Green and efficient method to acquire high-value phycobiliprotein from microalgal biomass involving deep eutectic solvent-based ultrasound-assisted extraction.

Phycoerythrin (PE) is a phycobiliprotein holding great potential as a high-value food colorant and medicine. Deep eutectic solvent (DES)-based ultrasound-assisted extraction (UAE) was applied to extract B-PE by disrupting the resistant polysaccharide cell wall of Porphyridium purpureum. The solubility of cell wall monomers in 31 DESs was predicted using COSMO-RS. Five glycerol-based DESs were tested for extraction, all of which showed significantly higher B-PE yields by up to 13.5 folds than water. The DES-dependent B-PE extraction efficiencies were proposedly associated with different cell disrupting capabilities and protein stabilizing effects of DESs. The DES-based UAE method could be considered green according to a metric assessment tool, AGREEprep. The crude extract containing DES was further subjected to aqueous two-phase system, two-step ammonium sulfate precipitation, and ultrafiltration processes. The final purified B-PE had a PE purity ratio of 3.60 and a PC purity ratio of 0.08, comparable to the purity of commercial products.

Non-Targeted Metabolomics Investigation of a Sub-Chronic Variable Stress Model Unveils Sex-Dependent Metabolic Differences Induced by Stress.

Depression is twice as prevalent in women as in men, however, most preclinical studies of depression have used male rodent models. This study aimed to examine how stress affects metabolic profiles depending on sex using a rodent depression model: sub-chronic variable stress (SCVS). The SCVS model of male and female mice was established in discovery and validation sets. The stress-induced behavioral phenotypic changes were similar in both sexes, however, the metabolic profiles of female plasma and brain became substantially different after stress, whereas those of males did not. Four stress-differential plasma metabolites-ß-hydroxybutyric acid (BHB), L-serine, glycerol, and myo-inositol-could yield biomarker panels with excellent performance to discern the stressed individuals only for females. Disturbances in BHB, glucose, 1,5-anhydrosorbitol, lactic acid, and several fatty acids in the plasma of stressed females implied a systemic metabolic shift to ß-oxidation in females. The plasma levels of BHB and corticosterone only in stressed females were observed not only in SCVS but also in an acute stress model. These results collectively suggest a sex difference in the metabolic responses by stress, possibly involving the energy metabolism shift to ß-oxidation and the HPA axis dysregulation in females.

Sn-Substituted Argyrodite Li6PS5Cl Solid Electrolyte for Improving Interfacial and Atmospheric Stability.

Sulfide-based solid electrolytes exhibit good formability and superior ionic conductivity. However, these electrolytes can react with atmospheric moisture to generate H2S gas, resulting in performance degradation. In this study, we attempted to improve the stability of the interface between Li metal and an argyrodite Li6Ps5Cl solid electrolyte by partially substituting P with Sn to form an Sn-S bond. The solid electrolyte was synthesized via liquid synthesis instead of the conventional mechanical milling method. X-ray diffraction analyses confirmed that solid electrolytes have an argyrodite structure and peak shift occurs as substitution increases. Scanning electron microscopy and energy-dispersive X-ray spectroscopy analyses confirmed that the particle size gradually increased, and the components were evenly distributed. Moreover, electrochemical impedance spectroscopy and DC cycling confirmed that the ionic conductivity decreased slightly but that the cycling behavior was stable for about 500 h at X = 0.05. The amount of H2S gas generated when the solid electrolyte is exposed to moisture was measured using a gas sensor. Stability against atmospheric moisture was improved. In conclusion, liquid-phase synthesis could be applied for the large-scale production of argyrodite-based Li6PS5Cl solid electrolytes. Moreover, Sn substitution improved the electrochemical stability of the solid electrolyte.

Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum.

Acetogenic bacteria are a unique biocatalyst that highly promises to develop the sustainable bioconversion of carbon oxides (e.g., CO and CO2) into multicarbon biochemicals. Genotype-phenotype relationships are important for engineering their metabolic capability to enhance their biocatalytic performance; however, systemic investigation on the fitness contribution of individual gene has been limited. Here, we report genome-scale CRISPR interference screening using 41,939 guide RNAs designed from the E. limosum genome, one of the model acetogenic species, where all genes were targeted for transcriptional suppression. We investigated the fitness contributions of 96% of the total genes identified, revealing the gene fitness and essentiality for heterotrophic and autotrophic metabolisms. Our data show that the Wood-Ljungdahl pathway, membrane regeneration, membrane protein biosynthesis, and butyrate synthesis are essential for autotrophic acetogenesis in E. limosum. Furthermore, we discovered genes that are repression targets that unbiasedly increased autotrophic growth rates fourfold and acetoin production 1.5-fold compared to the wild-type strain under CO2-H2 conditions. These results provide insight for understanding acetogenic metabolism and genome engineering in acetogenic bacteria.

Recent progress in the engineering of C1-utilizing microbes.

The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.

Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization.

C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood-Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.

Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks.

With a presence of the Wood-Ljungdahl pathway, acetogenic bacteria are capable of converting C1 feedstocks into biomass and various metabolites, receiving industrial interest in microbial production of biochemicals derived from C1 substrates. To understand C1 feedstock fermentation using acetogenic bacteria, most of the studies have focused on revealing their carbon assimilation and energy conservation systems. Despite the determination of the essential mechanisms, a fundamental understanding of acetogenic bacteria and the associated complex regulatory systems remains unclear and is needed for rational strain design. For this purpose, systems biology is a suitable approach for investigating genome, transcription, translation, regulation systems, and metabolic flux, providing a glimpse of the relationship between the genotype and phenotype of the organisms. This chapter will cover recent systems biology applications on acetogenic bacteria and discuss the cellular responses during C1 feedstock fermentation along with the regulatory systems that orchestrate cellular processes.

Poly-3-hydroxybutyrate production in acetate minimal medium using engineered Methylorubrum extorquens AM1.

Acetate is regarded as a sustainable microbial feedstock that is synthesized from biowastes such as synthesis gas (syngas), carbon dioxide, lignocellulose, or organic waste. In this study, Methylorubrum extorquens AM1 was engineered to improve the production of bioplastic poly-3-hydroxybutyrate (PHB) using acetate as the sole carbon source. To utilize acetate as a carbon source and methanol as an energy source, acs encoding acetyl-CoA synthetase and fdh from Burkholderia stabilis were overexpressed, while ftfL involved in the assimilation of methanol into formyl-tetrahydrofolate was deleted. The yields of biomass and PHB from acetate significantly improved, and the growth rate and PHB content of the bacteria increased. In addition, sustainability of the PHB production was demonstrated using acetate derived from carbon dioxide and syngas. This study shows that biopolymers could be synthesized efficiently using acetate as the sole carbon source through metabolic engineering and the supply of energy cofactors.

Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum.

Acetogenic bacteria demonstrate industrial potential for utilizing carbon dioxide (CO2) for biochemical production using the Wood-Ljungdahl pathway. However, the metabolic engineering of acetogenic bacteria has been hampered by the limited number of available genetic bioparts for gene expression. Here, we integrated RNA sequencing, ribosome profiling, differential RNA sequencing, and RNA 3'-end sequencing results of Eubacterium limosum to establish genetic bioparts, such as promoters, 5' untranslated regions, and transcript terminators, to regulate transcriptional and translational expression of genes composing of biosynthetic pathways. In addition, a transformation method for the strain was developed to efficiently deliver the obtained genetic bioparts into cells, resulting in a transformation efficiency of 2.5 × 105 CFU/µg DNA. Using this method, the genetic bioparts were efficiently introduced, and their strengths were measured, which were then applied to optimize the heterologous expression of acetolactate synthase and acetolactate decarboxylase for non-native biochemical acetoin production. The strategy developed in this study is the first report on integrating multi-omics data for biopart development of CO2 or syngas utilizing acetogenic bacteria, which lays a foundation for the efficient production of biochemicals from CO2 or syngas as a carbon feedstock under autotrophic growth conditions.

Carvone and its eutectic mixtures as novel, biodegradable, and tunable solvents to extract hydrophobic compounds in substitution for volatile toxic solvents.

Finding safe solvents with low viscosities has been in great demand in extraction processes. Herein, R-(-)-carvone, a natural monoterpenoid rich in spearmint, was mixed with naturally occurring fatty acids and terpenes. Most eutectic mixtures presented a wide liquid window in the solid-liquid equilibrium phase diagrams. Carvone mixtures at the ideal eutectic points were characterized for physicochemical properties. Despite varying properties, all the tested solvents were immiscible with water and displayed low viscosity with reasonable biodegradability. Sigma potentials of the mixtures were applied to machine learning algorithms, suggesting carvone mixtures as substitutes for polar protic and dipolar aprotic solvents. Carvone mixtures could be successfully applied to liquid-liquid extraction of a red algae called laver, which is rich in natural hydrophobic and hydrophilic pigments of high value. This study proposes carvone as a new bio-based source of hydrophobic solvents and the eutectic mixtures as biodegradable and tunable solvents to extract hydrophobic compounds.

Genome-Scale Analysis of Acetobacterium woodii Identifies Translational Regulation of Acetogenesis.

Acetogens synthesize acetyl-CoA via the CO2-fixing Wood-Ljungdahl pathway. Despite their ecological and biotechnological importance, their translational regulation of carbon and energy metabolisms remains unclear. Here, we report how carbon and energy metabolisms in the model acetogen Acetobacterium woodii are translationally controlled under different growth conditions. Data integration of genome-scale transcriptomic and translatomic analyses revealed that the acetogenesis genes, including those of the Wood-Ljungdahl pathway and energy metabolism, showed changes in translational efficiency under autotrophic growth conditions. In particular, genes encoding the Wood-Ljungdahl pathway are translated at similar levels to achieve efficient acetogenesis activity under autotrophic growth conditions, whereas genes encoding the carbonyl branch present increased translation levels in comparison to those for the methyl branch under heterotrophic growth conditions. The translation efficiency of genes in the pathways is differentially regulated by 5' untranslated regions and ribosome-binding sequences under different growth conditions. Our findings provide potential strategies to optimize the metabolism of syngas-fermenting acetogenic bacteria for better productivity. IMPORTANCE Acetogens are capable of reducing CO2 to multicarbon compounds (e.g., ethanol or 2,3-butanediol) via the Wood-Ljungdahl pathway. Given that protein synthesis in bacteria is highly energy consuming, acetogens living at the thermodynamic limit of life are inevitably under translation control. Here, we dissect the translational regulation of carbon and energy metabolisms in the model acetogen Acetobacterium woodii under heterotrophic and autotrophic growth conditions. The latter may be experienced when acetogen is used as a cell factory that synthesizes products from CO2 during the gas fermentation process. We found that the methyl and carbonyl branches of the Wood-Ljungdahl pathway are activated at similar translation levels during autotrophic growth. Translation is mainly regulated by the 5'-untranslated-region structure and ribosome-binding-site sequence. This work reveals novel translational regulation for coping with autotrophic growth conditions and provides the systematic data set, including the transcriptome, translatome, and promoter/5'-untranslated-region bioparts.

Th2 Cytokines Increase the Expression of Fibroblast Growth Factor 21 in the Liver.

Interleukin-4 (IL-4) and IL-13 are the major T helper 2 (Th2) cytokines, and they are involved in the regulation of metabolism in the adipose tissue. The liver contains diverse innate and adaptive immune cells, but it remains to be determined whether Th2 cytokines modulate energy metabolism in the liver. Here, using gene expression data from the Gene Expression Omnibus (GEO) and the BXD mouse reference population, we determined that the Th2 cytokines IL-4 and IL-13 increase the secretion of fibroblast growth factor 21 (FGF21) in the liver. In vitro experiments confirmed that FGF21 was highly expressed in response to IL-4 and IL-13, and this response was abolished by the Janus kinase (JAK)-signal transducer and activator of transcription 6 (STAT6) blockade. Moreover, FGF21 expression in response to Th2 cytokines was augmented by selective peroxisome proliferator-activated receptor α (PPARα) inhibition. In vivo administration of IL-4 increased FGF21 protein levels in the liver in a STAT6-dependent manner, but FGF21 secretion in response to IL-4 was not observed in the epididymal white adipose tissue (eWAT) despite the activation of STAT6. Intraperitoneal administration of IL-33, an activator of type 2 immune responses, significantly increased the level of FGF21 in the serum and liver after 24 h, but repeated administration of IL-33 attenuated this effect. Taken together, these data demonstrate that the IL-4/IL-13-STAT6 axis regulates metabolic homeostasis through the induction of FGF21 in the liver.

Acetogenic bacteria utilize light-driven electrons as an energy source for autotrophic growth.

Acetogenic bacteria use cellular redox energy to convert CO2 to acetate using the Wood-Ljungdahl (WL) pathway. Such redox energy can be derived from electrons generated from H2 as well as from inorganic materials, such as photoresponsive semiconductors. We have developed a nanoparticle-microbe hybrid system in which chemically synthesized cadmium sulfide nanoparticles (CdS-NPs) are displayed on the cell surface of the industrial acetogen Clostridium autoethanogenum The hybrid system converts CO2 into acetate without the need for additional energy sources, such as H2, and uses only light-induced electrons from CdS-NPs. To elucidate the underlying mechanism by which C. autoethanogenum uses electrons generated from external energy sources to reduce CO2, we performed transcriptional analysis. Our results indicate that genes encoding the metal ion or flavin-binding proteins were highly up-regulated under CdS-driven autotrophic conditions along with the activation of genes associated with the WL pathway and energy conservation system. Furthermore, the addition of these cofactors increased the CO2 fixation rate under light-exposure conditions. Our results demonstrate the potential to improve the efficiency of artificial photosynthesis systems based on acetogenic bacteria integrated with photoresponsive nanoparticles.

Recent Advances in the Understanding of Specific Efferent Pathways Emerging From the Cerebellum.

The cerebellum has a long history in terms of research on its network structures and motor functions, yet our understanding of them has further advanced in recent years owing to technical developments, such as viral tracers, optogenetic and chemogenetic manipulation, and single cell gene expression analyses. Specifically, it is now widely accepted that the cerebellum is also involved in non-motor functions, such as cognitive and psychological functions, mainly from studies that have clarified neuronal pathways from the cerebellum to other brain regions that are relevant to these functions. The techniques to manipulate specific neuronal pathways were effectively utilized to demonstrate the involvement of the cerebellum and its pathways in specific brain functions, without altering motor activity. In particular, the cerebellar efferent pathways that have recently gained attention are not only monosynaptic connections to other brain regions, including the periaqueductal gray and ventral tegmental area, but also polysynaptic connections to other brain regions, including the non-primary motor cortex and hippocampus. Besides these efferent pathways associated with non-motor functions, recent studies using sophisticated experimental techniques further characterized the historically studied efferent pathways that are primarily associated with motor functions. Nevertheless, to our knowledge, there are no articles that comprehensively describe various cerebellar efferent pathways, although there are many interesting review articles focusing on specific functions or pathways. Here, we summarize the recent findings on neuronal networks projecting from the cerebellum to several brain regions. We also introduce various techniques that have enabled us to advance our understanding of the cerebellar efferent pathways, and further discuss possible directions for future research regarding these efferent pathways and their functions.

Preparation and characterization of various chitin-glucan complexes derived from white button mushroom using a deep eutectic solvent-based ecofriendly method.

Deep eutectic solvents (DESs) have gained great interests as ecofriendly and safe solvents in diverse areas. Herein, various chitin-glucan complexes (CGCs) were prepared from white button mushroom (Agaricus bisporus) using DESs. Ultrasonication of mushroom in five DESs yielded two types of CGCs from each DES, one from the DES-insoluble residue (DES_P) and another from the DES-soluble extract (DES_S). The ten resulting CGCs with varying chitin-to-ß-glucan ratios were compared with alkali-insoluble matter (AIM), chemically prepared using NaOH. BU_S and BU_P, prepared using BU comprising betaine and urea, were obtained in the highest yields with reasonably low protein and mineral contents. Despite different acetylation degrees (77.3% and 57.3%, respectively), BU_S and BU_P both degraded at 318 °C and showed remarkably low crystallinity (32.0% and 37.0% for BU_S and BU_P, respectively) compared to AIM, commercial chitin, and the reported CGCs. The surface of BU_S and BU_P was very porous and rough compared with AIM as a result of reduced H-bonds and lowered crystallinity. The DES-based method can potentially enable the preparation of advanced biomaterials from mushrooms under mild and ecofriendly conditions.

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals.

Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.

Applications of deep eutectic solvents to quantitative analyses of pharmaceuticals and pesticides in various matrices: a brief review.

Pharmaceuticals and pesticides are important analytes of interest in clinical, environmental, and food analyses for ensuring public health. Sample pretreatment steps are often prerequisites for the quantitative analysis of these compounds, which are generally present in low concentrations in samples with complex matrices. In compliance with the current trend towards green analytical chemistry, the replacement of conventional toxic organic solvents with ecofriendly and safe solvents has been pursued in developing sample pretreatment methods. Subsequent to several reports in 2017, deep eutectic solvents (DESs) have been increasingly applied as desirable alternative solvents in numerous types of sample pretreatment methods for the analysis of pharmaceuticals and pesticides. The present review summarizes analytical methods involving DESs as extraction solvents and as the reaction media or functional materials for preparing adsorbents to quantify pharmaceuticals and pesticides in various matrices.

Insights into the Vastly Different Effects of Eutectic Solvents on the Stability of Phenolic Compounds.

Eutectic solvents (ESs) have shown stabilizing effects on several molecules. Due to the potential applicability of bioactive compounds, understanding how ESs stabilize them is of great interest in pharmaceutical and related fields. Here, among various ESs, CTU, which comprise thiourea and choline chloride (ChCl), exerted remarkably high stabilizing effects on various phenolic compounds, whereas CU consisting of urea and ChCl exhibited the opposite effects. Using a potent polyphenol, (-)-epigallocatechin gallate (EGCG), as a model compound, we conducted experimental and in silico studies to unravel the underlying mechanisms of the two very similar ESs for the contrasting effects. The results suggest that ESs can affect with great diversity the stability of EGCG by complicated interactions arising from the unique properties of both ESs and their components.

3D Printed Bioresponsive Devices with Selective Permeability Inspired by Eggshell Membrane for Effective Biochemical Conversion.

Eggshell membrane has selective permeability that enables gas or liquid molecules to pass through while effectively preventing migration of microbial species. Herein, inspired by the architecture of the eggshell membrane, we employ three-dimensional (3D) printing techniques to realize bioresponsive devices with excellent selective permeability for effective biochemical conversion. The fabricated devices show 3D conductive carbon nanofiber membranes in which precultured microbial cells are controllably deployed. The resulting outcome provides excellent selective permeability between chemical and biological species, which enables acquisition of target responses generated by biological species confined within the device upon input signals. In addition, electrically conductive carbon nanofiber networks provide a platform for real-time monitoring of metabolism of microbial cells in the device. The suggested platform represents an effort to broaden microbial applications by constructing biologically programmed devices for desired responses enabled by designated deployment of engineered cells in a securely confined manner within enclosed membranes using 3D printing methods.

Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide.

Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood-Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.