Potential Substrates Research Articles

Flower waste as a potential substrate for biosurfactant production

To know the potential of flower waste as a substrate for biosurfactant production, strains of pure isolated fungi F1, F2, F3, F4 and F5 were used for the study. Different screening methods were done to test the production of biosurfactant: Emulsification Index Test, Drop Collapse Test, Oil Spreading Test, CTAB Agar Test and Hemolytic Activity Test. The highest percentage of biosurfactant concentration for Emulsification Index Test i.e. E24 value was shown by F1 and F3 with 54.16%. The highest clearing zone for Oil Spreading Test was shown by F1 and F3 strain with 2.2 cm diameter. The Drop Collapse Test was shown positive by F1 and F3 strain with flattening of 1mm as compared with distilled water. The clearing zone around the wells for hemolytic activity was shown by both F1 and F3 strain. CTAB Agar Test showed that out of the five fungal strains, F1 and F3 showed blue halos around the wells and hence are anionic in nature. Thus, flower waste has the potential for the production of biosurfactant as a low-cost substrate which can yield high value biosurfactant.

UBC9 Deficiency Accelerates AML Progression By Downregulating PARP1 Sumoylation and Subsequently Activating the NF-ΚB Pathway

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and is a disease of heterogeneous clonal hematopoietic progenitor cells. Despite the relentless development of therapeutic options, including chemotherapy, and identification of many new therapeutic targets, the prognosis of AML is still poor, with a 5-year survival rate of approximately 35% in patients younger than 60 years old and 10% in patients older than 60 years, which may be due to the high degree of AML heterogeneity. Targeting the shared mechanisms of action among subclones has emerged led to find novel strategies, such as targeting protein post post-translational modification. Here we show that the impact of the UBC9 (the only E2 conjugation enzyme) and its related SUMOylation, a critical and reversible posttranslational modification as ubiquitination, on AML progression, to provide novel and potent sight for AML therapy. To identify the role of UBC9 expression in the clinical outcome of AML patients, we measured the expression of key SUMOylation genes, including SAE1, UBA2, UBC9, SUMO1, SUMO2, SUMO3, PIAS1, PIAS2, PIAS3, PIAS4, CBX4, and RANBP2, in the TCGA dataset (n=164) by using a multivariate survival curve based on the online tool SurvExpress. Our results showed that the survival probability curves of the low- and high-risk groups were significantly different due to the differences in the levels of expression of key SUMOylation genes ( p = 0.0011), and we found that the expression level of UBC9 was lower in the high-risk group than in the low-risk group. We next analyzed the UBC9 expression level and the prognosis of AML patients from the Therapeutically Applicable Research To Generate Effective Treatment dataset (n=156), which showed that AML patients with low UBC9 expression showed shorter overall survival ( p = 0.018)(Figure 1). In addition, real-time PCR showed that the UBC9 expression level in bone marrow samples from patients with de novo AML was significantly downregulated in both the high-risk patients based on National Comprehensive Cancer Network guidelines and the liver or spleen enlargement patients ( p = 0.01 and p = 0.001, respectively) (Figure 1). We used RNA interference system to knock out Ubc9 in a mouse model of MLL-AF9 and MLL-ENL induced AML. We observed the survival of AML mice and found that Ubc9 fl/+;Vav-Cre recipient mice showed a significantly shorter survival time than Ubc9 fl/+ mice (Figure 2). In addition, apoptosis experiments revealed reduced apoptosis of leukemia cells and leukemia stem cells in Ubc9 fl/+;Vav-cre mice. HE staining showed significantly higher leukemia cell infiltration in the livers, meninges, and kidneys of Ubc9 fl/+;Vav-cre mice compared to Ubc9 fl/+ mice. Transwell experiments indicated that Ubc9 deficiency resulted in increased migration of leukemia cells. Colony forming assay demonstrated that Ubc9-deficient leukemia cells formed significantly larger colonies. Flow cytometry analysis showed that Ubc9-deficient leukemia cells expressed high levels of c-kit and low levels of Mac1. To further elucidate the role of UBC9 in human AML cells, we constructed UBC9 deficient KG1 and K562 cell lines by using CRISPR-Cas9 technology. The UBC9 KD cell lines presented the same phenotype such as the increase of cell viability and the enhancement of invasiveness. To better understand the role that UBC9 plays in AML cell biology, we performed a system-level approach based on quantitative SUMO proteomic analysis to identify potential UBC9 substrates and then identified PARP1 with SUMOylation site lysine residue 486 (K486) by multiomics analysis. Finally, we validated that UBC9-mediated PARP1 SUMOylation played an important role in AML progression by activating the NF-kappa B pathway via the site-directed mutation of PARP1 (K486R) in UBC9-KO AML cells by using western blot and Co-immunoprecipitation. Together, our study revealed that UBC9 KO accelerated AML progression and enabled us to contrast global SUMOylation profiles of UBC9 in AML cells. In addition, we found that the PARP1 SUMOylation-mediated NF-κB pathway activation is a positive regulatory mechanism in the tumorigenesis of AML. These findings may provide potential clinical implications for AML treatment.

Structural and Biochemical Characterization of MppQ, an L-Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus.

MppQ is an enzyme of unknown function from Streptomyces hygroscopicus (ShMppQ) that operates in the biosynthesis of the nonproteinogenic amino acid L-enduracididine (L-End). Since L-End is a component of several peptides showing activity against antibiotic-resistant pathogens, understanding its biosynthetic pathway could facilitate the development of chemoenzymatic routes to novel antibiotics. Herein, we report on the crystal structures of ShMppQ complexed with pyridoxal-5'-phosphate (PLP) and pyridoxamine-5'-phosphate (PMP). ShMppQ is similar to fold-type I PLP-dependent aminotransferases like aspartate aminotransferase. The tertiary structure of ShMppQ is composed of an N-terminal extension, a large domain, and a small domain. The active site is placed at the junction of the large and small domains and includes residues from both protomers of the homodimer. We also report the first functional characterization of MppQ, which we incubated with the enzymatically produced 2-ketoenduracidine and observed the conversion to L-End, establishing ShMppQ as the final enzyme in L-End biosynthesis. Additionally, we have observed that MppQ has a relatively high affinity for 2-keto-5-guanidinovaleric acid (i.e., 2-ketoarginine), a shunt product of MppP, indicating the potential role of MppQ in increasing the efficiency of L-End biosynthesis by converting 2-ketoarginine back to the starting material, l-arginine. A panel of potential amino-donor substrates was tested for the transamination activity against a saturating concentration of 2-ketoarginine in end-point assays. Most l-Arg was produced with l-ornithine as the donor substrate. Steady-state kinetic analysis of the transamination reaction with l-Orn and 2-ketoarginine shows that the kinetic constants are in line with those for the amino donor substrate of other fold-type I aminotransferases.

Structural insight into the role of thiolase from Fusobacterium nucleatum

Fusobacterium nucleatum (F. nucleatum) is an anaerobic gram-negative bacterium that was previously thought to be related to the progression of colorectal cancer. In F. nucleatum, thiolase participates in fatty acid metabolism, and it can catalyse the transfer of an acetyl group from acetyl-CoA to another molecule, typically a fatty acid or another molecule in the synthesis of lipids. To gain deeper insight into the molecular mechanism governing the function of thiolase in F. nucleatum (Fn0495), we herein report the structure of Fn0495. The monomer of Fn0495 consists of three subdomains, namely, the N-terminal domain (residues 1–117 and 252–270), the C-terminal domain (residues 273–393), and the loop domain (residues 118–251). Fn0495 shows a unique difference in the charge and structure of the substrate binding pocket compared with homologous proteins. This research found three conserved residues (Cys88, His357, and Cys387) in Fn0495 arranged near a potential substrate binding pocket. In this study, the conformational changes between the covering loop, catalytic cysteine loop, regulatory determinant region, and homologous protein were compared. These results will enhance our understanding of the molecular characteristics and roles of the thiolase family.

Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.

In various autoimmune diseases, dysfunctional TREX1 (Three prime RepairExonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2'-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2'-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.

The Guaymas Basin – A hot spot for hydrothermal generation and anaerobic microbial degradation of hydrocarbons

Guaymas Basin is a young marginal rift basin in the Gulf of California characterized by active seafloor spreading, rapid deposition of organic-rich sediments, and steep geothermal gradients where sedimentary organic material of photosynthetic origin turns into hydrocarbons - potential microbial substrates. After introducing the sources of hydrocarbons in the subsurface, this short overview discusses the phylogenetic diversity, temperature range and occurrence patterns of novel alkane-oxidizing bacteria and archaea in the hydrothermal sediments of Guaymas Basin. Many of these alkane-degrading specialists function as syntrophic consortia, where sulfate-reducing bacteria accept electron from methane- or alkane-oxidizing archaea. As a source of metagenomes, enrichments, and cultures of these methodologically and conceptually challenging microorganisms, Guaymas Basin stands out as an indispensable field site that has consistently catalyzed new insights into the microbiology of anaerobic hydrocarbon oxidation and assimilation.

Anabolic and Catabolic Microbial Activity in Hydrocarbon-rich Sediments of Guaymas Basin

Guaymas Basin, located in the Gulf of California, Mexico, is a young marginal ocean basin with high sedimentation rates of >1 mm/year, active seafloor spreading, and steep geothermal gradients in its sediment. It hosts a unique microbial subseafloor biosphere as these conditions lead to thermal cracking of sedimentary organic matter and the production of bioavailable organic carbon compounds and hydrocarbons already at shallow depths. The abundance and diversity of potential microbial substrates raise the question of which substrates are being used for catabolic and anabolic microbial metabolism. We thus analyzed the microbial uptake of hydrocarbons and inorganic nitrogen using nanoscale secondary ion mass spectrometry (NanoSIMS) analysis after incubation with stable-isotope labeled substrates. Incubations were carried out with samples from two International Ocean Discovery Program (IODP) Exp. 385 drill sites. Site U1545 is characterized by undisturbed sedimentary strata and a temperature gradient of 225°C/km, whereas Site U1546 has experienced a sill intrusion at greater depth, below the cored interval. The intrusion led to temporary heating of the sediment, but a temperature gradient of 221°C/km indicates thermal equilibration with the surrounding sediment since sill emplacement. Incubations were carried out with 13C-benzene + 2H-hexadecane + 15NH4Cl or 13C-methane + 15NH4Cl at in-situ temperature (4-62°C) and pressure (25 MPa) for 42 days. Additionally, sulfate reduction rates (SRR) were measured by incubating the samples with four aliphatic hydrocarbons + four aromatic hydrocarbons or methane and radioisotope-labeled 35SO42- for 10 days, also at in-situ temperature and pressure. The NanoSIMS analyses reveal that a few samples showed detectable microbial assimilation of hydrocarbons. Nitrogen was significantly assimilated in some samples incubated with methane. The assimilation mostly occurred in samples from near the seafloor (2 and 44 meter below seafloor (mbsf)). Our results indicate that anaerobic microorganisms in Guaymas Basin take up measurable amounts of hydrocarbons and inorganic nitrogen even in the relatively short incubation time of 42 days. The results of the SRR measurements indicate that a mixture of hydrocarbons and methane increases the SRR in samples from near the seafloor (2 mbsf) and around the sulfate-methane transition zone (44 and 55 mbsf) but not in samples from greater depths. Our results show that anaerobic microorganisms in Guaymas Basin can use hydrocarbons for anabolic and catabolic metabolism in this extreme environment. Given the high abundance of various carbon compounds, nitrogen appears to be a limiting factor for cellular growth.

Structure and function of SPP/SPPL proteases: insights from biochemical evidence and predictive modeling.

More than 20 years ago, signal peptide peptidase (SPP) and its homologues, the signal peptide peptidase-like (SPPL) proteases have been identified based on their sequence similarity to presenilins, a related family of intramembrane aspartyl proteases. Other than those for the presenilins, no high-resolution structures for the SPP/SPPL proteases are available. Despite this limitation, over the years bioinformatical and biochemical data have accumulated, which altogether have provided a picture of the overall structure and topology of these proteases, their localization in the cell, the process of substrate recognition, their cleavage mechanism, and their function. Recently, the artificial intelligence-based structure prediction tool AlphaFold has added high-confidence models of the expected fold of SPP/SPPL proteases. In this review, we summarize known structural aspects of the SPP/SPPL family as well as their substrates. Of particular interest are the emerging substrate recognition and catalytic mechanisms that might lead to the prediction and identification of more potential substrates and deeper insight into physiological and pathophysiological roles of proteolysis.

SARS-CoV-2 papain-like protease plays multiple roles in regulating cellular proteins in the endoplasmic reticulum

Nsp3s are the largest nonstructural proteins of coronaviruses. These transmembrane proteins include papain-like proteases (PLpro) that play essential roles in cleaving viral polyproteins into their mature units. The PLpro of SARS-CoV viruses also have deubiquitinating and deISGylating activities. As Nsp3 is an endoplasmic reticulum (ER)-localized protein, we asked if the deubiquitinating activity of SARS-CoV-2 PLpro affects proteins that are substrates for ER-associated degradation (ERAD). Using full-length Nsp3 as well as a truncated transmembrane form we interrogated, by coexpression, three potential ERAD substrates, all of which play roles in regulating lipid biosynthesis. Transmembrane PLpro increases the level of INSIG-1 and decreases its ubiquitination. However, different effects were seen with SREBP-1 and SREBP-2. Transmembrane PLpro cleaves SREBP-1 at three sites, including two noncanonical sites in the N-terminal half of the protein, resulting in a decrease in precursors of the active transcription factor. Conversely, cleavage of SREBP-2 occurs at a single canonical site that disrupts a C-terminal degron, resulting in increased SREBP-2 levels. When this site is mutated and the degron can no longer be interrupted, SREBP-2 is still stabilized by transmembrane PLpro, which correlates with a decrease in SREBP-2 ubiquitination. All of these observations are dependent on PLpro catalytic activity. Our findings demonstrate that, when anchored to the ER membrane, SARS-CoV-2 Nsp3 PLpro can function as a deubiquitinating enzyme to stabilize ERAD substrates. Additionally, SARS-CoV-2 Nsp3 PLpro can cleave ER-resident proteins, including at sites that could escape analyses based on the established consensus sequence.

Aldehyde oxidase 1 activity and protein expression in human, rabbit, and pig ocular tissues

Aldehyde oxidase (AOX) is a cytosolic drug-metabolizing enzyme which has attracted increasing attention in drug development due to its high hepatic expression, broad substrate profile and species differences. In contrast, there is limited information on the presence and activity of AOX in extrahepatic tissues including ocular tissues. Because several ocular drugs are potential substrates for AOX, we performed a comprehensive analysis of the AOX1 expression and activity profile in seven ocular tissues from humans, rabbits, and pigs. AOX activities were determined using optimized assays for the established human AOX1 probe substrates 4-dimethylamino-cinnamaldehyde (DMAC) and phthalazine. Inhibition studies were undertaken in conjunctival and retinal homogenates using well-established human AOX1 inhibitors menadione and chlorpromazine. AOX1 protein contents were quantitated with targeted proteomics and confirmed by immunoblotting. Overall, DMAC oxidation rates varied over 10-fold between species (human ˃˃ rabbit ˃ pig) and showed 2- to 6-fold differences between tissues from the same species. Menadione seemed a more potent inhibitor of DMAC oxidation across species than chlorpromazine. Human AOX1 protein levels were highest in the conjunctiva, followed by most posterior tissues, whereas anterior tissues showed low levels. The rabbit AOX1 expression was high in the conjunctiva, retinal pigment epithelial (RPE), and choroid while lower in the anterior tissues. Quantification of pig AOX1 was not successful but immunoblotting confirmed the presence of AOX1 in all species. DMAC oxidation rates and AOX1 contents correlated quite well in humans and rabbits. This study provides, for the first time, insights into the ocular expression and activity of AOX1 among multiple species.

Atomic Insights into the Structural Properties and Displacement Cascades in Ytterbium Titanate Pyrochlore (Yb2Ti2O7) and High-Entropy Pyrochlores

Pyrochlore oxides (A2B2O7) are potential nuclear waste substrate materials due to their superior radiation resistance properties. We performed molecular dynamics simulations to study the structural properties and displacement cascades in ytterbium titanate pyrochlore (Yb2Ti2O7) and high-entropy alloys (HEPy), e.g., YbYTiZrO7, YbGdTiZrO7, and Yb0.5Y0.5Eu0.5Gd0.5TiZrO7. We computed lattice constants (LC) (ao) and threshold displacement energy (Ed). Furthermore, the calculation for ao and ionic radius (rionic) were performed by substituting a combination of cations at the A and B sites of the original pyrochlore structure. Our simulation results have demonstrated that the lattice constant is proportional to the ionic radius, i.e., ao α rionic. Moreover, the effect of displacement cascades of recoils of energies 1 keV, 2 keV, 5 keV, and 10 keV in different crystallographic directions ([100], [110], [111]) was studied. The number of defects is found to be proportional to the energy of incident primary knock-on atoms (PKA). Additionally, the Ed of pyrochlore exhibits anisotropy. We also observed that HEPy has a larger Ed as compared with Yb2Ti2O7. This establishes that Yb2Ti2O7 has characteristics of lower radiation damage resistance than HEPy. Our displacement cascade simulation result proposes that HEPy alloys have more tendency for trapping defects. This work will provide atomic insights into developing substrate materials for nuclear waste applications.

Systematic identification of CAZymes and transcription factors in the hypercellulolytic fungus Penicillium funiculosum NCIM1228 involved in lignocellulosic biomass degradation

BackgroundPenicillium funiculosum NCIM1228 is a filamentous fungus that was identified in our laboratory to have high cellulolytic activity. Analysis of its secretome suggested that it responds to different carbon substrates by secreting specific enzymes capable of digesting those substrates. This phenomenon indicated the presence of a regulatory system guiding the expression of these hydrolyzing enzymes. Since transcription factors (TFs) are the key players in regulating the expression of enzymes, this study aimed first to identify the complete repertoire of Carbohydrate Active Enzymes (CAZymes) and TFs coded in its genome. The regulation of CAZymes was then analysed by studying the expression pattern of these CAZymes and TFs in different carbon substrates—Avicel (cellulosic substrate), wheat bran (WB; hemicellulosic substrate), Avicel + wheat bran, pre-treated wheat straw (a potential substrate for lignocellulosic ethanol), and glucose (control).ResultsThe P. funiculosum NCIM1228 genome was sequenced, and 10,739 genes were identified in its genome. These genes included a total of 298 CAZymes and 451 TF coding genes. A distinct expression pattern of the CAZymes was observed in different carbon substrates tested. Core cellulose hydrolyzing enzymes were highly expressed in the presence of Avicel, while pre-treated wheat straw and Avicel + wheat bran induced a mixture of CAZymes because of their heterogeneous nature. Wheat bran mainly induced hemicellulases, and the least number of CAZymes were expressed in glucose. TFs also exhibited distinct expression patterns in each of the carbon substrates. Though most of these TFs have not been functionally characterized before, homologs of NosA, Fcr1, and ATF21, which have been known to be involved in fruiting body development, protein secretion and stress response, were identified.ConclusionsOverall, the P. funiculosum NCIM1228 genome was sequenced, and the CAZymes and TFs present in its genome were annotated. The expression of the CAZymes and TFs in response to various polymeric sugars present in the lignocellulosic biomass was identified. This work thus provides a comprehensive mapping of transcription factors (TFs) involved in regulating the production of biomass hydrolyzing enzymes.

Corticofugal regulation of predictive coding

Sensory systems must account for both contextual factors and prior experience to adaptively engage with the dynamic external environment. In the central auditory system, neurons modulate their responses to sounds based on statistical context. These response modulations can be understood through a hierarchical predictive coding lens: responses to repeated stimuli are progressively decreased, in a process known as repetition suppression, whereas unexpected stimuli produce a prediction error signal. A potential substrate for top-down predictive cues is the massive set of descending projections from the cortex to subcortical structures, although the role of these corticofugal neurons in predictive processing has never been directly assessed. We tested the effect of optogenetic inactivation of the auditory cortico-collicular feedback in awake mice on responses of auditory midbrain neurons to stimuli designed to test prediction error and repetition suppression. Inactivation of the cortico-collicular pathway led to a decrease in prediction error and repetition enhancement in these neurons. Overall, our results demonstrate that the auditory cortex provides cues about the statistical context of sound to subcortical brain regions via direct feedback, regulating processing of both prediction and repetition.

Cell culture design for homogeneous proliferation of cells in three-dimensional nonwoven polymer scaffolds

The objective of this study is to establish strategies to uniformly proliferate cells in a three-dimensional nonwoven polyethylene terephthalate (PET)/ethylene vinyl alcohol (EVOH) scaffold by simple adjustments in seeding and culture methods and the scaffold design. The combined dynamic and static seeding (intermittent agitations at 300 rpm with 1 h interval) resulted in the highest seeding efficiency (71%) comparing to the static and continuous agitating seeding methods. Cell-attached scaffolds were cultivated under different conditions. The stirring culture permitted cells to proliferate to a significantly greater extent than the static or agitating cultures, although faster cell proliferation in the outer region of the scaffold was observed. Next, based on this observation, scaffolds were opened with holes to alleviate the cell aggregation. The effect of hole size and number of scaffolds on the distribution of cells proliferated in the scaffold was evaluated. Two of 1-mm holes showed to be an optimal adjustment to allow cells to proliferate in a homogeneous manner. After 14 days culture, both of the holes were filled by cells proliferated with a fourfold increase in the cell number. The cell viability in the scaffolds was also high upon evaluating the live/dead and 3[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) staining examinations. Different cell types of 3T3-L1, C3H/10T1/2, and KUM6 cells showed similar behavior of cell proliferation and distribution in the scaffold, indicating the applicability of the established procedure. It is concluded that the nonwoven PET/EVOH scaffold serves as a potential cell culture substrate for an efficient cell proliferation.

Generation of Cannabigerolic Acid Derivatives and Their Precursors by Using the Promiscuity of the Aromatic Prenyltransferase NphB.

NphB is an aromatic prenyltransferase with high promiscuity for phenolics including flavonoids, isoflavonoids, and plant polyketides. It has been demonstrated that cannabigerolic acid is successfully formed by the reaction catalysed by NphB using geranyl diphosphate and olivetolic acid as substrates. In this study, the substrate specificity of NphB was further determined by using olivetolic acid derivatives as potential substrates for the formation of new synthetic cannabinoids. The derivatives differ in the hydrocarbon chain attached to C6 of the core structure. We performed in silico experiments, including docking of olivetolic acid derivatives, to identify differences in their binding modes. Substrate acceptance was predicted. Based on these results, a library of olivetolic acid derivatives was constructed and synthesized by using different organic synthetic routes. Conversion was monitored in in vitro assays with purified NphB versions. For the substrates leading to a high conversion olivetolic acid-C8, olivetolic acid-C2 and 2-benzyl-4,6-dihydroxybenzoic acid, the products were further elucidated and identified as cannbigerolic acid derivatives. Therefore, these substrates show potential to be adapted in cannabinoid biosynthesis.

Synergistic effect of YOD1 and USP21 on the Hippo signaling pathway

BackgroundDeubiquitinating enzymes (DUBs) comprise a family of proteases responsible for cleaving the peptide or isopeptide bond between ubiquitin and its substrate proteins. Ubiquitin is essential for regulating diverse cellular functions by attaching to target proteins. The Hippo signaling pathway plays a crucial role in controlling tissue size, cell proliferation, and apoptosis. In a previous study, we discovered that YOD1 regulates the Hippo signaling pathway by deubiquitinating the neural precursor cell expressed developmentally down-regulated protein 4 (NEDD4), an E3 ligase of large tumor suppressor kinase 1 (LATS1). Here, our aim was to investigate potential substrates of YOD1 implicated in the Hippo signaling pathway.MethodsWe employed various bioinformatics tools (BioGRID, STRING, and Cytoscape) to identify novel potential substrates of YOD1. Furthermore, we used western blotting, co-immunoprecipitation (co-IP), glutathione S-transferase (GST) pull-down, immunocytochemistry (ICC) assays to investigate cellular interactions. To evaluate cell proliferation, we performed cell counting kit-8 (CCK-8), wound healing, colony forming, and flow cytometry assays using A549, HEK293T, and HeLa cells. Additionally, we assessed the expression levels of YAP and p-YAP in A549, HEK293T, and HeLa cells through western blotting.ResultsOur investigations revealed that YOD1 interacts with ubiquitin-specific proteases 21 (USP21), a DUB involved in the Hippo signaling pathway, and deubiquitinates the microtubule-affinity regulating kinase (MARK). Intriguingly, YOD1 and USP21 mutually deubiquitinate each other; while YOD1 regulates the protein stability of USP21, USP21 does not exert a regulatory effect on YOD1. Moreover, we observed the synergistic effect of YOD1 and USP21 on cell proliferation through the modulation of the Hippo signaling pathway.ConclusionsOur study revealed multiple cellular interactions between YOD1 and USP21. Moreover, our findings suggest that the combined activities of YOD1 and USP21 synergistically influence cell proliferation in A549 cells by regulating the Hippo signaling pathway.

Polyaniline/Ti3C2Tx functionalized mask sensors for monitoring of CO2 and human respiration rate

Flexible and wearable gas-sensing devices have become increasingly crucial for monitoring air quality and human health. Disposable masks, mainly composed of polypropylene (PP) fibers, can serve as a potential flexible substrate for sensing devices yet have been largely overlooked during the COVID-19 pandemic. In the present work, flexible Ti3C2Tx/PANI-PP composite gas sensors were fabricated by spray-coating delaminated Ti3C2Tx MXene and in-situ polymerization of aniline on a disposable mask substrate. The resulting hybrid gas sensor displayed a wide detection range (25–1500 ppm), reliable reproducibility, long-term stability, and excellent flexibility and selectivity, a remarkable response (15.2%) towards 500 ppm CO2 gas, which is 6.5 times higher than pristine Ti3C2Tx and 2.4 times higher than pristine PANI. The enhanced sensing performance of the composite sensor is mainly attributed to the synergistic effects of the heterojunctions between Ti3C2Tx and PANI, the improved conductivity, and the enlarged specific surface area. We further investigated the influence of various parameters, including humidity, temperature, bending angles, and folding times on the sensing performance of the composite gas sensor. Finally, a wearable wireless Bluetooth sensing device was fabricated for human exhaled breath monitoring at room temperature, demonstrating the potential application of this Ti3C2Tx/PANI-PP composite sensor for respiratory disease diagnosis.

Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network

Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key posttranslational modification involved in physiology and disease. The ability to robustly and rapidly predict protease-substrate specificity would also enable targeted proteolytic cleavage by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pretrained PGCN model to guide the design of protease libraries for cleaving two noncanonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.

Recycling Fish Heads for the Production of Prodigiosin, a Novel Fungicide via Experimental and Molecular Docking Characterization

This report aims to characterize and reuse fish head powder (FHP) as a potential carbon/nitrogen source for microbial fermentation to produce prodigiosin (PG), and to evaluate its novel anti-fungal effect via an experimental and docking study. FHP has high protein (30.25%) and lipid (5.12%) content and a diversity of elements, which suggests that FHP is a potential substrate for microbial fermentation. Serratia marcescens TNU01 was screened as the most effective strain to produce PG from FHP. Further experiments indicated that the combination of FHP and crude chitin at the ratio of 9/1 and used at 1.5% as a C/N source for fermentation significantly enhanced PG production. Supplementing a minor amount of 0.05% Ca3(PO4)2, 0.03% K2SO4 also positively affects PG yield production. The fermentation using a bioreactor system (type of 14 L) achieved the highest PG yield production (6.4 mg/mL) in a short cultivation time (10 h) in comparison with the highest PG yield (5.8 mg/mL) obtained after 36 h of fermentation in a flask. In the anti-fungal evaluation of various plant pathogen fungal strains, PG demonstrated efficacy against Fusarium solani F04. The molecular docking results also showed that PG effectively interacted with targeting protein 3QPC of F. solani with good binding energy (DS—9.2 kcal/mol) and an acceptable RMSD value (0.94 Å). In this study, we provide a novel application of FHP for the eco-friendly production of PG, which can potentially used for the management of Fusarium solani.

The effect of acute high-intensity interval training and Tabata training on inhibitory control and cortical activation in young adults.

Physical exercise not only benefits peoples' health, but also improves their cognitive function. Although growing evidence suggests that high-intensity interval training (HIIT) is a time-efficient exercise regime that can improve inhibitory control performance by enhancing cortical activation in the prefrontal cortex, less is known about how Tabata training, a subset of HIIT that requires no equipment or facilities to perform, affects inhibitory control and cortical activation in young adults. Therefore, we aimed to reveal the effect of an acute bout of HIIT and Tabata training on inhibitory control and attempted to identify its potential neural substrates. Forty-two young adults (mean age: 19.36 ± 1.36 years; 21 females) performed the Stroop task and Simon task before and after acute HIIT, Tabata training, or a control session, and cortical hemodynamic changes in the prefrontal area were monitored by functional near-infrared spectroscopy (fNIRS) during the tasks. Both HIIT and Tabata interventions lasted for a total of 12 min. The HIIT participants performed ergometer cycling at their 80% maximal aerobic power at 90-100 rpm, and the Tabata participants performed a total of 8 intense activities, such as jumping jacks, high knees, and butt kickers, without using equipment or facilities, keeping the heart rate at 80-95% of their maximum heart rate. Participants in the control group watched a sport video while sedentary. Cognitive tasks data and fNIRS data were analyzed by repeated-measures three-way ANOVA. Our results indicated that both the HIIT and Tabata groups exhibited reduced reaction times after the intervention, and there were alterations in activation patterns in the dorsolateral and ventrolateral prefrontal cortices.