ABC transporters: the power to change. Nat Rev Mol Cell Biol. 2009;10:218-227. [PMID: 19234479 DOI: 10.1038/nrm2646]

Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942

Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.

The ATP-bound inward-open conformation of ABCC4 reveals asymmetric ATP binding for substrate transport

The multidrug resistance-associated protein (MRP) ABCC4 facilitates substrate transport across the cytoplasmic membrane, crucial for normal physiology and mediating multidrug resistance in tumor cells. Despite intensive studies on MRPs, ABCC4's transport mechanism remains incompletely understood. In this study, we unveiled an inward-open conformation with an ATP bound to degenerate NBD1. Additionally, we captured the structure with both ATP and substrate co-bound in the inward-open state. Our findings uncover the asymmetric ATP binding in ABCC4 and provide insights into substrate binding and transport mechanisms. ATP binding to NBD1 is parallel to substrate binding to ABCC4, and is a prerequisite for ATP-bound NBD2-induced global conformational changes. Our findings shed new light on targeting ABCC4 in combination with anticancer therapy.

Environmental and genetic regulation of Streptococcus pneumoniae galactose catabolic pathways

Efficient utilization of nutrients is crucial for microbial survival and virulence. The same nutrient may be utilized by multiple catabolic pathways, indicating that the physical and chemical environments for induction as well as their functional roles may differ. Here, we study the tagatose and Leloir pathways for galactose catabolism of the human pathogen Streptococcus pneumoniae. We show that galactose utilization potentiates pneumococcal virulence, the induction of galactose catabolic pathways is influenced differentially by the concentration of galactose and temperature, and sialic acid downregulates galactose catabolism. Furthermore, the genetic regulation and in vivo induction of each pathway differ, and both galactose catabolic pathways can be turned off with a galactose analogue in a substrate-specific manner, indicating that galactose catabolic pathways can be potential drug targets.

Modulation of the lytic apparatus by the FtsEX complex within the bacterial division machinery

The FtsEX membrane complex constitutes an essential component of the ABC transporter superfamily, widely distributed among bacterial species. It governs peptidoglycan degradation for cell division, acting as a signal transmitter rather than a substrate transporter. Through the ATPase activity of FtsE, it facilitates signal transmission from the cytosol across the membrane to the periplasm, activating associated peptidoglycan hydrolases. This review concentrates on the latest structural advancements elucidating the architecture of the FtsEX complex and its interplay with lytic enzymes or regulatory counterparts. The revealed three-dimensional structures unveil a landscape wherein a precise array of intermolecular interactions, preserved across diverse bacterial species, afford meticulous spatial and temporal control over the cell division process.

Artificial Phages with Biocatalytic Spikes for Synergistically Eradicating Antibiotic-Resistant Biofilms

Antibiotic-resistant pathogens have become a global public health crisis, especially biofilm-induced refractory infections. Efficient, safe, and biofilm microenvironment (BME)-adaptive therapeutic strategies are urgently demanded to combat antibiotic-resistant biofilms. Here, inspired by the fascinating biological structures and functions of phages, the de novo design of a spiky Ir@Co3O4 particle is proposed to serve as an artificial phage for synergistically eradicating antibiotic-resistant Staphylococcus aureus biofilms. Benefiting from the abundant nanospikes and highly active Ir sites, the synthesized artificial phage can simultaneously achieve efficient biofilm accumulation, extracellular polymeric substance (EPS) penetration, and superior BME-adaptive reactive oxygen species (ROS) generation, thus facilitating the in situ ROS delivery and enhancing the biofilm eradication. Moreover, metabolomics found that the artificial phage obstructs the bacterial attachment to EPS, disrupts the maintenance of the BME, and fosters the dispersion and eradication of biofilms by down-regulating the associated genes for the biosynthesis and preservation of both intra- and extracellular environments. The in vivo results demonstrate that the artificial phage can treat the biofilm-induced recalcitrant infected wounds equivalent to vancomycin. It is suggested that the design of this spiky artificial phage with synergistic "penetrate and eradicate" capability to treat antibiotic-resistant biofilms offers a new pathway for bionic and nonantibiotic disinfection.

The cluster model of energy transduction in biological systems

The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.

Anticyanobacterial effect of p-coumaric acid on Limnothrix sp. determined by proteomic and metabolomic analysis

Regulating photosynthetic machinery is a powerful but challenging strategy for selectively inhibiting bloom-forming cyanobacteria, in which photosynthesis mainly occurs in thylakoids. P-coumaric acid (p-CA) has several biological properties, including free radical scavenging and antibacterial effects, and studies have shown that it can damage bacterial cell membranes, reduce chlorophyll a in cyanobacteria, and effectively inhibit algal growth at concentrations exceeding 0.127 g/L. Allelochemicals typically inhibit cyanobacteria by inhibiting photosynthesis; however, research on inhibiting harmful algae using phenolic acids has focused mainly on their inhibitory and toxic effects and metabolite levels, and the molecular mechanism by which p-CA inhibits photosynthesis remains unclear. Thus, we examined the effect of p-CA on the photosynthesis of Limnothrix sp. in detail. We found that p-CA inhibits algal growth and damages photosynthesis-related proteins in Limnothrix sp., reduces carotenoid and allophycocyanin levels, and diminishes the actual quantum yield of Photosystem II (PSII). Moreover, p-CA significantly altered algal cell membrane protein systems, and PSII loss resulting from p-CA exposure promoted reactive oxygen species production. It significantly altered algae cell membrane protein systems. Finally, p-CA was found to be environmentally nontoxic; 80 % of 48-h-old Daphnia magna larvae survived when exposed to 0.15 g/L p-CA. These findings provide insight into the mechanism of cyanobacterial inhibition by p-CA, providing a more practical approach to controlling harmful algal blooms.

Metabolomics reveals metabolites associated with hair follicle cycle in cashmere goats

BACKGROUND

The hair follicle is a skin accessory organ that regulates hair development, and its activity varies on a regular basis. However, the significance of metabolites in the hair follicle cycle has long been unknown.

RESULTS

Targeted metabolomics was used in this investigation to reveal the expression patterns of 1903 metabolites in cashmere goat skin during anagen to telogen. A statistical analysis was used to investigate the potential associations between metabolites and the hair follicle cycle. The findings revealed clear changes in the expression patterns of metabolites at various phases and in various feeding models. The majority of metabolites (primarily amino acids, nucleotides, their metabolites, and lipids) showed downregulated expression from anagen (An) to telogen (Tn), which was associated with gene expression, protein synthesis and transport, and cell structure, which reflected, to some extent, that the cells associated with hair follicle development are active in An and apoptotic in An-Tn. It is worth mentioning that the expression of vitamin D3 and 3,3',5-triiodo-L-thyronine decreased and then increased, which may be related to the shorter and longer duration of outdoor light, which may stimulate the hair follicle to transition from An to catagen (Cn). In the comparison of different hair follicle development stages (An, Cn, and Tn) or feeding modes (grazing and barn feeding), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that common differentially expressed metabolites (DEMs) (2'-deoxyadenosine, L-valine, 2'-deoxyuridine, riboflavin, cytidine, deoxyguanosine, L-tryptophan, and guanosine-5'-monophosphate) were enriched in ABC transporters. This finding suggested that this pathway may be involved in the hair follicle cycle. Among these DEMs, riboflavin is absorbed from food, and the expression of riboflavin and sugars (D-glucose and glycogen) in skin tissue under grazing was greater and lower than that during barn feeding, respectively, suggesting that eating patterns may also alter the hair follicle cycle.

CONCLUSIONS

The expression patterns of metabolites such as sugars, lipids, amino acids, and nucleotides in skin tissue affect hair follicle growth, in which 2'-deoxyadenosine, L-valine, 2'-deoxyuridine, riboflavin, cytidine, deoxyguanosine, L-tryptophan, and guanosine-5'-monophosphate may regulate the hair follicle cycle by participating in ABC transporters. Feeding practices may regulate hair follicle cycles by influencing the amount of hormones and vitamins expressed in the skin of cashmere goats.

Wildfire Ashes from the Wildland-Urban Interface Alter Vibrio vulnificus Growth and Gene Expression

Climate change-induced stressors are contributing to the emergence of infectious diseases, including those caused by marine bacterial pathogens such as Vibrio spp. These stressors alter Vibrio temporal and geographical distribution, resulting in increased spread, exposure, and infection rates, thus facilitating greater Vibrio-human interactions. Concurrently, wildfires are increasing in size, severity, frequency, and spread in the built environment due to climate change, resulting in the emission of contaminants of emerging concern. This study aimed to understand the potential effects of urban interface wildfire ashes on Vibrio vulnificus (V. vulnificus) growth and gene expression using transcriptomic approaches. V. vulnificus was exposed to structural and vegetation ashes and analyzed to identify differentially expressed genes using the HTSeq-DESeq2 strategy. Exposure to wildfire ash altered V. vulnificus growth and gene expression, depending on the trace metal composition of the ash. The high Fe content of the vegetation ash enhanced bacterial growth, while the high Cu, As, and Cr content of the structural ash suppressed growth. Additionally, the overall pattern of upregulated genes and pathways suggests increased virulence potential due to the selection of metal- and antibiotic-resistant strains. Therefore, mixed fire ashes transported and deposited into coastal zones may lead to the selection of environmental reservoirs of Vibrio strains with enhanced antibiotic resistance profiles, increasing public health risk.

The central retinal thickness and its related genotype in ABCA4-related retinopathy

PURPOSE

To further explore the influence of genotype, including mutation type and structural domain, on the severity of macular atrophy, we measured the central retinal thickness (CRT) in patients with ABCA4-related retinopathy.

METHODS

A total of 66 patients were included in the cohort. This was a retrospective investigation. The patients were tested using whole exon sequencing and ophthalmic exams, including slip lamp exams, best-corrected visual acuity, optical coherence tomography, fundus photo, and fundus autofluorescence.

RESULTS

In this study, we discovered that mutations on nucleotide binding domains (NBD) lead to less CRT (45.00 ± 25.25μm, 95% CI: 31.54-58.46) had significantly less CRT than the others (89.75 ± 71.17μm, 95% CI: 30.25-149.25, p = 0.032), and could accelerate the rate of CRT decrease.

CONCLUSIONS

Our study provides new perspectives in the understanding of ABCA4-related retinopathy.

Hopping the Hurdle: Strategies to Enhance the Molecular Delivery to the Brain through the Blood-Brain Barrier

Modern medicine has allowed for many advances in neurological and neurodegenerative disease (ND). However, the number of patients suffering from brain diseases is ever increasing and the treatment of brain diseases remains an issue, as drug efficacy is dramatically reduced due to the existence of the unique vascular structure, namely the blood-brain barrier (BBB). Several approaches to enhance drug delivery to the brain have been investigated but many have proven to be unsuccessful due to limited transport or damage induced in the BBB. Alternative approaches to enhance molecular delivery to the brain have been revealed in recent studies through the existence of molecular delivery pathways that regulate the passage of peripheral molecules. In this review, we present recent advancements of the basic research for these delivery pathways as well as examples of promising ventures to overcome the molecular hurdles that will enhance therapeutic interventions in the brain and potentially save the lives of millions of patients.

Resistance role of Lactobacillus sp. and Lactococcus sp. to copper ions in healthy children's intestinal microorganisms

Heavy metal exposure is closely associated with gut microbe function and tolerance. However, intestinal microbe responses in children to different copper ion (Cu2+) concentrations have not yet been clarified. Here, in vitro cultivation systems were established for fecal microbe control and Cu2+-treated groups in healthy children. 16S rDNA high-throughput sequencing, meta-transcriptomics and metabolomics were used here to identify toxicity resistance mechanisms at microbiome levels. The results showed that Lactobacillus sp. and Lactococcus sp. exerted protective effects against Cu2+ toxicity, but these effects were limited by Cu2+ concentration. When the Cu2+ concentration was ≥ 4 mg/L, the abundance of Lactobacillus sp. and Lactococcus sp. significantly decreased, and the pathways of antioxidant activity and detoxification processes were enriched at 2 mg/L Cu2+, and beneficial metabolites accumulated. However, at high concentrations of Cu2+ (≥4 mg/L), the abundance of potential pathogen increased, and was accompanied by a downregulation of genes in metabolism and detoxification pathways, which meant that the balance of gut microbiota was disrupted and toxicity resistance decreased. From these observations, we identified some probiotics that are tolerant to heavy metal Cu2+, and warn that only when the concentration limit of Cu2+ in food is 2 mg/L, then a balanced gut microbiota can be guaranteed in children, thereby providing protection for their health.

Mechanistic insight into the impact of polystyrene microparticle on submerged plant during asexual propagules germination to seedling: Internalization in functional organs and alterations of physiological phenotypes

Asexual reproduction is one of the most important propagations in aquatic plants. However, there is a lack of information about the growth-limiting mechanisms induced by microplastics on the submerged plant during asexual propagule germination to seedling. Hence, we investigated the effects of two sizes (2 µm, 0.2 µm) and three concentrations (0.5 mg/L, 5 mg/L, and 50 mg/L) of polystyrene microplastics (PSMPs) on Potamogeton crispus turion germination and seedling growth. Both PSMPs sizes were found in P. crispus seedling tissues. Metabolic profile alterations were observed in leaves, particularly affecting secondary metabolic pathways and ATP-binding cassette transporters. Metal elements are indispensable cofactors for photosynthesis; however, alterations in the metabolic profile led to varying degrees of reduced concentrations in magnesium, iron, copper, and zinc within P. crispus. Therefore, the maximum quantum yield of photosystem II significantly decreased in all concentrations with 0.2 µm-PSMPs, and at 50 mg/L with 2 µm-PSMPs. These findings reveal that internalization of microplastics, nutrient absorption inhibition, and metabolic changes contribute to the negative impact on P. crispus seedlings.

Deciphering the functional role of clinical mutations in ABCB1, ABCC1, and ABCG2 ABC transporters in endometrial cancer

ATP-binding cassette transporters represent a superfamily of dynamic membrane-based proteins with diverse yet common functions such as use of ATP hydrolysis to efflux substrates across cellular membranes. Three major transporters-P-glycoprotein (P-gp or ABCB1), multidrug resistance protein 1 (MRP1 or ABCC1), and breast cancer resistance protein (BCRP or ABCG2) are notoriously involved in therapy resistance in cancer patients. Despite exhaustive individual characterizations of each of these transporters, there is a lack of understanding in terms of the functional role of mutations in substrate binding and efflux, leading to drug resistance. We analyzed clinical variations reported in endometrial cancers for these transporters. For ABCB1, the majority of key mutations were present in the membrane-facing region, followed by the drug transport channel and ATP-binding regions. Similarly, for ABCG2, the majority of key mutations were located in the membrane-facing region, followed by the ATP-binding region and drug transport channel, thus highlighting the importance of membrane-mediated drug recruitment and efflux in ABCB1 and ABCG2. On the other hand, for ABCC1, the majority of key mutations were present in the inactive nucleotide-binding domain, followed by the drug transport channel and membrane-facing regions, highlighting the importance of the inactive nucleotide-binding domain in facilitating indirect drug efflux in ABCC1. The identified key mutations in endometrial cancer and mapped common mutations present across different types of cancers in ABCB1, ABCC1, and ABCG2 will facilitate the design and discovery of inhibitors targeting unexplored structural regions of these transporters and re-engineering of these transporters to tackle chemoresistance.

Molecular and computational characterization of ABCB11 and ABCG5 variants in Tunisian patients with neonatal/infantile low-GGT intrahepatic cholestasis: Genetic diagnosis and genotype-phenotype correlation assessment

Many inherited conditions cause hepatocellular cholestasis in infancy, including progressive familial intrahepatic cholestasis (PFIC), a heterogeneous group of diseases with highly overlapping symptoms. In our study, six unrelated Tunisian infants with PFIC suspicion were the subject of a panel-target sequencing followed by an exhaustive bioinformatic and modeling investigations. Results revealed five disease-causative variants including known ones: (the p.Asp482Gly and p.Tyr354 * in the ABCB11 gene and the p.Arg446 * in the ABCC2 gene), a novel p.Ala98Cys variant in the ATP-binding cassette subfamily G member 5 (ABCG5) gene and a first homozygous description of the p.Gln312His in the ABCB11 gene. The p.Gln312His disrupts the interaction pattern of the bile salt export pump as well as the flexibility of the second intracellular loop domain harboring this residue. As for the p.Ala98Cys, it modulates both the interactions within the first nucleotide-binding domain of the bile transporter and its accessibility. Two additional potentially modifier variants in cholestasis-associated genes were retained based on their pathogenicity (p.Gly758Val in the ABCC2 gene) and functionality (p.Asp19His in the ABCG8 gene). Molecular findings allowed a PFIC2 diagnosis in five patients and an unexpected diagnosis of sisterolemia in one case. The absence of genotype/phenotype correlation suggests the implication of environmental and epigenetic factors as well as modifier variants involved directly or indirectly in the bile composition, which could explain the cholestasis phenotypic variability.

The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry

The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.

Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

Burkholderia pseudomallei Complex Subunit and Glycoconjugate Vaccines and Their Potential to Elicit Cross-Protection to Burkholderia cepacia Complex

Burkholderia are a group of Gram-negative bacteria that can cause a variety of diseases in at-risk populations. B. pseudomallei and B. mallei, the etiological agents of melioidosis and glanders, respectively, are the two clinically relevant members of the B. pseudomallei complex (Bpc). The development of vaccines against Bpc species has been accelerated in recent years, resulting in numerous promising subunits and glycoconjugate vaccines incorporating a variety of antigens. However, a second group of pathogenic Burkholderia species exists known as the Burkholderia cepacia complex (Bcc), a group of opportunistic bacteria which tend to affect individuals with weakened immunity or cystic fibrosis. To date, there have been few attempts to develop vaccines to Bcc species. Therefore, the primary goal of this review is to provide a broad overview of the various subunit antigens that have been tested in Bpc species, their protective efficacy, study limitations, and known or suspected mechanisms of protection. Then, we assess the reviewed Bpc antigens for their amino acid sequence conservation to homologous proteins found in Bcc species. We propose that protective Bpc antigens with a high degree of Bpc-to-Bcc sequence conservation could serve as components of a pan-Burkholderia vaccine capable of protecting against both disease-causing groups.

Abcb10 regulates murine hematopoietic stem cell potential and erythroid differentiation

Erythropoiesis in the adult bone marrow relies on mitochondrial membrane transporters to facilitate heme and hemoglobin production. Erythrocytes in the bone marrow are produced although the differentiation of erythroid progenitor cells that originate from hematopoietic stem cells (HSCs). Whether and how mitochondria transporters potentiate HSCs and affect their differentiation toward erythroid lineage remains unclear. Here, we show that the ATP-binding cassette (ABC) transporter 10 (Abcb10), located on the inner mitochondrial membrane, is essential for HSC maintenance and erythroid-lineage differentiation. Induced deletion of Abcb10 in adult mice significantly increased erythroid progenitor cell and decreased HSC number within the bone marrow (BM). Functionally, Abcb10-deficient HSCs exhibited significant decreases in stem cell potential but with a skew toward erythroid-lineage differentiation. Mechanistically, deletion of Abcb10 rendered HSCs with excess mitochondrial iron accumulation and oxidative stress yet without alteration in mitochondrial bioenergetic function. However, impaired hematopoiesis could not be rescued through the in vivo administration of a mitochondrial iron chelator or antioxidant to Abcb10-deficient mice. Abcb10-mediated mitochondrial iron transfer is thus pivotal for the regulation of physiologic HSC potential and erythroid-lineage differentiation.

Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration

Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates-thus reducing false positives as well as computation time.

Genetic Signatures for Distinguishing Chemo-Sensitive from Chemo-Resistant Responders in Prostate Cancer Patients

Prostate cancer remains a significant public health concern in sub-Saharan Africa, particularly impacting South Africa with high mortality rates. Despite many years of extensive research and significant financial expenditure, there has yet to be a definitive solution to prostate cancer. It is not just individuals who vary in their response to treatment, but even different nodules within the same tumor exhibit unique transcriptome patterns. These distinctions extend beyond mere differences in gene expression levels to encompass the control and networking of individual genes. Escalating chemotherapy resistance in prostate cancer patients has prompted increased research into its underlying mechanisms. The heterogeneous nature of transcriptomic organization among men makes the pursuit of universal biomarkers and one-size-fits-all treatments impractical. This study delves into the expression of drug resistance-associated genes, ABCB1 and CYP1B1, in cancer cells. Employing bioinformatics, we explored the molecular pathways and cascades linked to drug resistance following upregulation of these genes. Samples were obtained from archived prostate cancer patient specimens through pre-treatment biopsies of two categories: good vs. poor responders, with cDNAs synthesized from isolated RNAs subjected to qPCR analysis. The results revealed increased ABCB1 and CYP1B1 expression in tumor samples of the poor responders. Gene enrichment and network analysis associated ABCB1 with ABC transporters and LncRNA-mediated therapeutic resistance (WP3672), while CYP1B1 was linked to ovarian steroidogenesis, tryptophan metabolism, steroid hormone biosynthesis, benzo(a)pyrene metabolism, the sulindac metabolic pathway, and the estrogen receptor pathway, which are associated with drug resistance. Both ABCB1 and CYP1B1 correlated with microRNAs in cancer and the Nuclear Receptors Meta-Pathway. STRING analysis predicted protein-protein interactions of ABCB1 and CYP1B1 with Glutathione S-transferase Pi, Catechol O-methyltransferase, UDP-glucuronosyltransferase 1-6, Leucine-rich Transmembrane and O-methyltransferase (LRTOMT), and Epoxide hydrolase 1, with scores of 0.973, 0.971, 0.966, 0.966, and 0.966, respectively. Furthermore, molecular docking analysis of the chemotherapy drug, docetaxel, with CYP1B1 and ABCB1 revealed robust molecular interactions, with binding energies of -20.37 and -15.25 Kcal/mol, respectively. These findings underscore the susceptibility of cancer patients to drug resistance due to increased ABCB1 and CYP1B1 expression in tumor samples from patients in the poor-responders category that affects associated molecular pathways. The potent molecular interactions of ABCB1 and CYP1B1 with docetaxel further emphasize the potential basis for chemotherapy resistance.

Structures, Mechanisms, and Physiological Functions of Zinc Transporters in Different Biological Kingdoms

Zinc transporters take up/release zinc ions (Zn2+) across biological membranes and maintain intracellular and intra-organellar Zn2+ homeostasis. Since this process requires a series of conformational changes in the transporters, detailed information about the structures of different reaction intermediates is required for a comprehensive understanding of their Zn2+ transport mechanisms. Recently, various Zn2+ transport systems have been identified in bacteria, yeasts, plants, and humans. Based on structural analyses of human ZnT7, human ZnT8, and bacterial YiiP, we propose updated models explaining their mechanisms of action to ensure efficient Zn2+ transport. We place particular focus on the mechanistic roles of the histidine-rich loop shared by several zinc transporters, which facilitates Zn2+ recruitment to the transmembrane Zn2+-binding site. This review provides an extensive overview of the structures, mechanisms, and physiological functions of zinc transporters in different biological kingdoms.

Metabolomics reveals the phytotoxicity mechanisms of foliar spinach exposed to bulk and nano sizes of PbCO3

PbCO3 is an ancient raw material for Pb minerals and continues to pose potential risks to the environment and human health through mining and industrial processes. However, the specific effects of unintentional PbCO3 discharge on edible plants remain poorly understood. This study unravels how foliar application of PbCO3 induces phytotoxicity by potentially influencing leaf morphology, photosynthetic pigments, oxidative stress, and metabolic pathways related to energy regulation, cell damage, and antioxidant defense in Spinacia oleracea L. Additionally, it quantifies the resultant human health risks. Plants were foliarly exposed to PbCO3 nanoparticles (NPs) and bulk products (BPs), as well as Pb2+ at 0, 5, 10, 25, 50, and 100 mg·L-1 concentrations once a day for three weeks. The presence and localization of PbCO3 NPs inside the plant cells were confirmed by TEM-EDS analysis. The maximum accumulation of total Pb was recorded in the root (2947.77 mg·kg-1 DW for ion exposure), followed by the shoot (942.50 mg·kg-1 DW for NPs exposure). The results revealed that PbCO3 and Pb2+ exposure had size- and dose-dependent inhibitory effects on spinach length, biomass, and photosynthesis attributes, inducing impacts on the antioxidase activity of CAT, membrane permeability, and nutrient elements absorption and translocation. Pb2+ exhibited pronounced toxicity in morphology and chlorophyll; PbCO3 BP exposure accumulated the most lipid peroxidation products of MDA and H2O2; and PbCO3 NPs triggered the largest cell membrane damage. Furthermore, PbCO3 NPs at 10 and 100 mg·L-1 induced dose-dependent metabolic reprogramming in spinach leaves, disturbing the metabolic mechanisms related to amino acids, antioxidant defense, oxidative phosphorylation, fatty acid cycle, and the respiratory chain. The spinach showed a non-carcinogenic health risk hierarchy: Pb2+ > PbCO3 NPs > PbCO3 BPs, with children more vulnerable than adults. These findings enhance our understanding of PbCO3 particle effects on food security, emphasizing the need for further research to minimize their impact on human dietary health.

Maternal exposure to polystyrene nanoplastics causes defective retinal development and function in progeny mice by disturbing metabolic profiles

Microplastics (MPs) and nanoplastics (NPs) are widely spreading in our living environment, accumulating in the human body and potentially threating human health. The retina, which is a terminally differentiated extension of the central nervous system, is essential for the visual system. However, the effects and molecular mechanisms of MPs/NPs on retina development and function are still unclear. Here, we investigated the effects and modes of action of polystyrene NPs (PS-NPs) on the retina using mice as a mammalian model species. Maternal PS-NP exposure (100 nm) at an environmentally realistic concentration of 10 mg L-1 (or 2.07 *1010 particles mL-1) via drinking water from the first day of pregnancy till the end of lactation (21 days after birth) caused defective neural retinal development in the neonatal mice, by depositing in the retinal tissue and reducing the number of retinal ganglion cells and bipolar cells. Exposure to PS-NPs retarded retinal vascular development, while abnormal electroretinogram (ERG) responses and an increased level of oxidative stress were also observed in the retina of the progeny mice after maternal PS-NP exposure. Metabolomics showed significant dysregulation of amino acids that are pivotal to neuron retinal function, such as glutamate, aspartate, alanine, glycine, serine, threonine, taurine, and serotonin. Transcriptomics identified significantly dysregulated genes, which were enriched in processes of angiogenesis, visual system development and lens development. Regulatory analysis showed that Fos gene mediated pathways could be a potential key target for PS-NP exposure in retinal development and function. Our study revealed that maternal exposure to PS-NPs generated detrimental effects on retinal development and function in progeny mice, offering new insights into the visual toxicity of PS-NPs.

An integrated meta-omics approach reveals the different response mechanisms of two anammox bacteria towards fluoroquinolone antibiotics

The emerging fluoroquinolone antibiotics (FQs) are highly influential in nitrogen removal from livestock wastewater. However, beyond the capability of nitrogen removal, little is known about the molecular mechanisms (e.g., shift of core metabolism and energy allocation) of different anaerobic ammonium-oxidizing bacteria (AnAOB) under continuous FQ stress. This study investigated the effects of ciprofloxacin, ofloxacin and their mixture at concentrations detected in livestock wastewater on two key anammox species in membrane bioreactors. It was found 20 μg/L FQs promoted nitrogen removal efficiency and community stability, and42-51 % of FQs were removed simultaneously. Integrated meta-omics analysis revealed varied gene expression patterns between the two dominant AnAOB, Candidatus Brocadia sapporoensis (B AnAOB) and Candidatus Kuenenia stuttgartiensis (K AnAOB). The nitrogen metabolic processes were bolstered in B AnAOB, while those involved in anammox pathway of K AnAOB were inhibited. This difference was tentatively attributed to the up-regulation of reactive oxygen species scavenger genes (ccp and dxf) and FQ resistance gene (qnrB72) in B AnAOB. Importantly, most enhanced core biosynthesis/metabolism of AnAOB and close cross-feeding with accompanying bacteria were also likely to contribute to their higher levels of biomass yield and metabolism activity under FQ stress. This finding suggests that B AnAOB has the advantage of higher nitrogen metabolism capacity over K AnAOB in livestock wastewater containing FQs, which is helpful for efficient and stable nitrogen removal by the functional anammox species.

Structural View of Cryo-Electron Microscopy-Determined ATP-Binding Cassette Transporters in Human Multidrug Resistance

ATP-binding cassette (ABC) transporters, acting as cellular "pumps," facilitate solute translocation through membranes via ATP hydrolysis. Their overexpression is closely tied to multidrug resistance (MDR), a major obstacle in chemotherapy and neurological disorder treatment, hampering drug accumulation and delivery. Extensive research has delved into the intricate interplay between ABC transporter structure, function, and potential inhibition for MDR reversal. Cryo-electron microscopy has been instrumental in unveiling structural details of various MDR-causing ABC transporters, encompassing ABCB1, ABCC1, and ABCG2, as well as the recently revealed ABCC3 and ABCC4 structures. The newly obtained structural insight has deepened our understanding of substrate and drug binding, translocation mechanisms, and inhibitor interactions. Given the growing body of structural information available for human MDR transporters and their associated mechanisms, we believe it is timely to compile a comprehensive review of these transporters and compare their functional mechanisms in the context of multidrug resistance. Therefore, this review primarily focuses on the structural aspects of clinically significant human ABC transporters linked to MDR, with the aim of providing valuable insights to enhance the effectiveness of MDR reversal strategies in clinical therapies.

Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri)

BACKGROUND

ATP-binding cassette (ABC) transporter proteins constitute a plant gene superfamily crucial for growth, development, and responses to environmental stresses. Despite their identification in various plants like maize, rice, and Arabidopsis, little is known about the information on ABC transporters in pear. To investigate the functions of ABC transporters in pear development and abiotic stress response, we conducted an extensive analysis of ABC gene family in the pear genome.

RESULTS

In this study, 177 ABC transporter genes were successfully identified in the pear genome, classified into seven subfamilies: 8 ABCAs, 40 ABCBs, 24 ABCCs, 8 ABCDs, 9 ABCEs, 8 ABCFs, and 80 ABCGs. Ten motifs were common among all ABC transporter proteins, while distinct motif structures were observed for each subfamily. Distribution analysis revealed 85 PbrABC transporter genes across 17 chromosomes, driven primarily by WGD and dispersed duplication. Cis-regulatory element analysis of PbrABC promoters indicated associations with phytohormones and stress responses. Tissue-specific expression profiles demonstrated varied expression levels across tissues, suggesting diverse functions in development. Furthermore, several PbrABC genes responded to abiotic stresses, with 82 genes sensitive to salt stress, including 40 upregulated and 23 downregulated genes. Additionally, 91 genes were responsive to drought stress, with 22 upregulated and 36 downregulated genes. These findings highlight the pivotal role of PbrABC genes in abiotic stress responses.

CONCLUSION

This study provides evolutionary insights into PbrABC transporter genes, establishing a foundation for future research on their functions in pear. The identified motifs, distribution patterns, and stress-responsive expressions contribute to understanding the regulatory mechanisms of ABC transporters in pear. The observed tissue-specific expression profiles suggest diverse roles in developmental processes. Notably, the significant responses to salt and drought stress emphasize the importance of PbrABC genes in mediating adaptive responses. Overall, our study advances the understanding of PbrABC transporter genes in pear, opening avenues for further investigations in plant molecular biology and stress physiology.

Blood-brain barrier transporters: An overview of function, dysfunction in Alzheimer's disease and strategies for treatment

The blood-brain-barrier (BBB) has a major function in maintaining brain homeostasis by regulating the entry of molecules from the blood to the brain. Key players in BBB function are BBB transporters which are highly expressed in brain endothelial cells (BECs) and critical in mediating the exchange of nutrients and waste products. BBB transporters can also influence drug delivery into the brain by inhibiting or facilitating the entry of brain targeting therapeutics for the treatment of brain disorders, such as Alzheimer's disease (AD). Recent studies have shown that AD is associated with a disrupted BBB and transporter dysfunction, although their roles in the development in AD are not fully understand. Modulation of BBB transporter activity may pose a novel approach to enhance the delivery of drugs to the brain for enhanced treatment of AD. In this review, we will give an overview of key functions of BBB transporters and known changes in AD. In addition, we will discuss current strategies for transporter modulation for enhanced drug delivery into the brain.

Emerging roles of ncRNAs regulating ABCC1 on chemotherapy resistance of cancer - a review

In the process of chemotherapy, drug resistance of cancer cells is a common and difficult problem of chemotherapy failure, and it is also the main cause of cancer recurrence and metastasis. Non-coding RNAs (ncRNAs) refer to the RNA that does not encode proteins, including microRNA (miRNA), long non-coding RNA (lncRNA) and circularRNA (circRNA), etc. NcRNAs are involved in a series of important life processes and further regulate the expression of ABCC1 by directly or indirectly up-regulating or down-regulating the expression of targeted mRNAs, making cancer cells more susceptible to drug resistance. A growing number of studies have shown that ncRNAs have effects on cancer cell proliferation, invasion, metastasis, and drug sensitivity, by regulating the expression of ABCC1. In this review, we will discuss the emerging roles of ncRNAs regulating ABCC1 in chemotherapy resistance and mechanisms to reverse drug resistance as well as provide potential targets for future cancer treatment.

AaABCG20 transporter involved in cutin and wax secretion affects the initiation and development of glandular trichomes in Artemisia annua

Glandular trichomes are specialized structures found on the surface of plants to produce specific compounds, including terpenes, alkaloids, and other organic substances. Artemisia annua, commonly known as sweet wormwood, synthesizes and stores the antimalarial drug artemisinin in glandular trichomes. Previous research indicated that increasing the glandular trichome density could enhance artemisinin production, and the cuticle synthesis affected the initiation and development of glandular trichomes in A. annua. In this study, AaABCG12 and AaABCG20 were isolated from A. annua that exhibited similar expression patterns to artemisinin biosynthetic genes. Of the two, AaABCG20 acted as a specific transporter in glandular trichomes. Downregulating the expression of AaABCG20 resulted in a notable reduction in the density of glandular trichome, while overexpressing AaABCG20 resulted in an increase in glandular trichome density. GC-MS analysis demonstrated that AaABCG20 was responsible for the transport of cutin and wax in A. annua. These findings indicated that AaABCG20 influenced the initiation and development of glandular trichomes through transporting cutin and wax in A. annua. This glandular trichome specific half-size ABCG-type transporter is crucial in facilitating the transportation of cutin and wax components, ultimately contributing to the successful initiation and development of glandular trichomes.

Tracing the substrate translocation mechanism in P-glycoprotein

P-glycoprotein (Pgp) is a prototypical ATP-binding cassette (ABC) transporter of great biological and clinical significance.Pgp confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs (Juliano and Ling, 1976; Ueda et al., 1986; Sharom, 2011). Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds (Loo and Clarke, 2000; Loo et al., 2009; Aller et al., 2009; Alam et al., 2019; Nosol et al., 2020; Chufan et al., 2015), but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.

Systematic assessment of the antifungal mechanism of soil fumigant methyl isothiocyanate against Fusarium oxysporum

Fusarium oxysporum is an important phytopathogenic fungus, it can be controlled by the soil fumigant methyl isothiocyanate (MITC). However, the antimicrobial mechanism of MITC against F. oxysporum, especially at the transcriptional level, is still unclear. In this experiment, the antimicrobial mechanism of MITC against F. oxysporum was investigated. Our results indicated that when F. oxysporum was exposed to 6 mg/L MITC for 12 h, the inhibitory rate of MITC on F. oxysporum was 80%. Transmission electron microscopes showed that the cell wall and membrane of F. oxysporum had shrunk and folded, vacuoles increased, and mitochondria swelled and deformed. In addition, the enzyme activity of F. oxysporum treated with MITC showed a decrease of 32.50%, 8.28% and 74.04% in catalase, peroxidase and superoxide dismutase, respectively. Transcriptome sequencing of F. oxysporum was performed and the results showed that 1478 differentially expressed genes (DEGs) were produced in response to MITC exposure. GO and KEGG analysis showed that the DEGs identified were involved in substance and energy metabolism, signal transduction, transport and catalysis. MITC disrupted cell homeostasis by influencing the expression of some key genes involved in chitin synthase and detoxification enzymes production, but F. oxysporum also protected itself by up-regulating genes involved in energy synthesis (such as upregulating acnA, CS and LSC2 in TCA). qRT-PCR data validated the reliability of transcriptome data. Our research used biochemical and genetic techniques to identify molecular lesions in the mycelia of F. oxysporum exposed to MITC, and provide valuable insights into the toxic mechanism of pathogenic fungi mediated by MITC. These techniques are also likely to be useful for rapidly screening and identifying new, environmentally-friendly soil fumigants that are efficacious against fungal pathogens.

Metagenomic insights into the nitrogen metabolism, antioxidant pathway, and antibiotic resistance genes of activated sludge from a sequencing batch reactor under tetracycline stress

Tetracycline is prevalent in wastewater treatment plants and poses a potential threat to biological nitrogen removal under long-term exposure. In the present study, the influence of different tetracycline concentrations on the nitrogen removal, bioactivity response, and the spread of antibiotic resistance genes (ARGs) was assessed in sequencing batch reactor (SBR). The nitrogen removal efficiency, nitrification rate, and denitrification rate and their corresponding enzymatic activities gradually decreased with an increase in tetracycline concentration from 0.5 to 15 mg/L. The remarkable toxicity induced by tetracycline led to a significant increase in the peroxidation and the response of antioxidant system, as evidenced by strengthened antioxidant enzymatic activity and abundant genes (SOD12, katG, PXDN, gpx, and apx). Tetracycline addition significantly inhibited the ammonia-oxidizing bacterium Nitrosomonas and functional genes (amoA, amoB, and amoC). The presence of tetracycline decreased the abundance of citrate synthase and genes (CS, IDH3, and acnA) and interfered with carbon source metabolism, leading to impaired bioactivity and treatment performance. In addition, the presence of tetracycline induces diversity and differences in ARGs. The results provide reliable basic data for a deeper understanding of the effects of tetracycline on the nitrogen removal performance of bioreactors and provide a theoretical basis to build a promising strategy for relieving antibiotic-caused process fluctuations.

Knockdown of the ABCG23 Gene Disrupts the Development and Lipid Accumulation of Panonychus citri (Acari/Tetranychidae)

Panonychus citri is a worldwide citrus pest that is currently controlled through the use of insecticides. However, alternative strategies are required to manage P. citri. Recent studies suggest that the ATP-binding cassette (ABC) transporter G subfamily plays a crucial role in transporting cuticular lipids, which are essential for the insect's barrier function against microbial penetration. Therefore, investigating the potential of the ABC transporter G subfamily as a control measure for P. citri could be a promising approach. Based on the genome database, the gene was cloned, and the transcriptional response of ABCG23 for the different developmental stages of P. citri and under spirobudiclofen stress was investigated. Our results showed that the expression level of ABCG23 was significantly lower in adult females exposed to treatment compared to the control and was higher in females than males. The knockdown of ABCG23 using RNAi led to a decrease in the survival rate, fecundity, and TG contents of P. citri. Additionally, a lethal phenotype was characterized by body wrinkling and darkening. These results indicate that ABCG23 may be involved in cuticular lipid transportation and have adverse effects on the development and reproduction of P. citri, providing insight into the discovery of new targets for pest management based on the insect cuticle's penetration barrier function.

Antagonistic effects of Talaromyces muroii TM28 against Fusarium crown rot of wheat caused by Fusarium pseudograminearum

Fusarium crown rot (FCR) caused by Fusarium pseudograminearum is a serious threat to wheat production worldwide. This study aimed to assess the effects of Talaromyces muroii strain TM28 isolated from root of Panax quinquefolius against F. pseudograminearum. The strain of TM28 inhibited mycelial growth of F. pseudograminearum by 87.8% at 72 h, its cell free fermentation filtrate had a strong antagonistic effect on mycelial growth and conidial germination of F. pseudograminearum by destroying the integrity of the cell membrane. In the greenhouse, TM28 significantly increased wheat fresh weight and height in the presence of pathogen Fp, it enhanced the antioxidant defense activity and ameliorated the negative effects of F. pseudograminearum, including disease severity and pathogen abundance in the rhizosphere soil, root and stem base of wheat. RNA-seq of F. pseudograminearum under TM28 antagonistic revealed 2,823 differentially expressed genes (DEGs). Most DEGs related to cell wall and cell membrane synthesis were significantly downregulated, the culture filtrate of TM28 affected the pathways of fatty acid synthesis, steroid synthesis, glycolysis, and the citrate acid cycle. T. muroii TM28 appears to have significant potential in controlling wheat Fusarium crown rot caused by F. pseudograminearum.

An ABCB transporter regulates anisotropic cell expansion via cuticle deposition in the moss Physcomitrium patens

Anisotropic cell expansion is crucial for the morphogenesis of land plants, as cell migration is restricted by the rigid cell wall. The anisotropy of cell expansion is regulated by mechanisms acting on the deposition or modification of cell wall polysaccharides. Besides the polysaccharide components in the cell wall, a layer of hydrophobic cuticle covers the outer cell wall and is subjected to tensile stress that mechanically restricts cell expansion. However, the molecular machinery that deposits cuticle materials in the appropriate spatiotemporal manner to accommodate cell and tissue expansion remains elusive. Here, we report that PpABCB14, an ATP-binding cassette transporter in the moss Physcomitrium patens, regulates the anisotropy of cell expansion. PpABCB14 localized to expanding regions of leaf cells. Deletion of PpABCB14 resulted in impaired anisotropic cell expansion. Unexpectedly, the cuticle proper was reduced in the mutants, and the cuticular lipid components decreased. Moreover, induced PpABCB14 expression resulted in deformed leaf cells with increased cuticle lipid accumulation on the cell surface. Taken together, PpABCB14 regulates the anisotropy of cell expansion via cuticle deposition, revealing a regulatory mechanism for cell expansion in addition to the mechanisms acting on cell wall polysaccharides.

Characterization and transcriptional expression of ABCG genes in Bactrocera dorsalis: Insights into their roles in fecundity and insecticidal stress response

The ATP-binding cassette (ABC) transporters are essential for regulating various physiological processes and insecticide resistance across different living organisms. ABCG subfamily genes have diverse functions in insects, but little is known about the function of ABCGs in a serious agricultural pest, Bactrocera dorsalis. In this study, 15 BdABCG genes were identified, and BdABCG6 and BdABCG11 were highly expressed in the pupal and adult stages, especially during the transition period from pupae to adults. Silencing of these two genes resulted in a significant reduction of egg production in B. dorsalis, confirming their importance in reproduction. Analysis of tissue expression patterns showed that most genes, including BdABCG1, 3, 8, and 14, exhibited tissue-specificity, with significantly higher expression levels observed in the intestine, Malpighian tubule, and fat body compared to other tissues. Meanwhile, the induction of malathion and avermectin can significantly upregulate the expression of the above four genes. Furthermore, knockdown of BdABCG3 by RNAi significantly increased the mortality of B. dorsalis upon exposure to avermectin, which suggested that BdABCG3 is involved in the transport or metabolism of avermectin in B. dorsalis. Overall, our work provides valuable insights into the function of BdABCGs involved in the reproduction and detoxification system of B. dorsalis.

Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle

The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.

Computational analysis of long-range allosteric communications in CFTR

Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long-range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian network model, transfer entropy, and anisotropic normal mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease-causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP-binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses on dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTR's conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP-binding sites. We have also uncovered a previously undiscovered allosteric 'hotspot' located proximal to the docking site of the phosphorylated regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation-dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric 'hotspot' that could serve as a promising target for the development of novel therapeutic interventions.

Elucidating the structural and functional prophecy of the Rv2326c gene, an ABC transporter of Mycobacterium tuberculosis H37Rv through computational approach

Tuberculosis is a fatal disease caused by Mycobacterium tuberculosis. M. tuberculosis becoming drug-resistant day by day, necessitating to know the mechanism behind the drug resistance and how to overcome this deadly malady. Drug resistance and reduced drug bioavailability are caused by a class of transporter proteins called the ATP-binding cassette (ABC) transporters, which pump a range of medicines out of cells at the price of ATP hydrolysis. By using computational approaches, we tried to elaborate the probable function of the Rv2326c gene of M. tuberculosis, perhaps involved in drug resistance mechanism. The presence of the signature motif of ABC transporters (LSGGELQRLALAAAL and LSGGQMRRVVLAGLL) and ATP binding motif (GXXXXGKT and GXXXXGKS) in the protein sequence signifying its importance in the ATP binding and transportation of molecules. Further, this manuscript elaborated about tertiary structure and validation, functional category, localization, phosphorylation site prediction, mutational analysis of conserved motifs. Ligand docking study shows the highest affinity with ATP than GTP justified its function as an ATP binding protein. The Rv2326c protein is present in the inner membrane and working as an ATP binding protein and might be playing a dynamic role in transportation. In this study, we found that Rv2326c protein might be working as an ABC transporter by which the drugs and other molecules are imported or exported into the bacterium. As a result, the current study provides a means to better understand its normal functioning and basic biology, which can help in the development of novel therapeutic targeting approaches for Rv2326c protein.

Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases

Transposon-encoded tnpB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. This widespread gene family was repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas125,6. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. Here, using phylogenetics, structural predictions, comparative genomics, and functional assays, we uncover multiple instances of programmable transcription factors that we name TnpB-like nuclease-dead repressors (TldR). These proteins employ naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPRi technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of genes encoded by transposable elements, and reveals that RNA-guided transcription factors emerged long before the development of dCas9-based editors.

ABC Transporters 45 Years On

ABC transporters constitute one of the largest gene families among all species [...].

Single Live Cell Imaging of Multidrug Resistance Using Silver Ultrasmall Nanoparticles as Biosensing Probes in Triple-Negative Breast Cancer Cells

Silver ultrasmall nanoparticles (Ag UNPs) (size < 5 nm) were used as biosensing probes to analyze the efflux kinetics contributing to multidrug resistance (MDR) in single live triple-negative breast cancer (TNBC) cells by using dark-field optical microscopy to follow their size-dependent localized surface plasmon resonance. TNBC cells lack expression of estrogen (ER-), progesterone (PR-), and human epidermal growth factor 2 (HER2-) receptors and are more likely to acquire resistance to anticancer drugs due to their ability to transport harmful substances outside the cell. The TNBC cells displayed greater nuclear and cytoplasmic efflux, resulting in less toxicity of Ag UNPs in a concentration-independent manner. In contrast, more Ag UNPs and an increase in cytotoxic effects were observed in the receptor-positive breast cancer cells that have receptors for ER+, PR+, and HER2+ and are known to better respond to anticancer therapies. Ag UNPs accumulated in receptor-positive breast cancer cells in a time-and concentration-dependent mode and caused decreased cellular growth, whereas the TNBC cells due to the efflux were able to continue to grow. The TNBC cells demonstrated a marked increase in survival due to their ability to have MDR determined by efflux of Ag UNPs outside the nucleus and the cytoplasm of the cells. Further evaluation of the nuclear efflux kinetics of TNBC cells with Ag UNPs as biosensing probes is critical to gain a better understanding of MDR and potential for enhancement of cancer drug delivery.

Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter

Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.

Co-evolution at protein-protein interfaces guides inference of stoichiometry of oligomeric protein complexes by de novo structure prediction

The quaternary structure with specific stoichiometry is pivotal to the specific function of protein complexes. However, determining the structure of many protein complexes experimentally remains a major bottleneck. Structural bioinformatics approaches, such as the deep learning algorithm Alphafold2-multimer (AF2-multimer), leverage the co-evolution of amino acids and sequence-structure relationships for accurate de novo structure and contact prediction. Pseudo-likelihood maximization direct coupling analysis (plmDCA) has been used to detect co-evolving residue pairs by statistical modeling. Here, we provide evidence that combining both methods can be used for de novo prediction of the quaternary structure and stoichiometry of a protein complex. We achieve this by augmenting the existing AF2-multimer confidence metrics with an interpretable score to identify the complex with an optimal fraction of native contacts of co-evolving residue pairs at intermolecular interfaces. We use this strategy to predict the quaternary structure and non-trivial stoichiometries of Bacillus subtilis spore germination protein complexes with unknown structures. Co-evolution at intermolecular interfaces may therefore synergize with AI-based de novo quaternary structure prediction of structurally uncharacterized bacterial protein complexes.

ATP-dependent transporters: emerging players at the crossroads of immunity and metabolism

Nearly 50 ATP-binding cassette (ABC) transporters are encoded by mammalian genomes. These transporters are characterized by conserved nucleotide-binding and hydrolysis (i.e., ATPase) domains, and power directional transport of diverse substrate classes - ions, small molecule metabolites, xenobiotics, hydrophobic drugs, and even polypeptides - into or out of cells or subcellular organelles. Although immunological functions of ABC transporters are only beginning to be unraveled, emerging literature suggests these proteins have under-appreciated roles in the development and function of T lymphocytes, including many of the key effector, memory and regulatory subsets that arise during responses to infection, inflammation or cancers. One transporter in particular, MDR1 (Multidrug resistance-1; encoded by the ABCB1 locus in humans), has taken center stage as a novel player in immune regulation. Although MDR1 remains widely viewed as a simple drug efflux pump in tumor cells, recent evidence suggests that this transporter fills key endogenous roles in enforcing metabolic fitness of activated CD4 and CD8 T cells. Here, we summarize current understanding of the physiological functions of ABC transporters in immune regulation, with a focus on the anti-oxidant functions of MDR1 that may shape both the magnitude and repertoires of antigen-specific effector and memory T cell compartments. While much remains to be learned about the functions of ABC transporters in immunobiology, it is already clear that they represent fertile new ground, both for the definition of novel immunometabolic pathways, and for the discovery of new drug targets that could be leveraged to optimize immune responses to vaccines and cancer immunotherapies.

Multi-omics analysis revealed the selective enrichment of partial denitrifying bacteria for the stable coupling of partial-denitrification and anammox process under the influence of low strength magnetic field

The microbial consortium involving anaerobic ammonium oxidation (anammox) and partial denitrification (PD), known as PD-anammox, is an emerging energy-efficient and lower carbon nitrogen removal process from wastewater. However, maintaining a stable PD process by locking nitrate reduction until nitrite was challenging. This study established the first stable connection of anammox with constant nitrite generation by PD bacteria under a low-strength (1.3 mT) magnetic field (MF). When the nitrogen loading rate was 1.81 kg-N/m3/d, the nitrogen removal efficiency of the control reactor (R1) was 75%, lower than that of the experimental reactor (R2), which was 85%. The expression of Thauera and Zoogloea, potential PD bacteria was substantially lower in R1 (5.75% and 1.21%, respectively) than in R2 (10.25 and 6.61%, respectively), according to a meta-transcriptomic analysis. At the same time, the mRNA expression of anammox genera Candidatus Brocadia and Candidatus Kuenenia was 33.53% and 3.83% in R1 and 22.86% and 1.87% in R2. Moreover, carbon and nitrogen metabolism pathways were more abundant under the influence of low-strength MF. The selective enrichment of PD bacteria can be attributed to the increased expression of carbon metabolic pathways like the citrate cycle, glycolysis/gluconeogenesis, and pyruvate metabolism. Interestingly, the control reactor was dominated by a hydroxylamine-dependent anammox process while a low-strength MF-enhanced nitric-oxide-dependent anammox process. For successful anammox-centered nitrogen removal from wastewater, this study demonstrated that low-strength MF is a convenient and applicable technique to lock the nitrate reduction until nitrite.

Mechanisms of magnetic sensing and regulating extracellular electron transfer of electroactive bacteria under magnetic fields

Electroactive bacteria can display notable plasticity in their response to magnetic field (MF), which prompted bioelectrochemical system as promising candidates for magnetic sensor applications. In this study, we explored the sensing and stimulatory effect of MF on current generation by Geobacter sulfurreducens, and elucidated the related molecular mechanism at the transcriptomic level. MF treatment significantly enhanced electricity generation and overall energy efficiency of G. sulfurreducens by 50 % and 22 %, respectively. The response of current to MFs was instantaneous and reversible. Cyclic voltammetry analysis of the anode biofilm revealed that the redox couples changed from -0.31 to -0.39 V (vs. Ag/AgCl), suggesting that MFs could alter electron transfer related components. Differential gene expression analysis further verified this hypothesis, genes associated with electron transfer were upregulated in G. sulfurreducens under MF treatment relative to the control group, specifically, genes encoding periplasmic c-type cytochromes (ppcA and ppcD), outer membrane cytochrome (omcF, omcZ, omcB), pili (pilA-C, pilM, and pilV2), and ribosome. The enhanced bacterial extracellular electron transfer process was also linked to the overexpression of the NADH dehydrogenase I subunit, the ABC transporter, transcriptional regulation, and ATP synthase. Overall, our findings shed light on the molecular mechanism underlying the effects of magnetic field stimuli on EAB and provide a theoretical basis for its further application in magnetic sensors and other biological system.