Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS)

MFSD2A in Focus: the Molecular Mechanism of Omega-3 Fatty Acid Transport

Omega-3 fatty acids, such as docosahexaenoic acid (DHA), are essential nutrients required to support the growth, maintenance, and function of the central nervous system (CNS). While the brain has a high demand for DHA, it cannot synthesize it de novo and thus relies on its uptake from the bloodstream. Circulating DHA is primarily obtained from dietary sources and is transported across the blood-brain barrier (BBB) in the form of lysophosphatidylcholine (LPC-DHA) by the transmembrane transporter major facilitator superfamily domain containing 2A (MFSD2A) in a sodium-dependent manner. Here we provide a comprehensive analysis of recent insights gained from structural, functional, and computational studies of MFSD2A. We focus on the mechanism by which this transporter mediates sodium-dependent uptake of LPC-DHA, and lysolipids more broadly, highlighting different conformational states, substrate entry and release pathways, and the ligand binding sites. This review presents a detailed overview of the molecular mechanism that enables MFSD2A to supply the brain with this essential nutrient, while simultaneously providing biophysical insights into how lysolipids are transported across biological membranes.

Interaction of major facilitator superfamily domain containing 2A with the blood-brain barrier

The functional and structural integrity of the blood-brain barrier is crucial in maintaining homeostasis in the brain microenvironment; however, the molecular mechanisms underlying the formation and function of the blood-brain barrier remain poorly understood. The major facilitator superfamily domain containing 2A has been identified as a key regulator of blood-brain barrier function. It plays a critical role in promoting and maintaining the formation and functional stability of the blood-brain barrier, in addition to the transport of lipids, such as docosahexaenoic acid, across the blood-brain barrier. Furthermore, an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood-brain barrier dysfunction in a variety of neurological diseases; however, little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood-brain barrier. This paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood-brain barrier, including their basic structures and functions, cross-linking between major facilitator superfamily domain containing 2A and the blood-brain barrier, and the in-depth studies on lipid transport and the regulation of blood-brain barrier permeability. This comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood-brain barrier and the research progress to date. This will not only help to elucidate the pathogenesis of neurological diseases, improve the accuracy of laboratory diagnosis, and optimize clinical treatment strategies, but it may also play an important role in prognostic monitoring. In addition, the effects of major facilitator superfamily domain containing 2A on blood-brain barrier leakage in various diseases and the research progress on cross-blood-brain barrier drug delivery are summarized. This review may contribute to the development of new approaches for the treatment of neurological diseases.

Conformational Landscape of the Di- and Tripeptide Permease A Transport Cycle

Dipeptide and tripeptide permease A (DtpA) transporter is a bacterial homologue of the human PepT that is responsible for the uptake of di- and tripeptides from the small intestine and transports them across the cell membrane utilizing an inward-directed proton electrochemical gradient. Despite its importance, the structural dynamics governing the conformational transitions of DtpA remain poorly understood. In this study, we employed Adaptive Bandit enhanced sampling molecular dynamics simulations to investigate the five major conformational states of DtpA adopted during the transport cycle. We identified key metastable states and transitions underlying the transport cycle using Markov State Models (MSMs). Our findings reveal that intra- and interhelical interactions drive conformational changes by inducing bending and rotation of helices lining the pore, resulting in its opening and closure. This study explains the substrate transport mechanism in DtpA, enhancing our understanding of bacterial proton-dependent oligopeptide transporters (POTs) and opening new drug design and development opportunities.

Biodegradation of Poly(ε-caprolactone): Microorganisms, Enzymes, and Mechanisms

Poly(ε-caprolactone) (PCL) is a synthetic plastic known for its excellent physicochemical properties and a wide range of applications in packaging, coatings, foaming, and agriculture. In medicine, its versatility allows it to function as a scaffold for drug delivery, sutures, implants, tissue engineering, and 3D printing. In addition to its biocompatibility, PCL's most notable characteristic is its biodegradability. However, this property is affected by temperature, microbial activity, and environmental conditions, which means PCL can sometimes remain in nature for long periods. This review shows that various types of microorganisms can efficiently degrade PCL, including different strains of Pseudomonas spp., Streptomyces spp., Alcaligenes faecalis, and fungi like Aspergillus oryzae, Fusarium spp., Rhizopus delemar, and Thermomyces lanuginosus. These microorganisms produce enzymes such as lipases, esterases, and cutinases that break down PCL into smaller molecules that act as substrates. The review also examines the phylogenetic diversity of organisms capable of biodegrading PCL, the biochemical pathways involved in this process, and specific aspects of the genetic framework responsible for the expression of the enzymes that facilitate degradation. Targeted research on microbial PCL biodegradation and its practical applications could significantly aid in reducing and managing plastic waste on a global ecological scale.

Molecular basis of the urate transporter URAT1 inhibition by gout drugs

Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population. The human urate transporter 1 (URAT1) is responsible for the reabsorption of ~90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the recently developed compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor-dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.

Functional Outlook of Penicillium digitatum PdMFS6 Transporter to Elucidate Its Role in Fungicide Resistance and Virulence

A novel Penicillium digitatum MFS transporter, PdMFS6 (PDIP_42530), was recognized, and its function was studied to explain its relevance in the simultaneous development of resistance to different fungicide spectrums. No changes were detected after application of chemical fungicides in mutants with the deleted gene, but chemical susceptibility was severely impaired in overexpressing strains, that became persistent to different chemicals. Furthermore, P. digitatum deleted transformants showed less fungal virulence appraise upon citrus infection stored at 20 °C. In strains derived from Pd149-P. digitatum with low virulence and overexpressing PdMFS6, the signs of the disease were more evident. In addition, evaluation of gene transcription showed an increase in PdMFS6 gene expression over time in all P. digitatum strains tested. It is noteworthy that during citrus fruit infection, the wild-type Pd1 strain displayed an augmented level of transcription, indicating that this transporter plays a role in infectivity. The fungal transporter PdMFS6 could contribute to the susceptibility to chemicals commonly used in postharvest treatments, as well as to rise the virulence of P. digitatum during fruit infection.

Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution

The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.

Proteomics and physiologic analysis reveal different response strategies to cadmium stress in Lentinula edodes

Lentinula edodes (L. edodes) is the second most widely cultivated edible mushroom worldwide. However, it has the ability to accumulate cadmium (Cd), which poses significant health risks. Despite its significance, the protein-level response mechanisms to Cd stress remain insufficiently understood. This study aims to investigate the differential responses of the low-Cd-accumulating strain Le4606 and the high-Cd-accumulating strain Le4625 under Cd stress by biochemical and proteomic methodologies. The results indicate that Le4625 exhibits enhanced Cd absorption, proline accumulation, and vacuolar sequestration for detoxification, with ZRC1 detected exclusively at 7 h. Conversely, Le4606 demonstrates proficiency in glutathione-mediated detoxification, thioredoxin antioxidant activity, tricarboxylic acid cycle activity, autophagy, and Cd extrusion. Overall, vacuolar sequestration and glutathione-mediated detoxification are important for the differences in Cd accumulation. The distinct response strategies offer valuable insights into the underlying mechanisms of Cd accumulation. This research establishes a theoretical foundation for the breeding of low-Cd-accumulating cultivars, benefiting human health.

Structures of native SV2A reveal the binding mode for tetanus neurotoxin and anti-epileptic racetams

The synaptic vesicle glycoprotein 2A (SV2A) is a synaptic vesicle (SV) resident with homology to the major facilitator superfamily (MFS) and essential in vertebrate neurotransmission. Despite its unclear physiological role, SV2A is of high medical relevance as it is the target of the anti-epileptic drug Levetiracetam (LEV) and a receptor for clostridial neurotoxins (CNTs), among them presumably tetanus neurotoxin (TeNT). To obtain detailed insights about these molecular interactions we subjected native SV2A, purified from brain tissue, to cryo-EM. We discover that TeNT binds SV2A strikingly different from botulinum neurotoxin A and unveil the precise geometry of TeNT binding to dipartite SV2-ganglioside receptors. The structures deliver compelling support for SV2A as the protein receptor for TeNT in central neurons and reinforce the concepts of the dual receptor hypothesis for CNT entry into neurons. Further, our LEV-bound structure of SV2A reveals the drug-interacting residues, delineates a putative substrate pocket in SV2A and provides insights into the SV2-isoform-specificity of LEV. Our work has implications for CNT engineering from a hitherto unrecognized SV2 binding interface and for improved designs of anti-convulsant drugs in epilepsy treatment.

Structure and transport mechanism of human riboflavin transporters

Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which act as key cofactors of many enzymes, thus has essential roles in cell growth and functions. Animals cannot synthesize riboflavin in situ, the intake, distribution and metabolism of which are mediated by three riboflavin transporters (RFVT1-3). Many mutations in RFVTs cause severe consequences. How RFVTs recognize and transport riboflavin remains largely unknown. Here we describe the cryo-electron microscopy structures of human RFVT2 and RFVT3 in complex with riboflavin in outward-occluded and inward-open states, respectively. Riboflavin is recognized by a conserved binding pocket in the central cavity of RFVTs, whereas two acidic residues in RFVT3 determine its pH-dependent activity. By combining the structural, computational and functional analyses, this study demonstrates the structural basis of riboflavin recognition and provides a structural framework for the mechanistic comprehension of riboflavin recognition, transport, and pathology in human RFVTs.

Structural and functional insights into StnY, a ribbon-helix-helix (RHH) family transcription factor regulating antibiotic resistance in Streptomyces flocculus CGMCC4.1223

Deciphering how bacteria respond to antibiotic stress is essential for developing strategies to combat the increasing global antibiotic resistance gene (ARG) crisis. Here, we identified an unprecedented antibiotic resistance operon characterized by a single-domain transcription factor (TF) StnY, which responds to streptonigrin (STN) antibiotic and controls the activation of resistance genes stnK4 and stnG4 in Streptomyces flocculus CGMCC4.1223. To the best of our knowledge, StnY represents the first RHH family TF regulating ARG and it helically wraps around the promoter of the resistance operon in an octameric form. Unlike conventional TFs with distinct effector-binding domains, StnY utilizes its DNA-binding domain to bind the STN effector, facilitating the dissociation of StnY-DNA complex. Consequently, the vicinal oxygen chelates (VOC) family protein StnK4 sequesters STN to prevent cellular damage, while the major facilitator superfamily (MFS) protein StnG4 effluxes STN out of the cell. Furthermore, genome analysis reveals the widespread distribution of RHH-VOC-MFS gene cassettes in actinomycetes, the primary source of antibiotics. This study elucidates function mode of a resistance operon governed by a TF lacking an effector-binding domain, offering new insights into ARG regulation and the potential of ARG-guided antibiotics discovery, highlighting TFs as promising targets for addressing ARG.

Cryo-EM structure of the human monocarboxylate transporter 10

The monocarboxylate transporter (MCT) membrane protein family has 14 human members that perform key cellular functions, such as regulating metabolism. MCT8 and MCT10 have unique cargo specificity, transporting thyroid hormone and, in the case of MCT10, aromatic amino acids. Dysfunctional MCT8 causes the severe Allan-Herndon-Dudley syndrome, yet the (patho)physiology and function of MCT8 and MCT10 are not clearly understood, especially at a structural level. We present the cryoelectron microscopy (cryo-EM) structure of MCT10, displaying the classical major facilitator superfamily fold, caught in an inward-open configuration. Together with cargo docking models, the outward-open MCT10 AlphaFold model and validating functional analysis, cargo specificity and transport principles are proposed. These findings significantly enhance our understanding of the structure and function of MCTs, information that also may be valuable for the development of novel treatments against MCT-related disorders to address global challenges such as diabetes, obesity, and cancer.

Binding mechanism and antagonism of the vesicular acetylcholine transporter VAChT

The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. Dysregulation of its function can result in neurological disorders. It also serves as a target for developing radiotracers to quantify cholinergic neuron deficits in neurodegenerative conditions. Here we unveil the cryo-electron microscopy structures of human VAChT in its apo state, the substrate acetylcholine-bound state and the inhibitor vesamicol-bound state. These structures assume a lumen-facing conformation, offering a clear depiction of architecture of VAChT. The acetylcholine-bound structure provides a detailed understanding of how VAChT recognizes its substrate, shedding light on the coupling mechanism of protonation and substrate binding. Meanwhile, the vesamicol-bound structure reveals the binding mode of vesamicol to VAChT, laying the structural foundation for the design of the next generation of radioligands targeting VAChT.

The Fsr transporter of Sinorhizobium meliloti contributes to antimicrobial resistance and symbiosis with alfalfa

Major facilitator superfamily (MFS) transporters in bacteria participate in both the uptake and export of ions, metabolites or toxic compounds. In rhizobia, specific MFS transporters increase resistance to plant-produced compounds and may also affect other phenotypic traits, including symbiosis with legume host plants. Here, we describe the importance of the Sinorhizobium meliloti 1021 Fsr efflux pump in resistance to selected antimicrobial compounds and in modulating biofilm formation, motility and symbiotic efficiency with alfalfa. The fsr gene (smc00990) is annotated as encoding an MFS family fosmidomycin efflux pump. Unexpectedly, both the 1021 wild type and an fsr null mutant were highly resistant to fosmidomycin. Our assays indicate that this is due to an inability to transport the antibiotic. Unlike the wild type, the fsr mutant was highly sensitive to the fosmidomycin structural analogue fosfomycin, and moderately more sensitive to hydrogen peroxide (H2O2) and deoxycholate (DOC). Root and seed exudates from alfalfa did not inhibit the growth of the wild type or fsr mutant. fsr transcription significantly increased proportionally to the concentration of fosfomycin added to cultures but was unaffected by the addition of other antibiotics, H2O2, DOC or SDS. Alfalfa seed exudate moderately increased fsr transcriptional expression. Fluorometric assays using ethidium bromide as a substrate and carbonyl cyanide m-chlorophenyl hydrazone as an energy decoupler showed that Fsr was a proton-dependent efflux pump. Biofilm formation and swimming motility were decreased and increased, respectively, in the fsr mutant, and its symbiotic efficiency with alfalfa was decreased in terms of nodule numbers per plant and plant dry weights.

Comparative analysis of STP6 and STP10 unravels molecular selectivity in sugar transport proteins

The distribution of sugars is crucial for plant energy, signaling, and defense mechanisms. Sugar Transport Proteins (STPs) are Sugar Porters (SPs) that mediate proton-driven cellular uptake of glucose. Some STPs also transport fructose, while others remain highly selective for only glucose. What determines this selectivity, allowing STPs to distinguish between compounds with highly similar chemical composition, remains unknown. Here, we present the structure of Arabidopsis thaliana STP6 in an inward-occluded conformational state with glucose bound and demonstrate its role as both a glucose and fructose transporter. We perform a comparative analysis of STP6 with the glucose-selective STP10 using in vivo and in vitro systems, demonstrating how different experimental setups strongly influence kinetic transport properties. We analyze the properties of the monosaccharide binding site and show that the position of a single methyl group in the binding site is sufficient to shuffle glucose and fructose specificity, providing detailed insights into the fine-tuned dynamics of affinity-induced specificity for sugar uptake. Altogether, these findings enhance our understanding of sugar selectivity in STPs and more broadly SP proteins.

Structural basis of urate transport by glucose transporter 9

Glucose transporter 9 (GLUT9) is a critical urate transporter involved in renal reabsorption, playing a pivotal role in regulating physiological urate levels and representing a potential therapeutic target for gout. Despite such clinical significance, the structural basis of urate recognition and transport by GLUT9 remains elusive. Here, we present the cryoelectron microscopy (cryo-EM) structures of GLUT9 in the inward-open conformation in both apo and urate-bound states. Urate binds in a cleft between the N-terminal and C-terminal domains, interacting via hydrogen bonds and hydrophobic interactions. Structural comparison with sugar-transporting GLUTs highlights unique amino acid compositions in the substrate recognition pocket of GLUT9. Functional and mutational studies directly measuring GLUT9-mediated urate uptake further demonstrate the cooperative roles of multiple residues in urate recognition. Our findings elucidate the structural basis of urate transport by GLUT9 and provide valuable insights for the development of uricosuric drugs targeting GLUT9.

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology

The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo-electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.

Understanding, inhibiting, and engineering membrane transporters with high-throughput mutational screens

Promiscuous membrane transporters play vital roles across domains of life, mediating the uptake and efflux of structurally and chemically diverse substrates. Although many transporter structures have been solved, the fundamental rules of polyspecific transport remain inscrutable. In recent years, high-throughput genetic screens have solidified as powerful tools for comprehensive, unbiased measurements of variant function and hypothesis generation, but have had infrequent application and limited impact in the transporter field. In this primer, we describe the principles of high-throughput screening methods available for studying polyspecific transporters and comment on the necessity and potential of high-throughput methods for deciphering these transporters in particular. We present several screening approaches which could provide a fundamental understanding of the molecular basis of function and promiscuity in transporters. We further posit how this knowledge can be leveraged to design inhibitors that combat multidrug resistance and engineer transporters as needed tools for synthetic biology and biotechnology applications.

Bioinformatics analysis of oxidative phosphorylation-related differentially expressed genes in osteoporosis

BACKGROUND

Osteoporosis (OP) is a common metabolic bone disease characterized by decreased bone mass and increased fracture risk. Recent studies suggest that oxidative phosphorylation (OXPHOS) plays a crucial role in the pathogenesis of OP. This study aims to investigate the differential expression and potential functional roles of OXPHOS-related genes in OP.

METHODS

We downloaded gene expression data from two OP-related datasets, GSE56815 and GSE7429, using the GEOquery package. We also collected OXPHOS-related genes from the GeneCards and MsigDB databases. The limma package was used for differential expression analysis of GSE56815, and differentially expressed genes (DEGs) were identified. We intersected these DEGs with OXPHOS-related genes to identify OXPHOS-related differentially expressed genes. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), were conducted using the clusterProfiler package. Additionally, we performed gene set enrichment analysis (GSEA). The Mann-Whitney U test analyzed differences in the expression of OXPHOSRDEGs, and their diagnostic potential was assessed by Receiver Operating Characteristic (ROC) curves. Correlation analysis, Protein-Protein Interaction (PPI) network construction, mRNA-miRNA, mRNA-TF interaction network construction, and immune infiltration analysis using CIBERSORT were also conducted. RAW264.7 cells were induced in vitro for 3 days to differentiate towards osteoblasts, and RT-PCR assay was used to verify the differentiation and detect the differential expression of target genes.

RESULTS

Our results identified 31 DEGs in GSE56815, with 26 upregulated and 5 downregulated genes. Among these, we identified 10 OXPHOSRDEGs: VPS35, TBC1D2, UBQLN2, SH3GLB2, WWP1, NFKBIA, MFSD10, SLC2 A3, RP2, and ZNF91. GO and KEGG enrichment analyses revealed significant involvement of these genes in mechanisms such as the positive regulation of the protein catabolic process and the endocytosis pathway. ROC analysis demonstrated high diagnostic accuracy for VPS35 (AUC = 0.832) and TBC1D2 (AUC = 0.751). Correlation analysis indicated strong relationships between certain OXPHOSRDEGs. The PPI network highlighted 8 hub genes with significant functional similarity among them.

CONCLUSION

This study systematically elucidates the differential expression and potential mechanisms of OXPHOS-related genes in OP through comprehensive bioinformatics analyses. The identified key genes offer valuable insights into the molecular underpinnings of OP and present potential diagnostic biomarkers and therapeutic targets for further investigation.

Comparison and Analysis of Resistance Differences in Alternaria alternata from Fungicides with Three Different Mechanisms

The pathogen Alternaria alternata infects a variety of plants and crops, notably poplars, and results in large financial losses. Using twelve chemical fungicides for fungicide sensitivity tests (FSTs) on A. alternata, the result showed that prochloraz (PCZ), mancozeb (MZ), and fludioxonil (FLU) have potent inhibitory effects against the pathogen through different mechanisms. To investigate how the pathogen responded to fungicide-induced stress, transcriptome and physiological investigations were carried out after treatments with three fungicides at their corresponding 50% effective concentration (EC50) doses. The MZ treatment produced a distinct genetic response; FLU treatment produced the greatest number of differentially expressed genes (DEGs), followed by PCZ. DEGs from FLU treatment were mostly engaged in ribosome biosynthesis, those from MZ treatment in lipid and carbohydrate metabolism, and those from PCZ treatment in carbohydrate metabolism, according to Gene Ontology (GO) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that FLU and PCZ treatments were associated with ribosome biogenesis, whereas MZ treatment was linked to the pyruvate metabolic pathway. Collinear trend analysis indicates that MZ exhibits a unique pattern, with FLU treatment causing the most significant overexpression of genes, followed by PCZ. The six categories of 88 elevated DEGs associated with fungal resistance include tyrosinase, ATP-binding cassette (ABC) transporters, major facilitator superfamily (MFS) transporters, antioxidant and cellular resilience genes, as well as genes involved in cell wall and membrane biosynthesis. Notably, the pathways involved in the synthesis of melanin and ergosterol exhibited the strongest response to FLU. The results of a correlation analysis between physiological indices and resistance-related genes indicated that melanin content, malondialdehyde (MDA) content, and tyrosinase activity were positively correlated with the majority of resistance-related DEGs, whereas soluble protein content, superoxide dismutase (SOD) activity, and catalase (CAT) activity were negatively correlated, which is consistent with the observed trends in the measured physiological indicators. Taken together, this study provides a theoretical basis for developing more effective fungicides and chemical control strategies against A. alternata.

Energetic and structural control of polyspecificity in a multidrug transporter

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues extending beyond the binding site, with mutations that reshape binding, coupling, conformational flexibility, and membrane interactions. Further, we apply a pH-based selection scheme to measure the effect of mutation on pH-dependent transport efficiency. By integrating these data, we reveal a fundamental relationship between efficiency and promiscuity: highly efficient variants exhibit broad substrate profiles, while inefficient variants are narrower. These findings establish a direct link between energy coupling and polyspecificity, uncovering the biochemical logic underlying multidrug transport.

NIR-Activated Hollow Upconversion Nanocomposites for Tumor Therapy via GLUT1 Inhibition and Mitochondrial Function Disruption

Tumor remains a leading contributor to global mortality rates, necessitating urgent advancements in therapeutic interventions. Due to the intricate nature of the tumor microenvironment, individual differences make it difficult to achieve desired efficacy with a single strategy. To overcome these challenges, we develop for the first time hollow NaBiF4-based nanocomposites NaBiF4-W/R-D for tumor therapy by glucose transporter 1 (GLUT1) inhibition and mitochondrial function disruption. NaBiF4-W/R-D can inhibit GLUT1 function due to the presence of WZB117, which leads to a decrease in intracellular glucose in tumor cells, leaving them in a starved state. Meanwhile, the upconversion luminescence of NaBiF4-W/R-D under near-infrared (NIR) laser irradiation can stimulate the photosensitizer to efficiently generate singlet oxygen to disrupt the mitochondrial function and then kill the tumor cells. In addition, NIR-II emission from NaBiF4-W/R-D is used for fluorescence imaging to determine the optimal time point for tumor treatment. Finally, NaBiF4-W/R-D leads to mitochondrial membrane potential depolarization, impaired mitochondrial function, activation of caspase-3, and ultimately the amplification of apoptosis.

Polyethylene biodegradation: A multifaceted approach

The inert nature, durability, low cost, and wide applicability of plastics have made this material indispensable in our lives. This dependency has resulted in a growing number of plastic items, of which a substantial part is disposed in landfills or dumped in the environment, thereby affecting terrestrial and aquatic ecosystems. Among plastic materials, polyolefins are the most abundant and are impervious to biodegradation, owing to the presence of strong CC and CH bonds. Nevertheless, naturally occurring biodegradation of polyolefins, albeit limited, has been reported. This observation has sparked research on microbial polyolefin degradation. More efficient and targeted versions of this process could be developed also in the laboratory by designing synthetic microbial consortia with engineered enzymes. In this review, we discuss strategies for the development of such microbial consortia and identification of novel polyolefin-degrading microorganisms, as well as the engineering of polyethylene-oxidizing enzymes with greater catalytic efficacy. Finally, different techniques for the design of synthetic microbial consortia capable of successful polyolefin bioremediation will be outlined.

Mechanistic insights into proton-coupled substrate translocation of nucleoside proton symporters

The nucleoside proton symporter (NHS) family proteins are part of the major facilitator superfamily and are responsible for transporting nucleosides from the extracellular environment into the cell. Structural and biochemical analysis of NupG, a prototypical NHS member, have pinpointed the critical residues involved in substrate binding. However, the proton-coupled mechanism diving substrate translocation in NHS proteins has remained elusive. In previous research, we identified Asp323 in NupG as a potential protonation site. In this study, using X-ray crystallography, molecular dynamics simulations, and biochemical assays, we discovered that the deprotonation of Asp323 in NupG, or the equivalent Asp315 in YegT, (another NHS family member) triggers a local conformational change in the TM10 region of NHS transporters. Notably, this protonation site is part of a novel motif (GXXXD) located in the middle of the TM10 transmembrane helix in NHS proteins. Further biochemical studies suggest that this local conformational change in the GXXXD motif plays a role in coordinating substrate release, ultimately facilitating substrate translocation. Our findings provide valuable insights into the molecular mechanism of nucleoside transport and expand the understanding of the diverse transport mechanisms within the major facilitator superfamily.

Structural Basis for Inhibition of Urate Reabsorption in URAT1

The urate transporter 1 (URAT1) is the primary urate transporter in the kidney responsible for urate reabsorption and, therefore, is crucial for urate homeostasis. Hyperuricemia causes the common human disease gout and other pathological consequences. Inhibition of urate reabsorption through URAT1 has been shown as a promising strategy in alleviating hyperuricemia, and clinical and preclinical drug candidates targeting URAT1 are emerging. However, how small molecules inhibit URAT1 remains undefined, and the lack of accurate URAT1 complex structures hinders the development of better therapeutics. Here, we present cryoelectron microscopy structures of a humanized rat URAT1 bound with benzbromarone, lingdolinurad, and verinurad, elucidating the structural basis for drug recognition and inhibition. The three small molecules reside in the URAT1 central cavity with different binding modes, locking URAT1 in an inward-facing conformation. This study provides mechanistic insights into the drug modulation of URAT1 and sheds light on the rational design of potential URAT1-specific therapeutics for treating hyperuricemia.

Identification and functional characterization of major gene pcmfs, controlling cap color formation in Pleurotus cornucopiae

Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Cap color is an important commercial trait for oyster mushrooms. Little is known about the genetic mechanism of the cap color trait in oyster mushrooms, which limits molecular breeding for the improvement of cap color-type cultivars. In this study, an important candidate gene, pcmfs, for cap color in the oyster mushroom Pleurotus cornucopiae was identified based on the results of QTL (quantitative trait loci) mapping and comparative transcriptome analysis of our previous research. The pcmfs gene belonged to major facilitator superfamily (MFS) and was localized to the cell membrane. Expression pattern analysis and overexpression experiment demonstrated that pcmfs played an important positive role in cap color formation, with high expression levels leading to dark cap color. To our knowledge, this is the first reported gene that may be involved in the melanin transport in edible fungi. The results will enhance our understanding of the genetic basis for cap color formation in oyster mushrooms, ultimately facilitating the targeted molecular breeding of this phenotypic trait.IMPORTANCEOyster mushrooms are widely cultivated worldwide, particularly in developing countries, owing to their straightforward cultivation requirements and high biological efficiency. Cap color represents a significant commercial trait of oyster mushrooms. Despite its significance, the genetic basis of this trait remains poorly understood, limiting progress in molecular breeding to diversify cap color variants. Bridging this knowledge gap could improve the market appeal and consumer satisfaction of these cultivars by facilitating targeted breeding strategies. In our previous research, a major QTL of cap color in oyster mushroom P. cornucopiae was mapped and DEGs (differentially expressed genes) between the dark strains and white strains were identified. Based on this, the candidate gene for cap color pcmfs was further mined. The pcmfs gene, belonging to the major facilitator superfamily (MFS), is localized to the cell membrane. Expression pattern analysis and overexpression experiments have shown that pcmfs plays a significant role in cap color formation. To our knowledge, this is the first reported gene that may be involved in the melanin transport in edible fungi. The results contribute to elucidate the genetic mechanisms governing cap color formation in mushrooms, advancing targeted molecular breeding for this trait.

Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery

The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD+ and pumps ions (Na+ or H+) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na+-pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO2 reductases. Yet, the molecular principles that couple the long-range electron transfer to Na+ translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na+-pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na+ pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na+, and in turn, triggers an inward/outward transition with alternating membrane access driving the Na+ pump and the reduction of NAD+. Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.

Organic anion transporting polypeptides: Pharmacology, toxicology, structure, and transport mechanisms

Organic anion transporting polypeptides (OATPs) are membrane proteins that mediate the uptake of a wide range of substrates across the plasma membrane of various cells and tissues. They are classified into 6 subfamilies, OATP1 through OATP6. Humans contain 12 OATPs encoded by 11 solute carrier of organic anion transporting polypeptide (SLCO) genes: OATP1A2, OATP1B1, OATP1B3, the splice variant OATP1B3-1B7, OATP1C1, OATP2A1, OATP2B1, OATP3A1, OATP4A1, OATP4C1, OATP5A1, and OATP6A1. Most of these proteins are expressed in epithelial cells, where they mediate the uptake of structurally unrelated organic anions, cations, and even neutral compounds into the cytoplasm. The best-characterized members are OATP1B1 and OATP1B3, which have an important role in drug metabolism by mediating drug uptake into the liver and are involved in drug-drug interactions. In this review, we aimed to (1) provide a historical perspective on the identification of OATPs and their nomenclature and discuss their phylogenic relationships and molecular characteristics; (2) review the current knowledge of the broad substrate specificity and their role in drug disposition and drug-drug interactions, with a special emphasis on human hepatic OATPs; (3) summarize the different experimental systems that are used to study the function of OATPs and discuss their advantages and disadvantages; (4) review the available experimental 3-dimensional structures and examine how they can help elucidate the transport mechanisms of OATPs; and (5) finally, summarize the current knowledge of the regulation of OATP expression, discuss clinically important single-nucleotide polymorphisms, and outline challenges of physiologically based pharmacokinetic modeling and in vitro to in vivo extrapolation. SIGNIFICANCE STATEMENT: Organic anion transporting polypeptides (OATPs) are a family of 12 uptake transporters in the solute carrier superfamily. Several members, particularly the liver-expressed OATP1B1 and OATP1B3, are important drug transporters. They mediate the uptake of several endobiotics and xenobiotics, including statins and numerous other drugs, into hepatocytes, and their inhibition by other drugs or reduced expression due to single-nucleotide polymorphisms can lead to adverse drug effects. Their recently solved 3-dimensional structures should help to elucidate their transport mechanisms and broad substrate specificities.

Clinical Isolate of Candida tropicalis from a Patient in North Carolina: Identification, Whole-Genome Sequence Analysis, and Anticandidal Activity of Ganoderma lucidum

In North Carolina, candida infections are on the rise and pose a significant threat to human health in clinical settings. In addition, the rise of resistance to antifungal drugs has only heightened this concern. Importantly, misidentification of Candida spp. may result in underdiagnosis, patients getting the wrong treatment and incomplete infection prevention measures. The correct and rapid etiological identification of Candida infections is of paramount importance because it provides adequate therapy, reduces mortality, and controls outbreaks. Hence, this study aimed to identify Candida sp. up to species level of a clinical isolate from an infected patient treated in North Carolina using biochemical and molecular techniques. Due to the emergence of resistance, we explored whole genomic analysis to highlight polymorphisms that can impact candida resistance. Exploration for the effectiveness of bioactive compounds in natural products to treat Candida spp. resistant to present-day drugs could provide promising new treatment options for managing infected patients. Thus, this study also investigated anticandida activity of three solvent extracts of Ganoderma lucidum against the clinical isolate of Candida sp. The findings of this study provided evidence that Candida tropicalis MYA-3404 was the only strain present in the clinical isolate. The whole genome sequencing of C. tropicalis identified mutations in genes that most likely underscore drug resistance. All extracts from G. lucidum significantly (P < 0.05) inhibited the growth of C. tropicalis. Together, this work highlights the enormous potential of biochemical and molecular techniques in identifying clinical isolates of candida to species level and the use of bioactive compounds from extracts of G. lucidum as promising anticandidal agents. Further testing is needed to confirm the phenotypic expression of resistance.

Non-targeted Metabolomics Reveals the Potential Role of MFSD8 in Metabolism in Human Endothelial Cells

The major facilitator superfamily domain containing 8 (MFSD8) belongs to an orphan transporter protein expressed in a wide range of tissues. Nevertheless, the specific role of MFSD8 in human health and disease remains unknown. This study aimed to evaluate the role of MFSD8 protein on metabolic function using untargeted metabolomics analysis in human umbilical vein endothelial cells (HUVECs). HUVECs overexpressing MFSD8 were subjected to metabolomics analysis to evaluate changes in endogenous small molecules using LC-MS/MS analysis. In the positive scan mode, 634 metabolites from 1583 compounds were identified. In the negative scan mode, 169 metabolites from 405 compounds were identified. According to the established criteria for identifying differential metabolites, 96 metabolites exhibited significant differences between the MFSD8 and Vector groups. Among them, 62 metabolites were found to be up-regulated, whereas 34 metabolites were classified as down-regulated. Bioinformatics pipeline analysis revealed three common metabolic pathways, including arginine biosynthesis, beta-alanine metabolism, and pyrimidine metabolism, were found under the positive and negative scan modes. The semi-quantitative analysis was conducted on the differential metabolites, revealing that overexpression of MFSD8 resulted in increased levels of L-citrulline, L-aspartic acid, ornithine, N-acetyl-l-aspartic acid, L-histidine, beta-alanine metabolites and exhibited decreased levels of cytidine. The findings of our study indicated that MFSD8 had the most significant role in arginine biosynthesis, beta-alanine metabolism, and pyrimidine metabolism pathways within endothelial cells. The metabolomics data provide new insights into studying potential features of MFSD8 protein in the future.

From ancestor to pathogen: Expansion and evolutionary adaptations of multidrug resistance causing MFS efflux pumps in mycobacteria

Multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) is a growing threat. Efflux pumps, particularly those belonging to the Major Facilitator Superfamily (MFS), play a key role in MDR. This study investigated MFS transporters across Mycobacterium spp. to understand their evolution and role in drug resistance. We conducted a proteome-wide analysis of MFS proteins in Mtb, Mycobacterium smegmatis (non-pathogenic), and Mycobacterium canettii (closely related ancestor of Mtb). Mtb, known for its MDR, possessed the highest abundance of MFS drug efflux pumps, while Mycobacterium smegmatis had the least. This suggests a link between MFS drug efflux pump abundance and MDR phenotypes. Interestingly, Mycobacterium canettii displayed an intermediate level, possibly indicating the presence of these pumps before the emergence of Mtb as a pathogen. Further analysis of Mtb proteome revealed 31 putative MFS transporters and 3 proteins from expanded MFS subfamilies. Phylogenetic analysis categorized them into thirteen distinct families based on structural features. These findings highlight the potential importance of MFS transporters in MDR and the pathogenicity of Mtb. Overall, this study highlights the evolutionary role of MFS transporters in bacterial adaptation to antibiotics. The observed correlation between efflux pump abundance and MDR suggests MFS transporters as promising targets for future anti-tuberculosis therapies. Further research on specific transporter functions within MFS subfamilies can pave the way for novel therapeutic strategies.

Insight into the Mechanism of d-Glucose Accelerated Exchange in GLUT1 from Molecular Dynamics Simulations

Transmembrane glucose transport, facilitated by glucose transporters (GLUTs), is commonly understood through the simple mobile carrier model (SMCM), which suggests that the central binding site alternates exposure between the inside and outside of the cell, facilitating glucose exchange. An alternative "multisite model" posits that glucose transport is a stochastic diffusion process between ligand-operated gates within the transporter's central channel. This study aims to test these models by conducting atomistic molecular dynamics simulations of multiple glucose molecules docked along the central cleft of GLUT1 at temperatures both above and below the lipid bilayer melting point. Our results show that glucose exchanges occur on a nanosecond time-scale as glucopyranose rings slide past each other within the channel cavities, with minimal protein conformational movement. While bilayer gelation slows net glucose transit, the frequency of positional exchanges remains consistent across both temperatures. This supports the observation that glucose exchange at 0 °C is much faster than net flux, aligning with experimental data that show approximately 100 times the rate of exchange flux relative to net flux at 0 °C compared to 37 °C.

Characterization of bacterial transporters involved in the uptake of lignin-derived aromatic compounds

Chemically depolymerized low-molecular-weight lignin can be converted into polymer building blocks using bacterial convergent metabolic systems called biological funneling. Various bacterial enzyme genes involved in the catabolism of lignin-derived aromatic compounds have been identified and characterized in detail. This information is essential for developing the bioproduction of high-value-added chemicals from lignin. Transporters responsible for the first step in catabolism mediate the transport of substrates across biological membranes. Since substrate uptake in biological membranes can be an obstacle or a rate-limiting process in the bacterial production of value-added compounds, it is vital to understand not only enzyme functions but also uptake systems. In this chapter, we focus on the bacterial transporters for lignin-derived aromatic compounds that have been reported and introduce methods for the characterization of transporters, primarily through in vivo analyses. In addition, we will present an antibody-based analysis of the cellular localization of transporters.

Probing Ligand-Induced Conformational Changes in an MFS Transporter in vivo Using Site-Directed PEGylation

So far, site-directed alkylation (SDA) studies on transporters in the Major Facilitator Superfamily (MFS) are mostly performed at conditions different from the native cellular environment. In this study, using GFP-based site-directed PEGylation, ligand-induced conformational changes in the lactose permease of Escherichia coli (LacY), were examined in vivo for the first time. Accessibility/reactivity of single-Cys replacements in a Cys-less LacY-eGFP fusion background was tested using methoxy polyethylene glycol-maleimide-5K (mPEG-Mal-5K) in the absence or presence of a ligand, and the band-shift of the fusion upon PEGylation was detected by in-gel fluorescence. Ligand binding increases the rate of PEGylation at five out of eight tested positions on the periplasmic side in vivo, while decreasing the rate of PEGylation at both positions tested on the cytoplasmic side in situ. Upon ligand binding, the rate of PEGylation at two periplasmic positions, K42 and Q242, slightly decreases in vivo, but increases in situ, indicating the conformational behavior of these two residues in living cells may not be identical to that in isolated cell membranes. Furthermore, abolishing the electrochemical H+ gradient (Δμ∼H+) reduces the rate of PEGylation at all tested positions on the periplasmic side. We also found that, unlike the linear form, the branched (Y-shape) mPEG-Mal-5K cannot pass the outer membrane. This work characterizes the alternating access of LacY in the context of a living cell and demonstrates that this methodology is feasible and effective for dynamical studies of MFS transporters.

Turning antagonists into allies: Bacterial-fungal interactions enhance the efficacy of controlling Fusarium wilt disease

Intense microbial competition in soil has driven the evolution of resistance mechanisms, yet the implications of such evolution on plant health remain unclear. Our study explored the conversion from antagonism to coexistence between Bacillus velezensis (Bv) and Trichoderma guizhouense (Tg) and its effects on Fusarium wilt disease (FWD) control. We found a bacilysin transmembrane transporter (TgMFS4) in Tg, critical during cross-kingdom dialogue with Bv. Deleting Tgmfs4 (ΔTgmfs4) mitigated Bv-Tg antagonism, reduced bacilysin import into Tg, and elevated its level in the coculture environment. This increase acted as a feedback regulator, limiting overproduction and enhancing Bv biomass. ΔTgmfs4 coinoculation with Bv demonstrated enhanced FWD control relative to wild-type Tg (Tg-WT). In addition, the Tg-WT+ Bv consortium up-regulated antimycotic secretion pathways, whereas the ΔTgmfs4+ Bv consortium enriched the CAZyme (carbohydrate-active enzyme) family gene expression in the rhizosphere, potentiating plant immune responses. This study elucidates the intricacies of bacterial-fungal interactions and their ramifications for plant health.

Mechanisms of urate transport and uricosuric drugs inhibition in human URAT1

High urate levels in circulation lead to the accumulation of urate crystals in joints and ultimately inflammation and gout. The reabsorption process of urate in the kidney by the urate transporter URAT1 plays a pivotal role in controlling serum urate levels. Pharmacological inhibition of URAT1 by uricosuric drugs is a valid strategy for gout management. Despite the clinical significance of URAT1, its structural mechanism and dynamics remain incompletely understood. Here, we report the structures of human URAT1 (hURAT1) in complex with substrate urate or inhibitors benzbromarone and verinurad at resolution ranges from 3.0 to 3.3 Å. We observe urate in the central substrate-binding site of hURAT1 in the outward-facing conformation and urate is wrapped in the center of hURAT1 by five phenylalanines and coordinated by two positively charged residues on each side. Uricosuric compounds benzbromarone and verinurad occupy the urate-binding site of hURAT1 in the inward-facing conformation. Structural comparison between different conformations of hURAT1 reveals the rocker-switch-like mechanism for urate transport. Benzbromarone and verinurad exert their inhibitory effect by blocking not only the binding of urate but also the structural isomerization of hURAT1.

Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system

Hookworms are intestinal parasitic nematodes that chronically infect ~500 million people, with reinfection common even after clearance by drugs. How infecting hookworms successfully overcome host protective mechanisms is unclear, but it may involve hookworm proteins that digest host tissues, or counteract the host's immune system, or both. To find such proteins in the zoonotic hookworm Ancylostoma ceylanicum, we identified hookworm genes encoding excreted-secreted (ES) proteins, hookworm genes preferentially expressed in the hookworm intestine, and hookworm genes whose transcription is stimulated by the host immune system. We collected ES proteins from adult hookworms harvested from hamsters; mass spectrometry identified 565 A. ceylanicum genes encoding ES proteins. We also used RNA-seq to identify A. ceylanicum genes expressed both in young adults (12 days post-infection) and in intestinal and non-intestinal tissues dissected from mature adults (19 days post-infection), with hamster hosts that either had normal immune systems or were immunosuppressed by dexamethasone. In adult A. ceylanicum, we observed 1,670 and 1,196 genes with intestine- and non-intestine-biased expression, respectively. Comparing hookworm gene activity in normal versus immunosuppressed hosts, we observed almost no changes of gene activity in 12-day young adults or non-intestinal 19-day adult tissues. However, in intestinal 19-day adult tissues, we observed 1,951 positively immunoregulated genes (upregulated at least two-fold in normal hosts versus immunosuppressed hosts), and 137 genes that were negatively immunoregulated. Thus, immunoregulation was observed primarily in mature adult hookworm intestine directly exposed to host blood; it may include hookworm genes activated in response to the host immune system in order to neutralize the host immune system. We observed 153 ES genes showing positive immunoregulation in 19-day adult intestine; of these genes, 69 had ES gene homologs in the closely related hookworm Ancylostoma caninum, 24 in the human hookworm Necator americanus, and 24 in the more distantly related strongylid parasite Haemonchus contortus. Such a mixture of rapidly evolving and conserved genes could comprise virulence factors enabling infection, provide new targets for drugs or vaccines against hookworm, and aid in developing therapies for autoimmune diseases.

Metabolic gatekeepers: Dynamic roles of sugar transporters in insect metabolism and physiology

Sugars play multiple critical roles in insects, serving as energy sources, carbon skeletons, osmolytes and signalling molecules. The transport of sugars from source to sink via membrane proteins is essential for the uptake, distribution and utilization of sugars across various tissues. Sugar supply and distribution are crucial for insect development, flight, diapause and reproduction. Insect sugar transporters (STs) share significant structural and functional similarities with those in mammals and other higher eukaryotes. However, they exhibit unique characteristics, including differential regulation, substrate selectivity and kinetics. Here, we have discussed structural diversity, evolutionary trends, expression dynamics, mechanisms of action and functional significance of insect STs. The sequence and structural diversity of insect STs, highlighted by the analysis of conserved domains and evolutionary patterns, underpins their functional differentiation and divergence. The review emphasizes the importance of STs in insect metabolism, physiology and stress tolerance. It also discusses how variations in transporter regulation, expression, selectivity and activity contribute to functional differences. Furthermore, we have underlined the potential and necessity of studying these mechanisms and roles to gain a deeper understanding of insect glycobiology. Understanding the regulation and function of sugar transporters is vital for comprehending insect metabolism and physiological potential. This review provides valuable insights into the diverse functionalities of insect STs and their significant roles in metabolism and physiology.

Transcriptome analysis of Aureobasidium pullulans BL06 and identification of key factors affecting pullulan production

Pullulan, a versatile water-soluble polysaccharide, is widely used across various industries. To minimize byproduct interference, Aureobasidium pullulans BL06ΔPMAs was engineered, resulting in a higher yield and a lower molecular weight (MW) than the parent strain A. pullulans BL06. Comparative transcriptomic analysis revealed differentially expressed genes (DEGs) involved in sucrose metabolism, gluconeogenesis, glyoxylate metabolism, and amino acid metabolism. These DEGs may influence substrate consumption, energy production, and membrane composition, ultimately impacting pullulan synthesis. Additionally, further experimental validations were conducted on the genes with the most significant differential expression. Overexpressing glycosyltransferase gene (gta1, the third most differentially expressed gene) in A. pullulans BL06 increased pullulan production by 8.1 %, indicating its role in short α-1,4-glucan synthesis. Overexpression of the transmembrane transporter gene (st1, the most significantly differentially expressed gene) reduced pullulan molecular weight by 25 %, which potentially influences cell membrane fluidity and pullulan secretion. Furthermore, amylase (Amy1) was found to significantly impact molecular weight (MW) within the first 48 h of fermentation, an effect not previously reported for amylase, while its knockout resulted in a remarkable 7.6-fold increase in pullulan MW. These findings provide valuable insights for regulating pullulan yield and MW, offering innovative genetic targets for strains engineering in future industrial applications.

Structural insights into substrate transport and drug inhibition of the human vesicular monoamine transporter 2 (VMAT2)

Vesicular monoamine transporter 2 (VMAT2) is a proton-monoamine antiporter that is widely expressed in central and peripheral neurons and plays a crucial role in loading monoamine neurotransmitters into secretory vesicles. Dysfunction of VMAT2 causes many neuropsychiatric disorders, such as depression and Parkinson's disease. Consequently, VMAT2 is a valid and important therapeutic target. Reserpine alleviates symptoms of hypertension via potent inhibition of VMAT2. Tetrabenazine selectively inhibits VMAT2 and has been used for the management of chorea, including Huntington's disease. Decades of extensive studies have defined the substrate specificity and transport kinetics of VMAT2. However, the structure and precise mechanisms of monoamine recognition and drug inhibition in VMAT2 remain unknown. Recently, we determined an ensemble of high-resolution cryo-EM structures of human VMAT2 in three distinct states bound to multiple substrates and inhibitors. These results lay a structural foundation for a comprehensive understanding of substrate recognition and transport, drug inhibition, and proton coupling in VMAT2 and shed light on future therapeutic development.

Structural insights into the mechanism of phosphate recognition and transport by XPR1

XPR1 is the sole protein known to transport inorganic phosphate (Pi) out of cells, a function conserved across species from yeast to mammals. Human XPR1 variants lead to cerebral calcium-phosphate deposition and primary familial brain calcification (PFBC), a hereditary neurodegenerative disorder. Here, we present the cryo-EM structure of human XPR1 in both its Pi-unbound and various Pi-bound states. XPR1 features 10 transmembrane α-helices forming an ion channel-like structure, with multiple Pi recognition sites along the channel. Pathogenic mutations in two arginine residues, which line the translocation channel, disrupt Pi transport. Molecular dynamics simulations reveal that Pi ion undergoes a stepwise transition through the sequential recognition sites during the transport process. Together with functional analyses, our results suggest that this sequential arrangement allows XPR1 to facilitate Pi ion passage via a "relay" process, and they establish a framework for the interpretation of disease-related mutations and for the development of future therapeutics.

A fiducial-assisted strategy compatible with resolving small MFS transporter structures in multiple conformations using cryo-EM

Advancements in cryo-EM have stimulated a revolution in structural biology. Yet, for membrane proteins near the cryo-EM size threshold of approximately 40 kDa, including transporters and G-protein coupled receptors, the absence of distinguishable structural features makes image alignment and structure determination a significant challenge. Furthermore, resolving more than one protein conformation within a sample, a major advantage of cryo-EM, represents an even greater degree of difficulty. Here, we describe a strategy for introducing a rigid fiducial marker (BRIL domain) at the C-terminus of membrane transporters from the Major Facilitator Superfamily (MFS) with AlphaFold2. This approach involves fusion of the last transmembrane domain helix of the target protein with the first helix of BRIL through a short poly-alanine linker to promote helicity. Combining this strategy with a BRIL-specific Fab, we elucidated four cryo-EM structures of the 42 kDa Staphylococcus aureus transporter NorA, three of which were derived from a single sample corresponding to inward-open, inward-occluded, and occluded conformations. Hence, this fusion construct facilitated experiments to characterize the conformational landscape of NorA and validated our design to position the BRIL/antibody pair in an orientation that avoids steric clash with the transporter. The latter was enabled through AlphaFold2 predictions, which minimized guesswork and reduced the need for screening several constructs. We further validated the suitability of the method to three additional MFS transporters (GlpT, Bmr, and Blt), results that supported a rigid linker between the transporter and BRIL. The successful application to four MFS proteins, the largest family of secondary transporters in nature, and analysis of predicted structures for the family indicates this strategy will be a valuable tool for studying other MFS members using cryo-EM.

Drug inhibition and substrate transport mechanisms of human VMAT2

Vesicular monoamine transporter 2 (VMAT2) is crucial for packaging monoamine neurotransmitters into synaptic vesicles, with their dysregulation linked to schizophrenia, mood disorders, and Parkinson's disease. Tetrabenazine (TBZ) and valbenazine (VBZ), both FDA-approved VMAT2 inhibitors, are employed to treat chorea and tardive dyskinesia (TD). Our study presents the structures of VMAT2 bound to substrates serotonin (5-HT) and dopamine (DA), as well as the inhibitors TBZ and VBZ. Utilizing cryo-electron microscopy (cryo-EM), mutagenesis functional assays, and molecular dynamics (MD) simulations, we elucidate the mechanisms of substrate transport and drug inhibition. Our MD simulations indicate potential binding poses of substrate (5-HT) in both cytosol-facing and lumen-facing states, emphasizing the significance of protonation of key acidic residues for substrate release. We demonstrate that TBZ locks VMAT2 in a lumen-facing occluded state, while VBZ stabilizes it in a lumen-facing conformation. These insights enhance our understanding of VMAT2 function and provide valuable insights for the development of novel therapeutic strategies for psychiatric disorders.

Structural Dynamics of Neutral Amino Acid Transporter SLC6A19 in Simple and Complex Lipid Bilayers

B0AT1 (SLC6A19) is a major sodium-coupled neutral amino acid transporter that relies on angiotensin converting enzyme 2 (ACE2) or collectrin for membrane trafficking. Despite its significant role in disorders associated with amino acid metabolism, there is a deficit of comprehensive structure-function understanding of B0AT1 in lipid environment. Herein, we have employed molecular dynamics (MD) simulations to explore the architectural characteristics of B0AT1 in two distinct environments: a simplified POPC bilayer and a complex lipid system replicating the native membrane composition. Notably, our B0AT1 analysis in terms of structural stability and regions of maximum flexibility shows consistency in both the systems with enhanced structural features in the case of complex lipid system. Our findings suggest that diacylglycerol phospholipids significantly alter the pore radius, hydrophobic index, and surface charge distribution of B0AT1, thereby affecting the flexibility of transmembrane helices TM7, TM12, and loop connecting TM7-TM8, crucial for ACE2-B0AT1 interaction. Pro41, Ser190, Arg214, Arg240, Ser413, Pro414, Cys463, and Val582 are among the most prominent lipid binding residues that might influence B0AT1 functionality. We also perceive notable lipid mediated deviation in the degree of tilt and loss of helicity in TM1 and TM6 which might affect the substrate binding sites S1 and S2 in B0AT1. Considerably, destabilization in the structure of B0AT1 in lipid environment was evident upon mutation in TM domain, associated with Hartnup disorder through various structure-based protein stability tools. Our two-tiered approach allowed us to validate the use of POPC as a baseline for initial analyses of SLC transporters. Altogether, our all-atoms MD study provides a platform for future investigations into the structure-function mechanism of B0AT1 in realistic lipid mimetic bilayers and offers a framework for developing new therapeutic agents targeting this transporter.

Structural and Dynamic Assessment of Disease-Causing Mutations for the Carnitine Transporter OCTN2

Primary carnitine deficiency (PCD) is a rare autosomal recessive genetic disorder caused by missense mutations in the SLC22A5 gene encoding the organic carnitine transporter novel type 2 (OCTN2). This study investigates the structural consequences of PCD-causing mutations, focusing on the N32S variant. Using an alpha-fold model, molecular dynamics simulations reveal altered interactions and dynamics suggesting potential mechanistic changes in carnitine transport. In addition, we identify mutation hotspots (R169, E452) across the SLC family with the major facilitator superfamily (MFS) fold. Our data demonstrates the applicability of structural modeling for linking genetic information and clinical observations and providing a rationale for the influence of disease-causing mutations on protein dynamics.

Brassica rapa selenium transporter NPF2.20 (BrNPF2.20) accounts for Se-enrichment in Chinese cabbage

Selenium (Se) is an essential nutrient for the human body and breeding highly Se-enriched Chinese cabbage varieties is an important means of addressing Se deficiency in individuals in certain regions. The genus Brassica has a strong ability to enrich Se; however, the primary molecular mechanism of Se enrichment remains unclear. We screened for high- and low-Se-enriched Chinese cabbage varieties from 39 different genotypes and identified a key candidate gene for Se enrichment, namely, BrNPF2.20 (BraA07g035670.3.1 C), located on the cell membrane. The expression level of BrNPF2.20 in the high-Se-enriched Chinese cabbage variety P2 was significantly higher than that in the low-Se-enriched variety P6. Heterologous expression of BrNPF2.20 increased the sensitivity of yeast to Se. The overexpression of BrNPF2.20 significantly increased the Se content in Arabidopsis plants, whereas silencing BrNPF2.20 in Chinese cabbage leaves reduced the Se content. Cell selenium mainly in the cell wall may be the physiological and biochemical mechanism of the high-Se-enriched vareity in response to selenium stress. BrNPF2.20 promoted the transport and accumulation of Se from root to shoot in Chinese cabbage maybe by increasing GSH-Px activity or regulating sulfate transporter family genes related to Se absorption and transport. This study not only deepens our understanding of Se transport from Chinese cabbage root to the ground part, but also provides a new idea for breeding Se-rich Chinese cabbage varieties by promoting SeMet transport.

Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in California

Non-typhoidal Salmonella enterica is a leading cause of gastrointestinal illnesses in the United States. Among the 2,600 different S. enterica serovars, Infantis has been significantly linked to human illnesses and is frequently recovered from broilers and chicken parts in the U.S. A key virulence determinant in serovar Infantis is the presence of the megaplasmid pESI, conferring multidrug resistance. To further characterize the virulence potential of this serovar, the present study identified the types of plasmids harbored by Infantis strains, recovered from surface waters adjacent to leafy greens farms in California. Sequencing analysis showed that each of the examined 12 Infantis strains had a large plasmid ranging in size from 78 kb to 125 kb. In addition, a second 4-kb plasmid was detected in two strains. Plasmid nucleotide queries did not identify the emerging megaplasmid pESI in the examined Infantis strains; however, the detected plasmids each had similarity to a plasmid sequence already cataloged in the nucleotide databases. Subsequent comparative analyses, based on gene presence or absence, divided the detected plasmids into five distinct clusters, and the phylogram revealed these Infantis plasmids were clustered based either on the plasmid conjugation system, IncI and IncF, or on the presence of plasmid phage genes. Assignment of the putative genes to functional categories revealed that the large plasmids contained genes implicated in cell cycle control and division, replication and recombination and defense mechanisms. Further analysis of the mobilome, including prophages and transposons, demonstrated the presence of genes implicated in the release of the bactericidal peptide microcin in the IncF plasmids and identified a Tn10 transposon conferring tetracycline resistance in one of the IncI1 plasmids. These findings indicated that the plasmids in the environmental S. enterica serovar Infantis strains from surface waters harbored a wide variety of genes associated with adaptation, survivability and antimicrobial resistance.

Substrate transport and drug interaction of human thiamine transporters SLC19A2/A3

Thiamine and pyridoxine are essential B vitamins that serve as enzymatic cofactors in energy metabolism, protein and nucleic acid biosynthesis, and neurotransmitter production. In humans, thiamine transporters SLC19A2 and SLC19A3 primarily regulate cellular uptake of both vitamins. Genetic mutations in these transporters, which cause thiamine and pyridoxine deficiency, have been implicated in severe neurometabolic diseases. Additionally, various prescribed medicines, including metformin and fedratinib, manipulate thiamine transporters, complicating the therapeutic effect. Despite their physiological and pharmacological significance, the molecular underpinnings of substrate and drug recognition remain unknown. Here we present ten cryo-EM structures of human thiamine transporters SLC19A3 and SLC19A2 in outward- and inward-facing conformations, complexed with thiamine, pyridoxine, metformin, fedratinib, and amprolium. These structural insights, combined with functional characterizations, illuminate the translocation mechanism of diverse chemical entities, and enhance our understanding of drug-nutrient interactions mediated by thiamine transporters.

Design of an equilibrative nucleoside transporter subtype 1 inhibitor for pain relief

The current opioid crisis urgently calls for developing non-addictive pain medications. Progress has been slow, highlighting the need to uncover targets with unique mechanisms of action. Extracellular adenosine alleviates pain by activating the adenosine A1 receptor (A1R). However, efforts to develop A1R agonists have faced obstacles. The equilibrative nucleoside transporter subtype 1 (ENT1) plays a crucial role in regulating adenosine levels across cell membranes. We postulate that ENT1 inhibition may enhance extracellular adenosine levels, potentiating endogenous adenosine action at A1R and leading to analgesic effects. Here, we modify the ENT1 inhibitor dilazep based on its complex X-ray structure and show that this modified inhibitor reduces neuropathic and inflammatory pain in animal models while dilazep does not. Notably, our ENT1 inhibitor surpasses gabapentin in analgesic efficacy in a neuropathic pain model. Additionally, our inhibitor exhibits less cardiac side effect than dilazep via systemic administration and shows no side effects via local/intrathecal administration. ENT1 is colocalized with A1R in mouse and human dorsal root ganglia, and the analgesic effect of our inhibitor is linked to A1R. Our studies reveal ENT1 as a therapeutic target for analgesia, highlighting the promise of rationally designed ENT1 inhibitors for non-opioid pain medications.

Coelimycin inside out - negative feedback regulation by its intracellular precursors

Coelimycin (CPK) producer Streptomyces coelicolor A3(2) is a well-established model for the genetic studies of bacteria from the genus Streptomyces, renowned for their ability to produce a plethora of antibiotics and other secondary metabolites. Expression regulation of natural product biosynthetic gene clusters (BGCs) is highly complex, involving not only regulatory proteins, like transcription factors, but also the products of the biosynthetic pathway that may act as ligands for some regulators and modulate their activity. Here, we present the evidence that intracellular CPK precursor(s) (preCPK) is involved in a negative feedback loop repressing the CPK BGC. Moreover, we provide a characterization of the cluster-encoded efflux pump CpkF. We show that CpkF is essential for the extracellular CPK production. In order to track down which CPK compounds - intra- or extracellular - are the ones responsible for the feedback signal, a luciferase-based reporter system was applied to compare the activity of 13 CPK gene promoters in the wild-type (WT) and two mutated strains. The first strain, lacking the CPK-specific exporter CpkF (ΔcpkF), was unable to produce the extracellular CPK. The second one did not produce any CPK at all, due to the disruption of the CpkC polyketide synthase subunit (ΔcpkC). All tested promoters were strongly upregulated in ΔcpkC strain, while in the ΔcpkF strain, promoter activity resembled the one of WT. These results lead to the conclusion that the CPK polyketide acts as a silencer of its own production. Supposedly this function is exerted via binding of the preCPK by an unidentified regulatory protein. KEY POINTS: •Intracellular coelimycin precursor takes part in a negative cpk cluster regulation •CpkF exporter is essential for the extracellular coelimycin production •Simple method for the analysis of coelimycin P2 production in agar medium.