 1-year OS were 6.2 months and 20.5%, and PFS were 3.7 months and 3.5%. Total RT dose over 60 Gy significantly improved median OS (7.5 vs 4.1 months, p = 0.012) and median PFS (4.4 vs 3.0, p = 0.010). Patients with less than 10 initial metastatic tumors showed better median OS (9.1 vs 4.6 months, p = 0.002) but not PFS (5.1 vs 3.6, p = 0.485). At interim analysis, early response (CR, PR and SD) of primary tumor was not associated with survival, while progression of distant metastases showed significantly worse median OS (9.8 vs 4.6 months, p = 0.001). More than 10 metastatic tumors (HR 2.73, 95% CI 1.32-5.66) and stable metastasis at interim analysis (HR 2.39, 95% CI 1.04-5.48) remained as significant factor in the multivariable cox regression analysis. Median OS and PFS of patients with less than 10 metastases showing no progression at interim analysis were 9.1 months, and 5.1 months.

CONCLUSION

Local treatment combined with chemotherapy for M1 ATC patients showed outcome comparable to those of non-metastatic ATC results. Active local treatment should be considered especially for patients with less than 10 metastases, and patients without distant progression in early response evaluation.

Do media coverage of suicides and search frequency on suicides predict the number of tweets seeking others for a suicide pact?

We examined whether media coverage of suicides and frequencies of searching for suicide methods or suicide pacts predicted the number of users posting tweets seeking others for a suicide pact. Analyses of 6,119 tweets containing "suicide pact" posted on Twitter during a 6-month period revealed that the number of users posting tweets seeking others for a suicide pact had a positive association with media coverage of celebrity suicides, but not with that of suicide pact victims, and a greater positive association with the search frequency for suicide methods than for suicide pacts. We found that the search frequency on suicide methods was positively associated with media coverage of celebrity suicides, while that on suicide pacts was more strongly related to media coverage of suicide pacts.

Metabolic engineering of Corynebacterium glutamicum for the high-level production of valerolactam, a nylon-5 monomer

Valerolactam (VL) is an important precursor chemical for nylon-5 and nylon 6,5. It has been produced by petroleum-based route involving harsh reaction conditions and generating toxic wastes. Here, we report the complete biosynthesis of VL by metabolically engineered Corynebacterium glutamicum overproducing L-lysine. The pathway comprising L-lysine monooxygenase (davB) and 5-aminovaleramide amidohydrolase (davA) from Pseudomonas putida, and β-alanine CoA transferase (act) from Clostridium propionicum was introduced into the C. glutamicum GA16 strain. To increase the VL flux, competitive pathways predicted from sRNA knockdown target screening were deleted. This engineered C. glutamicum strain produced VL as a major product, but still secreted significant amount of its precursor, 5-aminovaleric acid (5AVA). To circumvent this problem, putative 5AVA transporter genes were screened and engineered in the genome, thereby reuptaking 5AVA excreted. Also, multiple copies of the act gene were integrated into the genome to strengthen the conversion of 5AVA to VL. The final VL10 (pVL1) strain was constructed by enhancing glucose uptake system, which produced 9.68 g/L of VL in flask culture. Fed-batch fermentation of the VL10 (pVL1) strain produced 76.1 g/L of VL from glucose with the yield and productivity of 0.28 g/g and 0.99 g/L/h, respectively, showcasing a high potential for bio-based production of VL from renewable resources.

Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli

Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.

A synthetic cell-free 36-enzyme reaction system for vitamin B12 production

Adenosylcobalamin (AdoCbl), a biologically active form of vitamin B12 (coenzyme B12), is one of the most complex metal-containing natural compounds and an essential vitamin for animals. However, AdoCbl can only be de novo synthesized by prokaryotes, and its industrial manufacturing to date was limited to bacterial fermentation. Here, we report a method for the synthesis of AdoCbl based on a cell-free reaction system performing a cascade of catalytic reactions from 5-aminolevulinic acid (5-ALA), an inexpensive compound. More than 30 biocatalytic reactions are integrated and optimized to achieve the complete cell-free synthesis of AdoCbl, after overcoming feedback inhibition, the complicated detection, instability of intermediate products, as well as imbalance and competition of cofactors. In the end, this cell-free system produces 417.41 μg/L and 5.78 mg/L of AdoCbl using 5-ALA and the purified intermediate product hydrogenobyrate as substrates, respectively. The strategies of coordinating synthetic modules of complex cell-free system describe here will be generally useful for developing cell-free platforms to produce complex natural compounds with long and complicated biosynthetic pathways.

Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes

CRISPR tools, especially Cas9n-sgRNA guided cytidine deaminase base editors such as CRISPR-BEST, have dramatically simplified genetic manipulation of streptomycetes. One major advantage of CRISPR base editing technology is the possibility to multiplex experiments in genomically instable species. Here, we demonstrate scaled up Csy4 based multiplexed genome editing using CRISPR-mcBEST in Streptomyces coelicolor. We evaluated the system by simultaneously targeting 9, 18, and finally all 28 predicted specialized metabolite biosynthetic gene clusters in a single experiment. We present important insights into the performance of Csy4 based multiplexed genome editing at different scales. Using multiomics analysis, we investigated the systems wide effects of such extensive editing experiments and revealed great potentials and important bottlenecks of CRISPR-mcBEST. The presented analysis provides crucial data and insights toward the development of multiplexed base editing as a novel paradigm for high throughput engineering of Streptomyces chassis and beyond.

Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs

Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including commensal, probiotic, pathogenic, and industrial bacteria, with >50% of target gene knockdown achieved in 12 bacterial species. For medical applications, virulence factors in Staphylococcus epidermidis and Klebsiella pneumoniae are knocked down to mitigate their virulence-associated phenotypes. For metabolic engineering applications, high performance Corynebacterium glutamicum strains capable of producing valerolactam (bulk chemical) and methyl anthranilate (fine chemical) are developed by combinatorial knockdown of target genes. A genome-scale sRNA library covering 2959 C. glutamicum genes is constructed for high-throughput colorimetric screening of indigoidine (natural colorant) overproducers. The BHR-sRNA platform will expedite engineering of diverse bacteria of both industrial and medical interest.

Efforts to install a heterologous Wood-Ljungdahl pathway in Clostridium acetobutylicum enable the identification of the native tetrahydrofolate (THF) cycle and result in early induction of solvents

Here, we report the construction of a Clostridium acetobutylicum strain ATCC 824 (pCD07239) by heterologous expression of carbonyl branch genes (CD630_0723∼CD630_0729) from Clostridium difficile, aimed at installing a heterologous Wood-Ljungdahl pathway (WLP). As part of this effort, in order to validate the methyl branch of the WLP in the C. acetobutylicum, we performed ¹³C-tracing analysis on knockdown mutants of four genes responsible for the formation of 5-methyl-tetrahydrofolate (5-methyl-THF) from formate: CA_C3201, CA_C2310, CA_C2083, and CA_C0291. While C. acetobutylicum 824 (pCD07239) could not grow autotrophically, in heterotrophic fermentation, it began producing butanol at the early growth phase (OD₆₀₀ of 0.80; 0.162 g/L butanol). In contrast, solvent production in the parent strain did not begin until the early stationary phase (OD₆₀₀ of 7.40). This study offers valuable insights for future research on biobutanol production during the early growth phase.

Biohybrid CO2 electrolysis for the direct synthesis of polyesters from CO2

Converting anthropogenic CO2 to value-added products using renewable energy has received much attention to achieve a sustainable carbon cycle. CO2 electrolysis has been extensively investigated, but the products have been limited to some C1-3 products. Here, we report the integration of CO2 electrolysis with microbial fermentation to directly produce poly-3-hydroxybutyrate (PHB), a microbial polyester, from gaseous CO2 on a gram scale. This biohybrid system comprises electrochemical conversion of CO2 to formate on Sn catalysts deposited on a gas diffusion electrode (GDE) and subsequent conversion of formate to PHB by Cupriavidus necator cells in a fermenter. The electrolyzer and the electrolyte solution were optimized for this biohybrid system. In particular, the electrolyte solution containing formate was continuously circulated through both the CO2 electrolyzer and the fermenter, resulting in the efficient accumulation of PHB in C. necator cells, reaching a PHB content of 83% of dry cell weight and producing 1.38 g PHB using 4 cm2 Sn GDE. This biohybrid system was further modified to enable continuous PHB production operated at a steady state by adding fresh cells and removing PHB. The strategies employed for developing this biohybrid system will be useful for establishing other biohybrid systems producing chemicals and materials directly from gaseous CO2.

Metabolic engineering of Escherichia coli for the production of an antifouling agent zosteric acid

Zosteric acid (ZA) is a Zostera species-derived, sulfated phenolic acid compound with antifouling activity and has gained much attention due to its nontoxic and biodegradable characteristics. However, the yield of Zostera species available for ZA extraction is limited by natural factors, such as season, latitude, light, and temperature. Here we report the development of metabolically engineered Escherichia coli strains capable of producing ZA from glucose and glycerol. First, intracellular availability of the sulfur donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) was enhanced by knocking out the cysH gene responsible for PAPS consumption and overexpressing the genes required for PAPS biosynthesis. Co-overexpression of the genes encoding tyrosine ammonia-lyase, sulfotransferase 1A1, ATP sulfurylase, and adenosine 5'-phosphosulfate kinase constructed ZA producing strain with enhanced PAPS supply. Second, the feedback-resistant forms of aroG and tyrA genes (encoding 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase and chorismate mutase, respectively) were overexpressed to relieve the feedback regulation of L-tyrosine biosynthesis. Third, the pykA gene involved in phosphoenolpyruvate-consuming reaction, the regulator gene tyrR, the competing pathway gene pheA, and the ptsHIcrr genes essential for the PEP:carbohydrate phosphotransferase system were deleted. Moreover, all genes involved in the shikimate pathway and the talA, tktA, and tktB genes in the pentose phosphate pathway were examined for ZA production. The PTS-independent glucose uptake system, the expression vector system, and the carbon source were also optimized. As a result, the best-performing strain successfully produced 1.52 g L^-1 ZA and 1.30 g L^-1p-hydroxycinnamic acid from glucose and glycerol in a 700 mL fed-batch bioreactor.

Rewiring the respiratory pathway of Lactococcus lactis to enhance extracellular electron transfer

Lactococcus lactis, a lactic acid bacterium with a typical fermentative metabolism, can also use oxygen as an extracellular electron acceptor. Here we demonstrate, for the first time, that L. lactis blocked in NAD⁺ regeneration can use the alternative electron acceptor ferricyanide to support growth. By electrochemical analysis and characterization of strains carrying mutations in the respiratory chain, we pinpoint the essential role of the NADH dehydrogenase and 2-amino-3-carboxy-1,4-naphtoquinone in extracellular electron transfer (EET) and uncover the underlying pathway systematically. Ferricyanide respiration has unexpected effects on L. lactis, e.g., we find that morphology is altered from the normal coccoid to a more rod shaped appearance, and that acid resistance is increased. Using adaptive laboratory evolution (ALE), we successfully enhance the capacity for EET. Whole-genome sequencing reveals the underlying reason for the observed enhanced EET capacity to be a late-stage blocking of menaquinone biosynthesis. The perspectives of the study are numerous, especially within food fermentation and microbiome engineering, where EET can help relieve oxidative stress, promote growth of oxygen sensitive microorganisms and play critical roles in shaping microbial communities.

Improved terephthalic acid production from p-xylene using metabolically engineered Pseudomonas putida

Terephthalic acid (TPA) is an important commodity chemical used as a monomer of polyethylene terephthalate (PET). Since a large quantity of PET is routinely manufactured and consumed worldwide, the development of sustainable biomanufacturing processes for its monomers (i.e. TPA and ethylene glycol) has recently gained much attention. In a previous study, we reported the development of a metabolically engineered Escherichia coli strain producing 6.7 g/L of TPA from p-xylene (pX) with a productivity and molar conversion yield of 0.278 g/L/h and 96.7 mol%, respectively. Here, we report metabolic engineering of Pseudomonas putida KT2440, a microbial chassis particularly suitable for the synthesis of aromatic compounds, for improved biocatalytic conversion of pX to TPA. To develop a plasmid-free, antibiotic-free, and inducer-free biocatalytic process for cost-competitive TPA production, all heterologous genes required for the synthetic pX-to-TPA bioconversion pathway were integrated into the chromosome of P. putida KT2440 by RecET-based markerless recombineering and overexpressed under the control of constitutive promoters. Next, TPA production was enhanced by integrating multiple copies of the heterologous genes to the ribosomal RNA genes through iteration of recombineering-based random integration and subsequent screening of high-performance strains. Finally, fed-batch fermentation process was optimized to further improve the performance of the engineered P. putida strain. As a result, 38.25 ± 0.11 g/L of TPA was produced from pX with a molar conversion yield of 99.6 ± 0.6%, which is equivalent to conversion of 99.3 ± 0.8 g pX to 154.6 ± 0.5 g TPA. This superior pX-to-TPA biotransformation process based on the engineered P. putida strain will pave the way to the commercial biomanufacturing of TPA in an industrial scale.

Metabolic engineering for sustainability and health

Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.

Whole-Cell P450 Biocatalysis Using Engineered Escherichia coli with Fine-Tuned Heme Biosynthesis

By exploiting versatile P450 enzymes, whole-cell biocatalysis can be performed to synthesize valuable compounds in Escherichia coli. However, the insufficient supply of heme limits the whole-cell P450 biocatalytic activity. Here a strategy for improving intracellular heme biosynthesis to enhance the catalytic efficiencies of P450s is reported. After comparing the effects of improving heme transport and biosynthesis on P450 activities, intracellular heme biosynthesis is optimized through the integrated expression of necessary synthetic genes at proper ratios and the assembly of rate-limiting enzymes using DNA-guided scaffolds. The intracellular heme level is fine-tuned by the combined use of mutated heme-sensitive biosensors and small regulatory RNA systems. The catalytic efficiencies of three different P450s, BM3, sca-2, and CYP105D7, are enhanced through fine-tuning heme biosynthesis for the synthesis of hydroquinone, pravastatin, and 7,3',4'-trihydroxyisoflavone as example products of chemical intermediate, drug, and natural product, respectively. This strategy of fine-tuned heme biosynthesis will be generally useful for developing whole-cell biocatalysts involving hemoproteins.

Metabolic engineering of Mannheimia succiniciproducens for malic acid production using dimethylsulfoxide as an electron acceptor

Microbial production of various TCA intermediates and related chemicals through the reductive TCA cycle has been of great interest. However, rumen bacteria that naturally possess strong reductive TCA cycle have been rarely studied to produce these chemicals, except for succinic acid, due to their dependence on fumarate reduction to transport electrons for ATP synthesis. In this study, malic acid (MA), a dicarboxylic acid of industrial importance, was selected as a target chemical for mass production using Mannheimia succiniciproducens, a rumen bacterium possessing a strong reductive branch of the TCA cycle. The metabolic pathway was reconstructed by eliminating fumarase to prevent MA conversion to fumarate. The respiration system of M. succiniciproducens was reconstructed by introducing the Actinobacillus succinogenes dimethylsulfoxide (DMSO) reductase to improve cell growth using DMSO as an electron acceptor. Also, the cell membrane was engineered by employing Pseudomonas aeruginosa cis-trans isomerase to enhance MA tolerance. High inoculum fed-batch fermentation of the final engineered strain produced 61 g/L of MA with an overall productivity of 2.27 g/L/h, which is the highest MA productivity reported to date. The systems metabolic engineering strategies reported in this study will be useful for developing anaerobic bioprocesses for the production of various industrially important chemicals.

Efficacy of Silkworm Pupae Extract on Muscle Strength and Mass in Middle-Aged and Older Individuals: A Randomized, Double-Blind, Placebo-Controlled Trial

OBJECTIVES

We investigated the efficacy and safety of silkworm pupae extract (SWP) consumption for 12 weeks on muscle mass and strength in middle-aged and older individuals with relatively low skeletal muscle mass who do regular low-intensity exercise.

DESIGN

A randomized double-blinded placebo-controlled trial.

PARTICIPANTS

The study was conducted with 54 participants with relatively low skeletal muscle mass (SMM) (64.4 ± 6.1 years; body mass index, 23.8 ± 2.4 kg/m2).

INTERVENTION AND MEASUREMENTS

Participants were randomly assigned to one of two groups: 1000 mg of SWP/day plus regular exercise (SWP group, n=27) or placebo plus regular exercise (placebo group, n=27). All participants were required to engage in 30-60 minutes/day of walking for ≥3 days/week for 12 weeks. The primary outcome was knee extension/flexion strength (Nm), measured at the velocity of 60°/s. Secondary outcomes included body composition, biomarkers (creatine kinase and creatinine), handgrip strength, and quality of life questionnaire.

RESULTS

Both the intention-to-treat (ITT) and per-protocol (PP) analyses revealed no significant impact of SWP on knee strength compared to the placebo group over 12 weeks. On the other hand, the SWP group had significantly greater increases in right-handgrip strength by 1.94 kg (95% CI: 0.08-3.79; p = 0.041) and left-handgrip strength by 1.83 kg (0.25-3.41; p = 0.024) compared to the placebo group in the ITT population, after 12 weeks. Moreover, in the PP population, the SWP group revealed an even greater increase in right-handgrip strength by 2.07 kg (0.15-3. 98; p = 0.035) and left-handgrip strength by 2.21 kg (0.60-3.83; p = 0.008) for the 12-week period. However, this study resulted in a failure to detect significant differences in the body composition, biomarkers, quality of life questionnaire, physical activity, and caloric intake between the groups. None of the participants in the SWP group experienced any significant adverse events. In the placebo group, two participants experienced urticaria and allergic side effects, leading to their withdrawal from the study and two exhibited elevated levels of liver enzyme and increased diastolic blood pressure, respectively at 12 weeks.

CONCLUSION

SWP, in addition to low-intensity exercise, may enhance handgrip strengths in middle-aged and older adults with relatively lower SMM. Future studies need to use a large sample size over longer periods to validate our findings. This trial was registered at clinicaltrials.gov as NCT04994054.

Can microbes be harnessed to reduce atmospheric loads of greenhouse gases?

Reducing atmospheric loads of greenhouse gases (GHGs), especially CO₂ and CH₄ , has been considered the key to alleviating global crises we are facing, such as climate change, sea level elevation and ocean acidification. To this end, development of strategies and technologies for carbon capture, sequestration and utilization (CCSU) is urgently needed. Although physicochemical methods have been the most actively studied in the early stages of developing CCSU technologies, there have recently been growing interests in developing microbe-based CCSU processes. In this article, we discuss advantages of microbe-based CCSU technologies over physicochemical approaches and even plant-based approaches. Next, various parts of the global carbon cycle where microorganisms can contribute, such as sequestering atmospheric GHGs, facilitating the carbon cycle, and slowing down the depletion of carbon reservoirs are described, emphasizing the impacts of microbes on the carbon cycle. Strategies to upgrade microbes and increase their performance in assimilating GHGs or converting GHGs to value-added chemicals are also provided. Moreover, several examples of exploiting microbes to address environmental crises are discussed. Finally, we discuss things to overcome in microbe-based CCSU technologies and provide future perspectives.

Factors affecting the competitiveness of bacterial fermentation

Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of 'net zero carbon' that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproducing an increasing number of chemicals and materials, some of which have been translated to industrial-scale production. Fermentation is one of the key processes determining the overall economics of bioprocesses, but has recently been attracting less research attention. In this Review, we revisit and discuss factors affecting the competitiveness of bacterial fermentation in connection to strain development by systems metabolic engineering. Future perspectives for developing efficient fermentation processes are also discussed.

Janus regulation of ice growth by hyperbranched polyglycerols generating dynamic hydrogen bonding

In this study, a new phenomenon describing the Janus effect on ice growth by hyperbranched polyglycerols, which can align the surrounding water molecules, has been identified. Even with an identical polyglycerol, we not only induced to inhibit ice growth and recrystallization, but also to promote the growth rate of ice that is more than twice that of pure water. By investigating the polymer architecture and population, we found that the stark difference in the generation of quasi-structured H₂O molecules at the ice/water interface played a crucial role in the outcome of these opposite effects. Inhibition activity was induced when polymers at nearly fixed loci formed steady hydrogen bonding with the ice surface. However, the formation-and-dissociation dynamics of the interfacial hydrogen bonds, originating from and maintained by migrating polymers, resulted in an enhanced quasi-liquid layer that facilitated ice growth. Such ice growth activity is a unique property unseen in natural antifreeze proteins or their mimetic materials.

Designing Microbial Cell Factories for the Production of Chemicals

The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising from our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined to produce chemicals of interests from renewable carbon sources. The biosynthetic pathways for the production of chemicals can be defined into three categories with reference to the microbial host selected for engineering: native-existing pathways, nonnative-existing pathways, and nonnative-created pathways. Recent trends in leveraging native-existing pathways, discovering nonnative-existing pathways, and designing de novo pathways (as nonnative-created pathways) are discussed in this Perspective. We highlight key approaches and successful case studies that exemplify these concepts. Once these pathways are designed and constructed in the microbial cell factory, systems metabolic engineering strategies can be used to improve the performance of the strain to meet industrial production standards. In the second part of the Perspective, current trends in design tools and strategies for systems metabolic engineering are discussed with an eye toward the future. Finally, we survey current and future challenges that need to be addressed to advance microbial cell factories for the sustainable production of chemicals.

Systematic strategies for developing phage resistant Escherichia coli strains

Phages are regarded as powerful antagonists of bacteria, especially in industrial fermentation processes involving bacteria. While bacteria have developed various defense mechanisms, most of which are effective against a narrow range of phages and consequently exert limited protection from phage infection. Here, we report a strategy for developing phage-resistant Escherichia coli strains through the simultaneous genomic integration of a DNA phosphorothioation-based Ssp defense module and mutations of components essential for the phage life cycle. The engineered E. coli strains show strong resistance against diverse phages tested without affecting cell growth. Additionally, the resultant engineered phage-resistant strains maintain the capabilities of producing example recombinant proteins, D-amino acid oxidase and coronavirus-encoded nonstructural protein nsp8, even under high levels of phage cocktail challenge. The strategy reported here will be useful for developing engineered E. coli strains with improved phage resistance for various industrial fermentation processes for producing recombinant proteins and chemicals of interest.

Phage contamination is a persistent problem in industrial biotechnology processes employing bacterial strains. Here, the authors report the construction of E. coli host strains with broad antiphase activities via the genomic integration of the Ssp defense system and mutations of components essential for phage infection cycles.

Improved production of heme using metabolically engineered Escherichia coli

Heme has recently attracted much attention due to its promising applications in food and healthcare industries. However, the current titers and productivities of heme produced by recombinant microorganisms are not high enough for a wide range of applications. In this study, the process for the fermentation of the metabolically engineered E. coli HAEM7 strain was optimized for the high-level production of heme. To improve the production of heme, different carbon sources, iron concentration in the medium, pH control strategies, induction points, and iron content in feeding solution were examined. Moreover, strategies of increasing cell density, regular iron supplementation, and supply of excess feeding solution were developed to further improve the production of heme. In the optimized fermentation process, the HAEM7 strain produced 1.03 g/L heme with a productivity of 21.5 mg/L/h. The fermentation process and strategies reported here will expedite establishing industry-level production of heme. This article is protected by copyright. All rights reserved.

Metabolic and cellular engineering for the production of natural products

Increased awareness of the environmental and health concerns of consuming chemically synthesized products has led to a rising demand for natural products that are greener and more sustainable. Despite their importance, however, industrial-scale production of natural products has been challenging due to the low yield and high cost of the bioprocesses. To cope with this problem, systems metabolic engineering has been employed to efficiently produce natural products from renewable biomass. Here, we review the recent systems metabolic engineering strategies employed for enhanced production of value-added natural products, together with accompanying examples. Particular focus is set on systems-level engineering and cell physiology engineering strategies. Future perspectives are also discussed.

Production of zinc protoporphyrin IX by metabolically engineered Escherichia coli

Zinc protoporphyrin IX (ZnPPIX) has been considered as a promising red colorant for food industries as well as an anti-cancer drug. However, bio-based production of ZnPPIX from a renewable carbon source has not been reported yet. In this study, a fermentation process of the metabolically engineered E. coli HAEM7 strain was optimized for the high-level production of ZnPPIX. To repurpose the HAEM7 strain that was originally developed for the production of heme into a producer of ZnPPIX, the concentrations of iron and zinc in the culture medium were rebalanced. Next, the concentration of zinc in the feeding solution was optimized to improve ZnPPIX production. Moreover, the pH control strategy, induction point, and the strategy of increasing the cell density, which were optimized in the accompanying paper (Choi et al., 2022) for the high-level production of heme, were applied together. In the optimized fermentation process, the HAEM7 strain produced 2.2 g/L ZnPPIX with a productivity of 39.9 mg/L/h. The fermentation process and strategies reported here will expedite establishing industry-level production of ZnPPIX. This article is protected by copyright. All rights reserved.

Online citizen petitions related to COVID-19 in South Korean cities: a big data analysis

What do citizens demand of their governing bodies to cope with the spread of emerging infectious diseases after recognizing the growing danger? What are the similarities and differences in political participation via online citizen petitions regarding COVID-19 across cities with different degrees of pandemic experience? This study aims to answer these questions by examining citizen petitions regarding the COVID-19 pandemic in urban areas of South Korea. The pattern of citizens' requests is a part of integrative socio-ecological and political systems with spatial and temporal dimensions. We compare the pattern of online citizen petitions in four Korean cities, namely Seoul, Busan, Daegu, and Incheon, some of which were epicenters of the COVID-19 outbreak. By applying relevant big data analysis techniques such as text mining, topic modeling, and network analysis, we compare the characteristics of citizen petitions on COVID-19 in the four cities, particularly whether (and how) they want financial or welfare support or COVID-19 prevention. We find that cities that experience a rapid spread are likely to have more petitions for prevention than for support. By comparison, cities without such experience are likely to have more petitions for support. This study contributes by tracing citizen and local government interactions in response to emerging infectious diseases by empirically analyzing the related big data on petitions. Policy implications suggest that urban authorities should listen to analyze and respond to the urgent needs of citizens.

Production of phenylpropanoids and flavonolignans from glycerol by metabolically engineered Escherichia coli

Phenylpropanoids are a group of plant natural products with medicinal importance derived from aromatic amino acids. Here, we report the production of two representative phenylpropanoids-coniferyl alcohol (CA) and dihydroquercetin (DHQ)-from glycerol by engineered Escherichia coli. First, an E. coli strain capable of producing 187.7 mg/L of CA from glycerol was constructed by the introduction of hpaBC from E. coli and OMT1, 4CL4, and CCR1 from Arabidopsis thaliana to the p-coumaric acid producer. Next, an E. coli strain capable of producing 239.4 mg/L of DHQ from glycerol was constructed by the introduction of F3H, TT7, and CPR from A. thaliana to the naringenin producer, followed by engineering the signal peptide of a cytochrome P450 TT7. Furthermore, to demonstrate the production of flavonolignans, a group of heterodimeric phenylpropanoids, from glycerol, ascorbate peroxidase 1 from Silybum marianum was employed and engineered to produce 0.04 μg/L of silybin and 1.29 μg/L of isosilybin from glycerol by stepwise culture. Finally, a single strain harboring all the 16 necessary genes was constructed, resulting in 0.12 μg/L of isosilybin production directly from glycerol. The strategies described here will be useful for the production of pharmaceutically important yet complex natural products.

Media Coverage of Senior and Celebrity Suicides and Its Effects on Copycat Suicides among Seniors

This study examined whether suicide rates in the elderly population are associated with media coverage of senior or celebrity suicides. Analyzing data from 2012 to 2015, we found that seniors were likely to be more influenced by media coverage of senior suicides than by celebrity suicides. Furthermore, the effects of media coverage of senior suicides were more significant when the reported reason was either health (mental or physical problems) or financial issues, such as poverty than other reasons.