Principles and functions of metabolic compartmentalization

Nanohybrid urate oxidase with magnetically switchable catalytic potential for precise gout therapy

Spatiotemporal regulation of therapeutic enzymes is desirable for enhancing the efficacy and safety of enzyme-based treatments for metabolic diseases, yet the absence of techniques capable of on-demand manipulating the in vivo catalytic activity of urate oxidase (UOx) represents a significant challenge in achieving precise gout therapy. Herein, we report a cyclic cascade nanohybrid urate oxidase (NUOx) comprised of a Fe3O4 nanoring core and a UOx shell, whose activity can be switched on and off on-demand using a deep-penetrated alternating magnetic field (AMF). The Fe3O4 nanoring under AMF exposure functions as a nanoheater to stimulate its intrinsic catalase (CAT) activity for oxygen recycling, which in turn activates UOx/CAT cascade for controlled uric acid degradation. Through the synergistic magnetothermal and UOx/CAT cyclic cascade, NUOx exhibited greatly enhanced AMF-tunability with an ON/OFF ratio as high as 7.6 and robust reversibility. This magnetically switchable NUOx enabled dynamic control of uric acid homeostasis without inducing hypouricemia and more efficient dissolution of monosodium urate crystals in vitro. In vivo experiments in a rat model of acute gout arthritis demonstrated that intra-articular administrated NUOx combined with AMF can more effectively relieve joint hypoxia, reduce uric acid levels and suppress joint inflammation, leading to a magneto-catalytic therapy with tunable therapeutic potential to enhance efficacy while minimizing potential side effects in gout treatment. These findings provide new insights into the development of nanohybrid enzymes with robust magnetic responsiveness for metabolic reprogramming and disease treatment.

Interfacial hydrogen bonding reorganization-assisted aqueous assembly of hydroxypropyl cellulose for robust construction of hollow nanocapsules

In nature, the assembly of biomolecules (e.g., saccharides, protein) spontaneously occurs in water into highly ordered compartmentalized hollow architecture such as cells. Cell-mimetic compartmentalized saccharide nanocapsules have emerged as important colloidal materials with great utility in the pharmaceutical and food fields. However, it remains challenging to fabricate hollow nanocapsules using highly hydrophilic natural saccharides in water. Herein, we report on the one-pot fabrication of hollow nanocapsules through a two-stepwise interfacial hydrogen bonding reorganization-assisted aqueous assembly of thermo-responsive hydroxypropyl cellulose (HPC) with pH-sensitive curcumin. A first-step solution mixing-triggered pH/temperature shifting significantly weakens the hydrogen bonding interaction of HPC with water molecules and leads to the protonation of curcumin, simultaneously driving supersaturation-induced phase separation and ordered co-aggregation in aqueous solution. A second-step temperature shifting rapidly rebuilds hydrogen bonding between HPC and curcumin at their interface to stabilize curcumin-entrapped amphiphilic nanostructures, robustly generating hollow nanocapsules with high loading capacity (up to 44 %) and good colloidal stability. The careful establishment of phase diagrams provides the conditions for producing nanocapsules under which the particle sizes, compositions and loading capacities can be regulated conveniently. The versatility of approach enables robust construction of compartmentalized polysaccharide nanomaterials with well-customized properties and functions, showing considerable potential in various fields.

Liquid-liquid phase separation in normal hematopoiesis and hematological diseases

Liquid-liquid phase separation (LLPS) is an emerging research field in cellular biology. LLPS-driven biomolecular condensates act as reaction chambers and regulatory hubs for critical processes, including chromatin architecture, gene expression, and metabolism. The dysregulation of these processes frequently impedes the proper execution of physiological functions. Current research indicates that abnormal phase separation plays a significant role in the pathogenesis of diseases and aging. This review briefly overviews the fundamental concepts and research methods related to phase separation. We also summarize studies concerning its physiological functions, particularly emphasizing its role in hematopoiesis. We further discuss how abnormal phase separation can lead to hematological disorders, specifically summarizing its involvement in the pathogenesis of leukemia. Despite recent advancements, elucidating LLPS mechanisms in hematopoiesis remains challenging due to the intricate interplay between biomolecular condensates and cellular function. Future research efforts aiming to reveal the role of LLPS in hematological diseases hold promise for novel therapeutic interventions and a deeper understanding of hematopoietic processes.

Metabolic mapping of the human solute carrier superfamily

Solute carrier (SLC) transporters govern most of the chemical exchange across cellular membranes and are integral to metabolic regulation, which in turn is linked to cellular function and identity. Despite their key role, individual functions of the SLC superfamily members were not evaluated systematically. We determined the metabolic and transcriptional profiles upon SLC overexpression in knock-out or wild-type isogenic cell backgrounds for 378 SLCs and 441 SLCs, respectively. Targeted metabolomics provided a fingerprint of 189 intracellular metabolites, while transcriptomics offered insights into cellular programs modulated by SLC expression. Beyond the metabolic profiles of 102 SLCs directly related to their known substrates, we identified putative substrates or metabolic pathway connections for 71 SLCs without previously annotated bona fide substrates, including SLC45A4 as a new polyamine transporter. By comparing the molecular profiles, we identified functionally related SLC groups, including some with distinct impacts on osmolyte balancing and glycosylation. The assessment of functionally related human genes presented here may serve as a blueprint for other systematic studies and supports future investigations into the functional roles of SLCs.

Recent Advances in Multiple Strategies for the Biosynthesis of Sesquiterpenols

Sesquiterpenols, a class of natural compounds composed of three isoprene units that form a 15-carbon skeleton with hydroxyl (-OH) group, are characterized by their volatility and potent aromatic properties. These compounds exhibit a wide range of biological activities, including antitumor, antibacterial, anti-inflammatory, anti-neurotoxic, antiviral, immunosuppressive, hepatoprotective, and cardiotonic effects. Due to their diverse physiological functionalities, sesquiterpenols serve as critical raw materials in the pharmaceutical, food, and cosmetic industries. In recent years, research on the heterologous synthesis of sesquiterpenol compounds using microbial systems has surged, attracting significant scientific interest. However, challenges such as low yields and high production costs have impeded their industrial-scale application. The rapid development of synthetic biology has introduced innovative methodologies for the microbial production of sesquiterpenol compounds. Herein, we examine the latest synthetic biology strategies and progress in microbial sesquiterpenol production, focusing on adaptive sesquiterpenol synthase screening and expression, synthesis pathway regulation, intracellular compartmentalized expression strategies, and tolerance to terpenoid-related toxicity. Critical challenges and future directions are also discussed to advance research in sesquiterpenol biosynthesis.

Oxidation of retromer complex controls mitochondrial translation

Reactive oxygen species (ROS) underlie human pathologies including cancer and neurodegeneration1,2. However, the proteins that sense ROS levels and regulate their production through their cysteine residues remain ill defined. Here, using systematic base-editing and computational screens, we identify cysteines in VPS35, a member of the retromer trafficking complex3, that phenocopy inhibition of mitochondrial translation when mutated. We find that VPS35 underlies a reactive metabolite-sensing pathway that lowers mitochondrial translation to decrease ROS levels. Intracellular hydrogen peroxide oxidizes cysteine residues in VPS35, resulting in retromer dissociation from endosomal membranes and subsequent plasma membrane remodelling. We demonstrate that plasma membrane localization of the retromer substrate SLC7A1 is required to sustain mitochondrial translation. Furthermore, decreasing VPS35 levels or oxidation of its ROS-sensing cysteines confers resistance to ROS-generating chemotherapies, including cisplatin, in ovarian cancer models. Thus, we identify that intracellular ROS levels are communicated to the plasma membrane through VPS35 to regulate mitochondrial translation, connecting cytosolic ROS sensing to mitochondrial ROS production.

Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis

Mitochondria serve as central hubs in cellular metabolism by sensing, integrating, and responding to metabolic demands. This integrative function is achieved through inter-organellar communication, involving the exchange of metabolites, lipids, and signaling molecules. The functional diversity of metabolite exchange and pathway interactions is enabled by compartmentalization within organelle membranes. Membrane contact sites (MCSs) are critical for facilitating mitochondria-organelle communication, creating specialized microdomains that enhance the efficiency of metabolite and lipid exchange. MCS dynamics, regulated by tethering proteins, adapt to changing cellular conditions. Dysregulation of mitochondrial-organelle interactions at MCSs is increasingly recognized as a contributing factor in the pathogenesis of multiple diseases. Emerging technologies, such as advanced microscopy, biosensors, chemical-biology tools, and functional genomics, are revolutionizing our understanding of inter-organellar communication. These approaches provide novel insights into the role of these interactions in both normal cellular physiology and disease states. This review will highlight the roles of metabolite transporters, lipid-transfer proteins, and mitochondria-organelle interfaces in the coordination of metabolism and transport.

Targeting B7-H3 inhibition-induced activation of fatty acid synthesis boosts anti-B7-H3 immunotherapy in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is the most malignant breast cancer, highlighting the need for effective immunotherapeutic targets. The immune checkpoint molecule B7-H3 has recently gained attention as a promising therapeutic target due to its pivotal role in promoting tumorigenesis and cancer progression. However, the therapeutic impact of B7-H3 inhibitors (B7-H3i) remains unclear.

METHODS

Transcriptomic and metabolomic analyses were conducted to explore the underlying mechanisms of B7-H3 inhibition in TNBC. The therapeutic efficacy of the combined treatment strategy was substantiated through comprehensive phenotypic assays conducted in vitro and validated in vivo using animal models.

RESULTS

B7-H3 blockade induces a "primed for death" stress state in cancer cells, leading to distinct alterations in metabolic pathways. Specifically, B7-H3 knockdown activated the AKT signaling pathway and upregulated sterol regulatory element-binding protein 1 (SREBP1), which in turn elevated FASN expression. The simultaneous inhibition of both B7-H3 and FASN more effectively attenuated the malignant progression of TNBC.

CONCLUSIONS

Our findings propose an "immune attack-metabolic compensation" dynamic model and suggest the feasibility of a dual-targeting strategy that concurrently inhibits both B7-H3 and FASN to enhance therapeutic efficacy in TNBC patients.

SAM transmethylation pathway and adenosine recycling to ATP are essential for systemic regulation and immune response

During parasitoid wasp infection, activated immune cells of Drosophila melanogaster larvae release adenosine to conserve nutrients for immune response. S-adenosylmethionine (SAM) is a methyl group donor for most methylations in the cell and is synthesized from methionine and ATP. After methylation, SAM is converted to S-adenosylhomocysteine, which is further metabolized to adenosine and homocysteine. Here, we show that the SAM transmethylation pathway is up-regulated during immune cell activation and that the adenosine produced by this pathway in immune cells acts as a systemic signal to delay Drosophila larval development and ensure sufficient nutrient supply to the immune system. We further show that the up-regulation of the SAM transmethylation pathway and the efficiency of the immune response also depend on the recycling of adenosine back to ATP by adenosine kinase and adenylate kinase. We therefore hypothesize that adenosine may act as a sensitive sensor of the balance between cell activity, represented by the sum of methylation events in the cell, and nutrient supply. If the supply of nutrients is insufficient for a given activity, adenosine may not be effectively recycled back into ATP and may be pushed out of the cell to serve as a signal to demand more nutrients.

Ergothioneine controls mitochondrial function and exercise performance via direct activation of MPST

Ergothioneine (EGT) is a diet-derived, atypical amino acid that accumulates to high levels in human tissues. Reduced EGT levels have been linked to age-related disorders, including neurodegenerative and cardiovascular diseases, while EGT supplementation is protective in a broad range of disease and aging models. Despite these promising data, the direct and physiologically relevant molecular target of EGT has remained elusive. Here, we use a systematic approach to identify how mitochondria remodel their metabolome in response to exercise training. From these data, we find that EGT accumulates in muscle mitochondria upon exercise training. Proteome-wide thermal stability studies identify 3-mercaptopyruvate sulfurtransferase (MPST) as a direct molecular target of EGT; EGT binds to and activates MPST, thereby boosting mitochondrial respiration and exercise training performance in mice. Together, these data identify the first physiologically relevant EGT target and establish the EGT-MPST axis as a molecular mechanism for regulating mitochondrial function and exercise performance.

A structural perspective on enzymes and their catalytic mechanisms

In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.

Vesicle-Encapsulated Chemosensing Ensembles Allow Monitoring of Transmembrane Uptake Coupled with Enzymatic Reactions

Compartmentalized models with coupled catalytic networks are considered as "protocells" in the context of research related to the origin of life. To model the kinetics of a simple cellular uptake-metabolism process, we use a compartmentalized protocell system that combines liposome-encapsulated intravesicular reporter pairs with co-encapsulated enzymes to monitor the membrane transport of a substrate (analyte uptake) and its subsequent enzymatic reaction inside the vesicles (metabolism to the product). The intravesicular chemosensing ensembles consist of the macrocycles cucurbit[7]uril or p-sulfonatocalix[4]arene and matching fluorescent dyes to set up suitable reporter pairs. When these macrocycle/dye reporter pairs are co-encapsulated with enzymes (trypsin, protein kinase A, or butyrylcholinesterase), it is possible to monitor first the transport of different substrates (polylysine, protamine, H-LRRWSLG-OH, or butyrylcholine) through added pores (outer membrane proteins F and C), with synthetic carriers (amphiphilic calixarenes), or by direct permeation (only for butyrylcholine). The subsequent enzymatic conversions of the substrates after they have entered the corresponding protocells can be monitored as consecutive reactions. The new type of in vitro assays can be applied to different enzymes and analytes, affording a comprehensive chemosensing system of high chemical complexity.

Membrane Transport Modulates the pH-Regulated Feedback of an Enzyme Reaction Confined within Lipid Vesicles

Understanding ion transport dynamics in reactive vesicles is pivotal for exploring biological and chemical processes and essential for designing synthetic cells. In this work, we investigate how proton transport and membrane potential regulate pH dynamics in an autocatalytic enzyme reaction within lipid vesicles. Combining experimental and numerical methods, we demonstrate that compartmentalization within lipid membranes accelerates internal reactions, attributed to protection from the external acidic environment. In experiments, we explored how proton movement significantly impacts internal reactions by changing bilayer thickness, adding ion transporters, and varying buffers. Numerical investigations incorporated electrical membrane potential and capacitance into a kinetic model of the process, elucidating the mechanisms that dictate the control of reaction time observed in the experiment, driven by both electrical and chemical potential gradients. These findings establish a framework for controlling pH clock reactions via membrane changes and targeted manipulation of proton movement, which could aid in the design of synthetic cells with precise, controlled functionalities.

Building Localized NADP(H) Recycling Circuits to Advance Enzyme Cascadetronics

The catalytic action of enzymes in a cascade trapped within a mesoporous electrode material is simultaneously energized, controlled and observed through the efficient, reversible electrochemical NAD(P)(H) recycling catalyzed by one of the enzymes. In their nanoconfined state, nicotinamide cofactors are tightly channeled current carriers, mediating multi-step reactions in either direction (oxidation or reduction) with a rapid response time. By incorporating a hydrogen-borrowing enzyme pair, the internal action of which opposes the external voltage bias driving oxidation or reduction, a reduction process can be performed under overall oxidizing conditions, and vice versa. The power of the method to control and resolve complex metabolic pathways is demonstrated using a non-linear, three-enzyme cascade extended by incorporating a fourth enzyme, urease. The latter generates in situ ammonia, which is enzymatically consumed in a reductive process, but the immediate current response to each addition of urea is observed, unusually, by applying an oxidizing potential. A practical consequence is that enzyme-catalyzed electrochemical reduction reactions requiring anaerobic conditions (to avoid O2 interference) can readily be studied under ambient aerobic conditions. The results illustrate how a complex enzyme cascade confined within a porous electrode and connected to an electrical power source manifests characteristics associated with electronic circuits.

Engineering metabolic flux for the microbial synthesis of aromatic compounds

Microbial cell factories have emerged as a sustainable alternative to traditional chemical synthesis and plant extraction methods for producing aromatic compounds. However, achieving economically viable production of these compounds in microbial systems remains a significant challenge. This review summarizes the latest advancements in metabolic flux regulation during the microbial production of aromatic compounds, providing an overview of its applications and practical outcomes. Various strategies aimed at improving the utilization of extracellular substrates, enhancing the efficiency of synthetic pathways for target products, and rewiring intracellular metabolic networks to boost the titer, yield, and productivity of aromatic compounds are discussed. Additionally, the persistent challenges in this field and potential solutions are highlighted.

Normothermic Machine Perfusion of Explanted Human Metabolic Livers: A Proof of Concept for Studying Inborn Errors of Metabolism

The human liver plays a central metabolic role; however, its physiology may become imbalanced in inborn errors of metabolism (IEM), a broad category of monogenic disorders. Liver transplantation has been increasingly used to improve patient metabolic control, especially in diseases related to amino acid metabolism, such as urea cycle disorders and organic acidurias, to provide enzyme replacement. Ex vivo liver normothermic machine perfusion (NMP) techniques have recently been developed to increase the number of transplantable grafts and improve transplantation outcomes. This study used seven NMP of explanted livers from patients with IEM undergoing transplantation as models to investigate disease-related liver metabolism and function. The perfused livers demonstrated positive viability indicators and disease-specific targeted metabolomics providing the proof-of-principle that our ex vivo model expresses the biochemical disease characteristics and responds to therapeutical intervention in a unique "physiological" milieu, offering an ideal tool to study novel treatments, in a setting closely mirroring human disease.

Rational pore engineering reveals the relative contribution of enzymatic sites and self-assembly towards rapid ferroxidase activity and mineralization: impact of electrostatic guiding and cage-confinement in bacterioferritin

The self-assembled ferritin protein nanocage plays a pivotal role during oxidative stress, iron metabolism, and host-pathogen interaction by executing rapid iron uptake, oxidation and its safe-storage. Self-assembly creates a nanocompartment and various pores/channels for the uptake of charged substrates (Fe2+) and develops a concentration gradient across the protein shell. This phenomenon fuels rapid ferroxidase activity by an upsurge in the substrate concentration at the catalytic sites. However, it is difficult to segregate the relative contributions of the catalytic sites and self-assembly towards rapid ferroxidase/mineralization activity owing to the inherent self-assembly propensity of ferritins. In the current work, 3-fold pore electrostatics of bacterioferritin from Mycobacterium tuberculosis were rationally altered by site-directed mutagenesis to generate self-assembled (E121A and E121Q) and assembly-defective (E121K and E121F) variants. In comparison to the autoxidation of Fe2+ in buffer, the assembly-defective variants exhibited significantly faster ferroxidase/mineralization activity and O2 consumption kinetics due to their functional catalytic sites, but failed to level-up with the self-assembled variants even at 100-fold higher Fe2+ concentration. Only the self-assembled variants exhibited cooperativity in iron oxidation, maintained biomineral solubility, and protected DNA against the Fenton reaction. This report highlights the concerted effect of self-assembly and ferroxidase sites that propels the rapid Fe2+ uptake, its oxidation and biomineralization in bacterioferritin. The findings also establish the importance of electrostatic guiding and nanoconfinement offered by ferritin self-assembly towards its enzymatic activity and antioxidative properties. Moreover, this work identifies the key electrostatic interactions ("hot-spots") at the subunit contact points that control the cage/pore formation, impart cage stability and influence ferritin's natural functions. Manipulation of hot-spot residues can be further extended towards the encapsulation of cargo, for various bio-medical applications, by strategically inducing its disassembly and subsequent reassembly through adjustments in ionic strength. This would bypass the need for extreme/harsh reaction conditions and minimize the loss of cargo/protein.

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Defining the subcellular distribution of all human proteins and their remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immunocapture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membraneless compartments. A graph-based analysis assigns the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following HCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides key insights for elucidating cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org.

Synthetic Biomolecular Condensates: Phase-Separation Control, Cytomimetic Modelling and Emerging Biomedical Potential

Liquid-liquid phase separation towards the formation of synthetic coacervate droplets represents a rapidly advancing frontier in the fields of synthetic biology, material science, and biomedicine. These artificial constructures mimic the biophysical principles and dynamic features of natural biomolecular condensates that are pivotal for cellular regulation and organization. Via adapting biological concepts, synthetic condensates with dynamic phase-separation control provide crucial insights into the fundamental cell processes and regulation of complex biological pathways. They are increasingly designed with the ability to display more complex and ambitious cell-like features and behaviors, which offer innovative solutions for cytomimetic modeling and engineering active materials with sophisticated functions. In this minireview, we highlight recent advancements in the design and construction of synthetic coacervate droplets; including their biomimicry structure and organization to replicate life-like properties and behaviors, and the dynamic control towards engineering active coacervates. Moreover, we highlight the unique applications of synthetic coacervates as catalytic centers and promising delivery vehicles, so that these biomimicry assemblies can be translated into practical applications.

Programming biological communication between distinct membraneless compartments

Distinct membraneless organelles within cells collaborate closely to organize crucial functions. However, biosynthetic communicating membraneless organelles have yet to be created. Here we report a binary population of membraneless compartments capable of coexistence, biological communication and controllable feedback under cellular environmental conditions. The compartment consortia emerge from two orthogonally phase-separating proteins in a cell-free expression system. Their appearance can be programmed in time and order for on-demand delivery of molecules. In particular, the consortia can sense, process and deliver functional protein cargo in response to a protease message or a DNA message that encodes the protease. Such DNA-based molecular programs can be further harnessed by installing a feedback loop that controls the information flow at the messenger RNA level. These results contribute to understanding crosstalk among membraneless organelles and provide a design principle that can guide construction of functional compartment consortia.

Confinement Induces Morphological and Topological Transitions in Multivesicles

The study of self-assembly in confined spaces has gained significant attention among amphiphilic superstructures and colloidal design. The additional complexity introduced by interactions between contents and their containers, along with the effects of shape and lipid mixing, makes multivesicular bodies an interesting subject of study. Despite its promising applications in biomedicine, such as drug delivery and biomimetic materials, much remains unexplored. Here we investigate the effects of confinement on vesicles with varying lipid tail lengths. We first analyze the morphological changes of single spherical vesicles undergoing dehydration, which leads to a prolate-to-oblate transition. Our findings reveal that reductions in water content induce changes of shape while minimally affecting the surface area needed to maintain the hydration layer of lipid phosphate groups. Additionally, using extensive coarse-grained molecular dynamics simulations, we explore how vesicles confined within other vesicles evolve through topological changes into unexpected structures, mainly influenced by the lipid hydrocarbon lengths. Our results highlight the interplay between confinement, curvature-induced lipid sorting, and lipid-mixing entropy, leading to exquisitely self-assembled superstructures.

Construction of Compartmentalized Meso/Micro Spaces in Hierarchically Porous MOFs with Long-Chain Functional Ligands Inspired by Biological Signal Amplification

The creation of spatially coupled meso-/microenvironments with biomimetic compartmentalized functionalities is of great significance to achieve efficient signal transduction and amplification. Herein, using a soft-template strategy, UiO-67-type hierarchically mesoporous metal-organic frameworks (HMMOFs) were constructed to satisfy the requirements of such an artificial system. The key to the successful synthesis of HMUiO-67 is rooted in the utilization of the preformed cerium-oxo clusters as metal precursors, aligning the growth of MOF crystals with the mild conditions required for the self-assembly of the soft template. The adoption of long-chain functional 2,2'-bipyridine-5,5'-dicarboxylic acid ligands not only resulted in larger microporous sizes, facilitating the transport of various cascade reaction intermediates, but also provided anchorages for the introduction of enzyme-mimicking active sites. A cascade amplification system was designed based on the developed HMUiO-67, in which enzyme cascade reactions were initiated and relayed by a target analyte in the separate but coupled meso/micro spaces. As a proof of concept, natural acetylcholinesterase (AChE) and Cu-based laccase mimetics were integrated into HMMOFs, establishing a spatially coupled nanoreactor. The activity of AChE was triggered by the target analyte of carbaryl, while the amplified products of AChE catalysis mediated the activity of biomimetic enzyme in the closely proximate microporous spaces, producing further amplification of detectable signal. This enabled the entire cascade system to respond to minimal carbaryl with a limit of detection as low as approximately 2 nM. Such a model of cascade amplification is expected to set a conceptual guideline for the rational design of various bioreactors, serving as a sensitive response system for quantifying numerous target analytes.

Divide and conquer, mitochondrial edition: Subpopulations direct cellular energy and nutrient supply

Mitochondria produce energy and building blocks essential for cell growth. How these competing processes are balanced and sustained during nutrient scarcity remains unclear. Ryu et al. uncover distinct mitochondrial subpopulations, one dedicated to ATP production and another to macromolecule synthesis, enabling cell growth and proliferation under nutrient-limiting conditions.

Wars1 downregulation in hepatocytes induces mitochondrial stress and disrupts metabolic homeostasis

Several laboratories, including ours, have employed the Slc25a47tm1c(EUCOMM)Hmgu mouse model to investigate the role of SLC25A47, a hepatocyte-specific mitochondrial carrier, in regulating hepatic metabolism and systemic physiology. In this study, we reveal that the hepatic and systemic phenotypes observed following recombination of the Slc25a47-Wars1 locus in hepatocytes are primarily driven by the unexpected downregulation of Wars1, the cytosolic tryptophan aminoacyl-tRNA synthetase located adjacent to Slc25a47. While the downregulation of Wars1 predictably affects cytosolic translation, we also observed a significant impairment in mitochondrial protein synthesis within hepatocytes. This disturbance in mitochondrial function leads to an activation of the mitochondrial unfolded protein response (UPRmt), a critical component of the mitochondrial stress response (MSR). Our findings clarify the distinct roles of Slc25a47 and Wars1 in maintaining both systemic and hepatic metabolic homeostasis. This study sheds new light on the broader implications of aminoacyl-tRNA synthetases in mitochondrial physiology and stress responses.

The endosomal-vacuolar transport system acts as a docking platform for the Pmk1 MAP kinase signaling pathway in Magnaporthe oryzae

In Magnaporthe oryzae, the Pmk1 MAP kinase signaling pathway regulates appressorium formation, plant penetration, effector secretion, and invasive growth. While the Mst11-Mst7-Pmk1 cascade was characterized two decades ago, knowledge of its signaling in the intracellular network remains limited. In this study, we demonstrate that the endosomal surface scaffolds Pmk1 MAPK signaling and Msb2 activates Ras2 on endosomes in M. oryzae. Protein colocalization demonstrated that Msb2, Ras2, Cap1, Mst50, Mst11, Mst7, and Pmk1 attach to late endosomal membranes. Damage to the endosome-vacuole transport system influences Pmk1 phosphorylation. When Msb2 senses a plant signal, it internalizes and activates Ras2 on endosome membrane surfaces, transmitting the signal to Pmk1 via Mst11 and Mst7. Signal-sensing and delivery proteins are ubiquitinated and sorted for degradation in late endosomes and vacuoles, terminating signaling. Plant penetration and lowered intracellular turgor are required for the transition from late endosomes to vacuoles in appressoria. Our findings uncover an effective mechanism that scaffolds and controls Pmk1 MAPK signaling through endosomal-vacuolar transport, offering new knowledge for the cytological and molecular mechanisms by which the Pmk1 MAPK pathway modulates development and pathogenicity in M. oryzae.

Biosynthesis-Encoded Lipogenic Acetyl-CoA Measurement Using NMR Reveals Glucose-Driven Lipogenesis and Glutamine's Alternative Roles in Kidney Cancer

Fatty acid de novo synthesis (FADNS) is a critical process in lipogenesis that is characteristically altered in clear cell renal cell carcinoma (ccRCC), which is the major type of kidney cancer. An important challenge in studying the FADNS process has been the accurate measurement of cytosolic lipogenic acetyl-CoA (AcCoA), the precursor in FADNS, due to its compartmentalization within cells. Here, we describe a novel NMR-based method to decode the isotopic enrichment of lipogenic AcCoA, which, as we demonstrated, is encoded in the simple signal ratios of the geminal methyl groups of lanosterol during its biosynthesis. The approach was validated based on the independence of the tracer enrichment and species along with the expected FADNS modulation using differentially enriched tracers and a well-studied drug. Application of this technique to 786-O ccRCC cells showed that glucose may serve as a major carbon source for lipogenic AcCoA in FADNS at physiological nutrient concentrations, at odds with previous studies that indicated glutamine's dominant role through reductive carboxylation under higher nutrient conditions. Further investigation into glutamine's alternative roles in ccRCC cells suggested its major involvement in the bioenergetic TCA cycle, pyrimidine synthesis, and glutathione synthesis, which is also critical in ccRCC growth. The glutamine-dependent glutathione synthesis was also suggested as a possible metabolic vulnerability compared to normal kidney cells using a glutathione synthesis inhibitor. The current study provides a simple tool for studying an important aspect of lipid metabolism and suggests translational implications for targeting glucose-driven lipogenesis and glutamine-supported glutathione synthesis in ccRCC.

Compartmentalised single-chain nanoparticles and their function

Single-chain nanoparticles (SCNPs) are generated by intramolecular collapse and crosslinking of single polymer chains, thus conceptually resembling the structures of folded proteins. Their chemical flexibility and ability to form compartmentalised nanostructures sized ∼1 nm make them perfect candidates for numerous applications, such as in catalysis and drug delivery. In this review we discuss principles for the design, synthesis and analysis of SCNPs, with a focus on their compartmentalised structures, highlighting our own previous work. As such compartments offer the potential to generate a specific nanoenvironment e.g. for the covalent and non-covalent encapsulation of catalysts or drugs, they represent a novel, exciting, and expanding research area. Starting from the architectural and chemical design of the starting copolymers by controlling their amphiphilic profile, the embedding of blocks-, or secondary-structure-mimetic arrangements, we discuss design principles to form internal compartments inside the SCNPs. While the generation of compartments inside SCNPs is straightforward, their analysis is still challenging and often demands special techniques. We finally discuss applications of SCNPs, also linked to the compartment formation, predicting a bright future for these special nanoobjects.

Enzyme-Responsive DNA Condensates

Membrane-less compartments and organelles are widely acknowledged for their role in regulating cellular processes, and there is an urgent need to harness their full potential as both structural and functional elements of synthetic cells. Despite rapid progress, synthetically recapitulating the nonequilibrium, spatially distributed responses of natural membrane-less organelles remains elusive. Here, we demonstrate that the activity of nucleic-acid cleaving enzymes can be localized within DNA-based membrane-less compartments by sequestering the respective DNA or RNA substrates. Reaction-diffusion processes lead to complex nonequilibrium patterns, dependent on enzyme concentration. By arresting similar dynamic patterns, we spatially organize different substrates in concentric subcompartments, which can be then selectively addressed by different enzymes, demonstrating spatial distribution of enzymatic activity. Besides expanding our ability to engineer advanced biomimetic functions in synthetic membrane-less organelles, our results may facilitate the deployment of DNA-based condensates as microbioreactors or platforms for the detection and quantitation of enzymes and nucleic acids.

p53 engagement is a hallmark of an unfolded protein response in the nucleus of mammalian cells

Exposure to exogenous and endogenous stress is associated with the intracellular accumulation of aberrant unfolded and misfolded proteins. In eukaryotic cells, protein homeostasis within membrane-bound organelles is regulated by specialized signaling pathways, with the unfolded protein response in the endoplasmic reticulum serving as a foundational example. Yet, it is unclear if a similar surveillance mechanism exists in the nucleus. Here we leveraged engineered proteins called destabilizing domains to acutely expose mammalian cells to nuclear- or cytosolic- localized unfolded protein. We show that the appearance of unfolded protein in either compartment engages a common transcriptional response associated with the transcription factors Nrf1 and Nrf2. Uniquely, only in the nucleus does unfolded protein activate a robust p53-driven transcriptional response and a transient p53-independent cell cycle delay. These studies highlight the distinct effects of localized protein folding stress and the unique protein quality control environment of the nucleus.

Mitochondrial Phosphopantetheinylation is Required for Oxidative Function

4'-phosphopantetheinyl (4'PP) groups are essential co-factors added to target proteins by p hospho p antetheinyl transferase (PPTase) enzymes. Although mitochondrial 4'PP-modified proteins have been described for decades, a mitochondrially-localized PPTase has never been found in mammals. We discovered that the cytoplasmic PPTase a mino a dipate s emialdehyde d ehydrogenase p hospho p antetheinyl t ransferase (AASDHPPT) is required for mitochondrial respiration and oxidative metabolism. Loss of AASDHPPT results in failed 4'-PP modification of the mitochondrial acyl carrier protein and blunted activity of the mitochondrial fatty acid synthesis (mtFAS) pathway. We found that in addition to its cytoplasmic localization, AASDHPPT localizes to the mitochondrial matrix via an N-terminal mitochondrial targeting sequence contained within the first 13 amino acids of the protein. Our data show that this novel mitochondrial localization of AASDHPPT is required to support mtFAS activity and oxidative function. We further identify two variants of uncertain significance in AASDHPPT that are likely pathogenic in humans due to loss of mtFAS activity.

The key metabolic signatures and biomarkers of polycyclic aromatic hydrocarbon-induced blood glucose elevation in chinese individuals exposed to diesel engine exhaust

Due to the complexity of environmental exposure factors and the low levels of exposure in the general population, identifying the key environmental factors associated with diabetes and understanding their potential mechanisms present significant challenges. This study aimed to identify key polycyclic aromatic hydrocarbons (PAHs) contributing to increased fasting blood glucose (FBG) concentrations and to explore their potential metabolic mechanisms. We recruited a highly PAH-exposed diesel engine exhaust testing population and healthy controls. Our findings found a positive association between FBG concentrations and PAH metabolites, identifying 1-OHNa, 2-OHPh, and 9-OHPh as major contributors to the rise in FBG concentrations induced by PAH mixtures. Specifically, each 10 % increase in 1-OHNa, 2-OHPh, and 9-OHPh concentrations led to increases in FBG concentrations of 0.201 %, 0.261 %, and 0.268 %, respectively. Targeted metabolomics analysis revealed significant alterations in metabolic pathways among those exposed to high levels of PAHs, including sirtuin signaling, asparagine metabolism, and proline metabolism pathway. Toxic function analysis highlighted differential metabolites involved in various dysglycemia-related conditions, such as cardiac arrhythmia and renal damage. Mediation analysis revealed that 2-aminooctanoic acid mediated the FBG elevation induced by 2-OHPh, while 2-hydroxyphenylacetic acid and hypoxanthine acted as partial suppressors. Notably, 2-aminooctanoic acid was identified as a crucial intermediary metabolic biomarker, mediating significant portions of the associations between the multiple different structures of OH-PAHs and elevated FBG concentrations, accounting for 16.73 %, 10.84 %, 10.00 %, and 11.90 % of these effects for 1-OHPyr, 2-OHFlu, the sum concentrations of 2- and 9-OHPh, and the sum concentrations of total OH-PAHs, respectively. Overall, our study explored the potential metabolic mechanisms underlying the elevated FBG induced by PAHs and identified 2-aminooctanoic acid as a pivotal metabolic biomarker, presenting a potential target for intervention.

Hunting the Cell Cycle Snark

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the 'prebiotic ecology' and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like "why do cells replicate their DNA?", "why is DNA replication semi-conservative?", "why is DNA a double helix?", "why do cells divide?", "is cell division a spandrel?", and "how are catabolism and anabolism balanced?". Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria.

Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles

Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.

An Ultrasensitive Biosensor for Probing Subcellular Distribution and Mitochondrial Transport of l-2-Hydroxyglutarate

l-2-Hydroxyglutarate (l-2-HG) is a functionally compartmentalized metabolite involved in various physiological processes. However, its subcellular distribution and mitochondrial transport remain unclear owing to technical limitations. In the present study, an ultrasensitive l-2-HG biosensor, sfLHGFRH, composed of circularly permuted yellow fluorescent protein and l-2-HG-specific transcriptional regulator, is developed. The ability of sfLHGFRH to be used for analyzing l-2-HG metabolism is first determined in human embryonic kidney cells (HEK293FT) and macrophages. Then, the subcellular distribution of l-2-HG in HEK293FT cells and the lower abundance of mitochondrial l-2-HG are identified by the sfLHGFRH-supported spatiotemporal l-2-HG monitoring. Finally, the role of the l-glutamate transporter SLC1A1 in mitochondrial l-2-HG uptake is elucidated using sfLHGFRH. Based on the design of sfLHGFRH, another highly sensitive biosensor with a low limit of detection, sfLHGFRL, is developed for the point-of-care diagnosis of l-2-HG-related diseases. The accumulation of l-2-HG in the urine of patients with kidney cancer is determined using the sfLHGFRL biosensor.

Rhythms in lipid droplet content driven by a metabolic oscillator are conserved throughout evolution

The biological clock in eukaryotes controls daily rhythms in physiology and behavior. It displays a complex organization that involves the molecular transcriptional clock and the redox oscillator which may coordinately work to control cellular rhythms. The redox oscillator has emerged very early in evolution in adaptation to the environmental changes in O2 levels and has been shown to regulate daily rhythms in glycerolipid (GL) metabolism in different eukaryotic cells. GLs are key components of lipid droplets (LDs), intracellular storage organelles, present in all living organisms, and essential for energy and lipid homeostasis regulation and survival; however, the cell bioenergetics status is not constant across time and depends on energy demands. Thus, the formation and degradation of LDs may reflect a time-dependent process following energy requirements. This work investigated the presence of metabolic rhythms in LD content along evolution by studying prokaryotic and eukaryotic cells and organisms. We found sustained temporal oscillations in LD content in Pseudomonas aeruginosa bacteria and Caenorhabditis elegans synchronized by temperature cycles, in serum-shock synchronized human embryonic kidney cells (HEK 293 cells) and brain tumor cells (T98G and GL26) after a dexamethasone pulse. Moreover, in synchronized T98G cells, LD oscillations were altered by glycogen synthase kinase-3 (GSK-3) inhibition that affects the cytosolic activity of the metabolic oscillator or by knocking down LIPIN-1, a key GL synthesizing enzyme. Overall, our findings reveal the existence of metabolic oscillations in terms of LD content highly conserved across evolutionary scales notwithstanding variations in complexity, regulation, and cell organization.

The iAAA-mitochondrial protease YME1L1 regulates the degradation of the short-lived mitochondrial transporter SLC25A38

Mitochondrial transporters facilitate the exchange of diverse metabolic intermediates across the inner mitochondrial membrane, ensuring an adequate supply of substrates and cofactors to support redox and biosynthetic reactions within the mitochondrial matrix. However, the regulatory mechanisms governing the abundance of these transporters, crucial for maintaining metabolic compartmentalization and mitochondrial functions, remain poorly defined. Through analysis of protein half-life data and mRNA-protein correlations, we identified SLC25A38, a mitochondrial glycine transporter, as a short- lived protein with a half-life of 4 hours under steady-state conditions. Pharmacological inhibition and genetic depletion of various cellular proteolytic systems revealed that SLC25A38 is rapidly degraded by the iAAA-mitochondrial protease YME1L1. Depolarization of the mitochondrial membrane potential induced by the mitochondrial uncoupler carbonyl cyanide m-chlorophenylhydrozone prevented the degradation of SLC25A38. This dual regulation of SLC25A38 abundance by YME1L1 and mitochondrial membrane potential suggests a link between SLC25A38 turnover, the integrity of the inner mitochondrial membrane, and electron transport chain function. These findings open avenues for investigating whether mitochondrial glycine import coordinates with mitochondrial bioenergetics.

Liquid-Liquid Phase Separation-Mediated Photocatalytic Subcellular Hybrid System for Highly Efficient Hydrogen Production

Plant chloroplasts have a highly compartmentalized interior, essential for executing photocatalytic functions. However, the construction of a photocatalytic reaction compartment similar to chloroplasts in inorganic-biological hybrid systems (IBS) has not been reported. Drawing inspiration from the compartmentalized chloroplast and the phenomenon of liquid-liquid phase separation, herein, a new strategy is first developed for constructing a photocatalytic subcellular hybrid system through liquid-liquid phase separation technology in living cells. Photosensitizers and in vivo expressed hydrogenases are designed to coassemble within the cell to create subcellular compartments for synergetic photocatalysis. This compartmentalization facilitates efficient electron transfer and light energy utilization, resulting in highly effective H2 production. The subcellular compartments hybrid system (HM/IBSCS) exhibits a nearly 87-fold increase in H2 production compared to the bare bacteria/hybrid system. Furthermore, the intracellular compartments of the photocatalytic reactor enhance the system's stability obviously, with the bacteria maintaining approximately 81% of their H2 production activity even after undergoing five cycles of photocatalytic hydrogen production. The research brings forward visionary prospects for the field of semi-artificial photosynthesis, offering new possibilities for advancements in areas such as renewable energy, biomanufacturing, and genetic engineering.

Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering

Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.

Molecular vessels from preorganised natural building blocks

Supramolecular vessels emerged as tools to mimic and better understand compartmentalisation, a central aspect of living matter. However, many more applications that go beyond those initial goals have been documented in recent years, including new sensory systems, artificial transmembrane transporters, catalysis, and targeted drug or gene delivery. Peptides, carbohydrates, nucleobases, and steroids bear great potential as building blocks for the construction of supramolecular vessels, possessing complexity that is still difficult to attain with synthetic methods - they are rich in functional groups and well-defined stereogenic centers, ready for noncovalent interactions and further functions. One of the options to tame the functional and dynamic complexity of natural building blocks is to place them at spatially designed positions using synthetic scaffolds. In this review, we summarise the historical and recent advances in the construction of molecular-sized vessels by the strategy that couples synthetic predictability and durability of various scaffolds (cyclodextrins, porphyrins, crown ethers, calix[n]arenes, resorcin[n]arenes, pillar[n]arenes, cyclotriveratrylenes, coordination frameworks and multivalent high-symmetry molecules) with functionality originating from natural building blocks to obtain nanocontainers, cages, capsules, cavitands, carcerands or coordination cages by covalent chemistry, self-assembly, or dynamic covalent chemistry with the ultimate goal to apply them in sensing, transport, or catalysis.

Functional interplay of lipid droplets and mitochondria

Our body stores energy mostly in form of fatty acids (FAs) in lipid droplets (LDs). From there the FAs can be mobilized and transferred to peroxisomes and mitochondria. This transfer is dependent on close opposition of LDs and mitochondria and peroxisomes and happens at membrane contact sites. However, the composition and the dynamics of these contact sites is not well understood, which is in part due to the dependence on the metabolic state of the cell and on the cell- and tissue-type. Here, we summarize the current knowledge on the contacts between lipid droplets and mitochondria both in mammals and in the yeast Saccharomyces cerevisiae, in which various contact sites are well studied. We discuss possible functions of the contact site and their implication in disease.

Ergothioneine boosts mitochondrial respiration and exercise performance via direct activation of MPST

Ergothioneine (EGT) is a diet-derived, atypical amino acid that accumulates to high levels in human tissues. Reduced EGT levels have been linked to age-related disorders, including neurodegenerative and cardiovascular diseases, while EGT supplementation is protective in a broad range of disease and aging models in mice. Despite these promising data, the direct and physiologically relevant molecular target of EGT has remained elusive. Here we use a systematic approach to identify how mitochondria remodel their metabolome in response to exercise training. From this data, we find that EGT accumulates in muscle mitochondria upon exercise training. Proteome-wide thermal stability studies identify 3-mercaptopyruvate sulfurtransferase (MPST) as a direct molecular target of EGT; EGT binds to and activates MPST, thereby boosting mitochondrial respiration and exercise training performance in mice. Together, these data identify the first physiologically relevant EGT target and establish the EGT-MPST axis as a molecular mechanism for regulating mitochondrial function and exercise performance.

Metabolic rewiring of macrophages by epidermal-derived lactate promotes sterile inflammation in the murine skin

Dysregulated macrophage responses and changes in tissue metabolism are hallmarks of chronic inflammation in the skin. However, the metabolic cues that direct and support macrophage functions in the skin are poorly understood. Here, we show that during sterile skin inflammation, the epidermis and macrophages uniquely depend on glycolysis and the TCA cycle, respectively. This compartmentalisation is initiated by ROS-induced HIF-1α stabilization leading to enhanced glycolysis in the epidermis. The end-product of glycolysis, lactate, is then exported by epithelial cells and utilized by the dermal macrophages to induce their M2-like fates through NF-κB pathway activation. In addition, we show that psoriatic skin disorder is also driven by such lactate metabolite-mediated crosstalk between the epidermis and macrophages. Notably, small-molecule inhibitors of lactate transport in this setting attenuate sterile inflammation and psoriasis disease burden, and suppress M2-like fate acquisition in dermal macrophages. Our study identifies an essential role for the metabolite lactate in regulating macrophage responses to inflammation, which may be effectively targeted to treat inflammatory skin disorders such as psoriasis.

Chemical proteomics to study metabolism, a reductionist approach applied at the systems level

Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.

The solute carrier SLC25A17 sustains peroxisomal redox homeostasis in diverse mammalian cell lines

Despite the crucial role of peroxisomes in cellular redox maintenance, little is known about how these organelles transport redox metabolites across their membrane. In this study, we sought to assess potential associations between the cellular redox landscape and the human peroxisomal solute carrier SLC25A17, also known as PMP34. This carrier has been reported to function as a counter-exchanger of adenine-containing cofactors such as coenzyme A (CoA), dephospho-CoA, flavin adenine dinucleotide, nicotinamide adenine dinucleotide (NAD+), adenosine 3',5'-diphosphate, flavin mononucleotide, and adenosine monophosphate. We found that inactivation of SLC25A17 resulted in a shift toward a more reductive state in the glutathione redox couple (GSSG/GSH) across HEK-293 cells, HeLa cells, and SV40-transformed mouse embryonic fibroblasts, with variable impact on the NADPH levels and the NAD+/NADH redox couple. This phenotype could be rescued by the expression of Candida boidinii Pmp47, a putative SLC25A17 orthologue reported to be essential for the metabolism of medium-chain fatty acids in yeast peroxisomes. In addition, we provide evidence that the alterations in the redox state are not caused by changes in peroxisomal antioxidant enzyme expression, catalase activity, H2O2 membrane permeability, or mitochondrial fitness. Furthermore, treating control and ΔSLC25A17 cells with dehydroepiandrosterone, a commonly used glucose-6-phosphate dehydrogenase inhibitor affecting NADPH regeneration, revealed a kinetic disconnection between the peroxisomal and cytosolic glutathione pools. Additionally, these experiments underscored the impact of SLC25A17 loss on peroxisomal NADPH metabolism. The relevance of these findings is discussed in the context of the still ambiguous substrate specificity of SLC25A17 and the recent observation that the mammalian peroxisomal membrane is readily permeable to both GSH and GSSG.

Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis

Organelle transporters define metabolic compartmentalization, and how this metabolite transport process can be modulated is poorly explored. Here, we discovered that human SLC25A39, a mitochondrial transporter critical for mitochondrial glutathione uptake, is a short-lived protein under dual regulation at the protein level. Co-immunoprecipitation mass spectrometry and CRISPR knockout (KO) in mammalian cells identified that mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. SLC25A39 senses mitochondrial iron-sulfur cluster using four matrix cysteine residues and inhibits its degradation. SLC25A39 protein regulation is robust in developing and mature neurons. This dual transporter regulation, by protein quality control and metabolic sensing, allows modulating mitochondrial glutathione level in response to iron homeostasis, opening avenues for exploring regulation of metabolic compartmentalization. Neuronal SLC25A39 regulation connects mitochondrial protein quality control, glutathione, and iron homeostasis, which were previously unrelated biochemical features in neurodegeneration.

Reductive stress in cancer: coming out of the shadows

Redox imbalance is defined by disruption in oxidative and reductive pathways and has a central role in cancer initiation, development, and treatment. Although redox imbalance has traditionally been characterized by high levels of oxidative stress, emerging evidence suggests that an overly reductive environment is just as detrimental to cancer proliferation. Reductive stress is defined by heightened levels of antioxidants, including glutathione and elevated NADH, compared with oxidized NAD, which disrupts central biochemical pathways required for proliferation. With the advent of new technologies that measure and manipulate reductive stress, the sensors and drivers of this overlooked metabolic stress are beginning to be revealed. In certain genetically defined cancers, targeting reductive stress pathways may be an effective strategy. Redox-based pathways are gaining recognition as essential 'regulatory hubs,' and a broader understanding of reductive stress signaling promises not only to reveal new insights into metabolic homeostasis but also potentially to transform therapeutic options in cancer.

Designer protein compartments for microbial metabolic engineering

Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.

Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Precise coupling between cellular physiology and metabolism is emerging as a vital relationship underpinning tissue health and longevity. Nevertheless, functional-metabolic coupling within heterogenous microenvironments in vivo remains poorly understood due to tissue complexity and metabolic plasticity. Here, we establish the Drosophila renal system as a paradigm for linking mechanistic analysis of metabolism, at single-cell resolution, to organ-wide physiology. Kidneys are amongst the most energetically-demanding organs, yet exactly how individual cell types fine-tune metabolism to meet their diverse, unique physiologies over the life-course remains unclear. Integrating live-imaging of metabolite and organelle dynamics with spatio-temporal genetic perturbation within intact functional tissue, we uncover distinct cellular metabolic signatures essential to support renal physiology and healthy ageing. Cell type-specific programming of glucose handling, PPP-mediated glutathione regeneration and FA β-oxidation via dynamic lipid-peroxisomal networks, downstream of differential ERR receptor activity, precisely match cellular energetic demands whilst limiting damage and premature senescence; however, their dramatic dysregulation may underlie age-related renal dysfunction.

Helping students see bacteria in 3D: cellular models increase student learning about cell size and diffusion

In the microbial world, cell size and shape impact physiology, but students struggle to visualize spatial relationships between cells and macromolecules. In prokaryotic cells, cell size is limited by reliance on diffusion for nutrient uptake and the transport of nutrients within the cell. Cells must also meet a minimum size threshold to accommodate essential cellular components such as ribosomes and DNA. Using 3D printing allows for the creation of custom models that can be influential teaching tools in the biology classroom. This lesson uses 3D cell models to teach students enrolled in an introductory microbiology course about bacterial cell size and the biological importance of surface-area-to-volume ratio. During the lesson, students interact with 3D cell models and discuss a series of questions in small groups. Student learning was assessed using quantitative and qualitative student response data collected pre- and post-lesson. Student achievement of learning objectives, and their confidence in their knowledge of these concepts, improved post-lesson, and these gains were statistically significant. Our findings suggest that interacting with 3D-printed cell models improves student understanding about bacterial cell size and diffusion.