Search Results (63)

Plastic, a ubiquitous part of our daily lives, has become a global necessity, with annual production exceeding 300 million tons. However, the accumulation of synthetic polymers in our environment poses a pressing global challenge. To address this urgent issue, fungi have emerged as potential agents for plastic degradation. In our previous manuscript, ‘A Review of the Fungi That Degrade Plastic’, we explored the taxonomic placement of plastic-degrading fungi across three main phyla: Ascomycota, Basidiomycota, and Mucoromycota. In this review, we built upon that foundation and aimed to further explore the taxonomic relationships of these fungi in a comprehensive and detailed manner, leaving no stone unturned. Moreover, we linked metabolic activity and enzyme production of plastic-degrading fungi to their taxonomy and summarized a phylogenetic tree and a detailed table on enzyme production of plastic-degrading fungi presented here. Microbial enzymes are key players in polymer degradation, operating intra-cellularly and extra-cellularly. Fungi, one of the well-studied groups of microbes with respect to plastic degradation, are at the forefront of addressing the global issue of plastic accumulation. Their unique ability to hydrolyze synthetic plastic polymers and produce a wide range of specific enzymes is a testament to their potential. In this review, we gather and synthesize information concerning the metabolic pathways of fungi involved in the degradation of plastics. The manuscript explores the diverse range of specific enzymes that fungi can produce for plastic degradation and the major pathways of plastic metabolism. We provide a listing of 14 fungal enzymes (Esterase, Cutinase, Laccase, Peroxidases, Manganese peroxidase, Lignin peroxidase, Oxidoreductases, Urease, Protease, Lipase, Polyesterase, Dehydrogenase, Serine hydrolase, and PETase) involved in pathways for plastic degradation alongside the relevant fungi known to produce these enzymes. Furthermore, we integrate the fungi’s enzyme-producing capabilities with their taxonomy and phylogeny. Taxonomic and phylogenetic investigations have pinpointed three primary fungal classes (Eurotiomycetes, Sordariomycetes (Ascomycota), and Agaricomycetes (Basidiomycota)) as significant plastic degraders that produce the vital enzymes mentioned earlier. This paper provides a foundational resource for recognizing fungal involvement in the biodegradation of synthetic polymers. It will ultimately advance fungal biotechnology efforts to address the global issue of plastic accumulation in natural environments. Full article

Alpha/beta hydrolase (ABHs) fold esterase/lipase proteins represent a prominent family within the serine hydrolase (SH) superfamily that includes esterases and lipases and other catalytic and non-catalytic proteins. ABHs play crucial roles in both the fundamental and secondary metabolic pathways, including the synthesis and degradation of triacylglycerols (TAGs), key components of plant oils. Despite their importance in oil production, the ABH gene family in the oil crop Brassica napus has not been comprehensively analyzed. In the present study, we identified 777 BnABH genes in the B. napus cultivar ‘Zhongshuang 11’ (ZS11). Phylogenetic analysis categorized these BnABH genes into 10 distinct groups. Twenty-four BnABHs were identified through esterase activity staining and mass spectrometry, 11 of which were classified into clade C3. Examination of the gene and protein structures, expression patterns, and cis-elements of the BnABHs in clade C3 suggested diverse functional roles across different tissues and in response to various environmental stresses. In particular, BnABH205 was highly induced by high temperatures. Subcellular localization analysis revealed that the BnABH205 protein was localized to the plastid. Further analysis revealed five haplotypes within the coding and 3′ untranslated regions of BnABH205 that were significantly associated with seed oil content (SOC). Overall, this study provides a comprehensive understanding of BnABHs and introduces a robust methodology for identifying potential esterase/lipase genes that regulate seed oil content (SOC) in response to environmental hazards, especially heat waves during seed maturation. Full article

Background: Multi-antibiotic resistance has become an alarming issue in treating bacterial infections in both community and medical environments. Globally, the scientific community has been exploring multi-antibiotic techniques to find new ways to address this challenge. To address this critical challenge and explore alternative antibiotic treatments, we investigated the potential of Solanum trilobatum, an edible and medicinally important herb plant in Ayurvedic medicine. Methods: Our research focused on a 60 kDa serine protease isolated and purified from the leaves of S. trilobatum, which showed evidence of possessing hydrolase activity. In this study, we examined the capability of the purified enzyme to eradicate preformed biofilms of S. aureus in combination with ampicillin. Additionally, we assessed the stability of the enzyme in the presence of metal ions and detergents. Results: Enzyme kinetics revealed a Vmax of 48.63 µM/min and a Km of 14.08 µM, indicating efficient enzymatic activity. Furthermore, the enzyme exhibited maximum activity at physiological pH, suggesting its potential effectiveness under physiological conditions. Conclusions: Our preliminary findings highlight the promising role of this enzyme as a potential agent to combat S. aureus biofilms, especially when used in conjunction with ampicillin, as an alternative antibiotic approach. Full article

Reproduction and breeding are crucial to maintaining abalone aquaculture. Understanding the molecular underpinnings of sexual maturation is essential for advancing knowledge in reproductive biology. However, the molecular mechanisms of gonadal development in abalones remain poorly understood, particularly in microRNA (miRNA)-mediated regulation. Thus, this study conducted a comprehensive transcriptomic analysis of abalone Haliotis discus hannai (H. discus hannai) to identify genes and miRNAs associated with ovarian and testicular discovery. This study identified 685 differentially expressed (DE) genes between the H. discus hannai ovary (DD_ovary) and testis (DD_testis) groups, comprising 479 upregulated and 206 downregulated genes in the DD_ovary. Moreover, 137 miRNAs, including 83 novel and 54 known miRNAs, were detected, with 30 upregulated and 27 downregulated in the DD_ovary compared to the DD_testis. Bioinformatics analysis revealed that these miRNAs regulate key processes such as carbohydrate metabolic processes, kinase and hydrolase activity, and starch and sucrose metabolism, all potentially associated with reproductive traits. Further, key mRNA candidates, including Vitelline envelope sperm lysin receptor (Verl) and Testis-specific serine/threonine-protein kinase (Tssk) 1, and miRNAs such as novel_90 and novel_120, were identified as components of a functional miRNA-mRNA network associated with sexual maturity and sex determination. These key genes were verified using qRT-PCR and fluorescence in situ hybridization (FISH). These transcriptomic and miRNA datasets provide valuable resources for understanding abalone reproductive biology and may support molecular breeding strategies. Full article

Zygophyllum coccineum L. and Haloxylon salicornicum are dominant plant species in the natural habitats of Saudi Arabia. The soil microbiome is indispensable for nutrient cycling and stress resilience. In the present study, the analysis of soil nutrients under the two plants displayed variable differences in total N, K, Zn, Mn and Cu, with significant differences in both K and Mn (p ≤ 0.05). In general, the available soil nutrients were higher under Haloxylon than Zygophyllum plants, reflecting higher N, K, Fe and Cu contents in the leaves of the Haloxylon plant. Metagenomic analysis of soil microbiome revealed that the top abundant bacteria at the phylum level were Actinobacteriota, Chloroflexi and Proteobacteria, whereas the uppermost fungal communities were Ascomycota, followed by Basidiomycota. The predicted abundant enzymes in the bacterial communities included Phosphoadenylyl-sulfate reductase, Serine-type D-Ala-carboxypeptidase, ADP-glyceromanno-heptose 6-epimerase and glutathione hydrolase. The fungal communities associated with Haloxylon possessed more than 48 enzymes that differed in their richness from the communities of Zygophyllum. Pentose-P and Sulphate-Cys pathways disclosed the extreme abundant pathways in Zygophyllum bacterial communities, while the nonoxipent pathway was overabundant in the Haloxylon fungal communities. While genomic predictions provide insights into functional potential, integrating these data with environmental parameters remains key to managing soil health. Full article

Despite extensive research on Bacillus sp. as lignin degraders, the enzyme mechanisms involved, particularly in Bacillus cereus isolated from termite guts, remain unclear. In this study, the selected Bacillus cereus was fermented to extract the lignin-degrading enzymes to identify the enzymes responsible for lignin degradation using the sample substrate empty fruit bunch (EFB) as their sole carbon source. After 7 days of submerged fermentation (SmF), the crude enzyme was extracted, and SDS-PAGE gel was used to determine the weight of the proteins, and bands with sizes of 20 kDa–97 kDa were extracted for further analysis. The extracted proteins were partially characterized and sequenced using liquid chromatography–mass spectrometry (LC–MS/MS). The results identified 11 enzymes that are responsible for lignin degradation, such as 4-aminobutyrate aminotransferase (GABA), amidohydrolase, chemotaxis protein, serine hydrolase, GMC family protein, glycosyltransferase, phosphate binding protein PstS, ABC transporter ATP-binding protein, heme peroxidase, nitrate reductase, and nitrite reductase. The value of the mutual relationships between all the enzymes in Bacillus cereus indicates the synergistic mechanism under carbon scrutinization. Also, the peptides sequenced in this study identified various uncharacterized proteins and hypothetical proteins that might not be discovered for their protein functions. Further analysis is essential to uncover more lignin degradation enzymes that can work synergically for paper and pulp bioprocessing. Full article

Flavonoids are naturally occurring polyphenolic compounds known for their extensive range of biological activities. This review focuses on the inhibitory effects of flavonoids on acetylcholinesterase (AChE) and their potential as therapeutic agents for cognitive dysfunction. AChE, a serine hydrolase that plays a crucial role in cholinergic neurotransmission, is a key target in the treatment of cognitive impairments due to its function in acetylcholine hydrolysis. Natural polyphenolic compounds, particularly flavonoids, have demonstrated significant inhibition of AChE, positioning them as promising alternatives or adjuncts in neuropharmacology. This study specifically examines flavonoids such as quercetin, apigenin, kaempferol, and naringenin, investigating their inhibitory efficacy, binding mechanisms, and additional neuroprotective properties, including their antioxidant and anti-inflammatory effects. In vitro, in vivo, and in silico analyses reveal that these flavonoids effectively interact with both the active and peripheral anionic sites of AChE, resulting in increased acetylcholine levels and the stabilization of cholinergic signaling. Their mechanisms of action extend beyond mere enzymatic inhibition, as they also exhibit antioxidant and anti-amyloidogenic properties, thereby offering a multifaceted approach to neuroprotection. Given these findings, flavonoids hold considerable therapeutic potential as modulators of AChE, with implications for enhancing cognitive function and treating neurodegenerative diseases. Future studies should prioritize the enhancement of flavonoid bioavailability, evaluate their efficacy in clinical settings, and explore their potential synergistic effects when combined with established therapies to fully harness their potential as neurotherapeutic agents. Full article

Subtilisin-like proteins are serine proteases that use two types of catalytic triads: Ser-His-Asp and Ser-Glu-Asp. Here, we investigate the two known families of subtilisin-like proteins, the subtilases (Ser-His-Asp triad) and the serine-carboxyl proteinases (Ser-Glu-Asp triad), and describe the local structural arrangements (cores) that govern the catalytic residues in these proteins. We show the separation of the cores into conserved structural zones, which can be repeatedly found in different structures, and compare the structural cores in subtilisin-like proteins with those in trypsin-like serine proteases and alpha/beta-hydrolases. Full article

(1) Background: Weaning is a challenging and stressful event in the pig’s life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student’s t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses—350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages. Full article

The ability of Mycobacterium tuberculosis to derive lipids from the host, store them intracellularly, and then break them down into energy requires a battery of serine hydrolases. Serine hydrolases are a large, diverse enzyme family with functional roles in dormant, active, and reactivating mycobacterial cultures. To rapidly measure substrate-dependent shifts in mycobacterial serine hydrolase activity, we combined a robust mycobacterial growth system of nitrogen limitation and variable carbon availability with nimble in-gel fluorogenic enzyme measurements. Using this methodology, we rapidly analyzed a range of ester substrates, identified multiple hydrolases concurrently, observed functional enzyme shifts, and measured global substrate preferences. Within every growth condition, mycobacterial hydrolases displayed the full, dynamic range of upregulated, downregulated, and constitutively active hydrolases independent of the ester substrate. Increasing the alkyl chain length of the ester substrate also allowed visualization of distinct hydrolase activity likely corresponding with lipases most responsible for lipid breakdown. The most robust expression of hydrolase activity was observed under the highest stress growth conditions, reflecting the induction of multiple metabolic pathways scavenging for energy to survive under this high stress. The unique hydrolases present under these high-stress conditions could represent novel drug targets for combination treatment with current front-line therapeutics. Combining diverse fluorogenic esters with in-gel activity measurements provides a rapid, customizable, and sensitive detection method for mycobacterial serine hydrolase activity. Full article

Naja nivea (N. nivea) is classed as a category one snake by the World Health Organization since its envenomation causes high levels of mortality and disability annually. Despite this, there has been little research into the venom composition of N. nivea, with only one full venom proteome published to date. Our current study separated N. nivea venom using size exclusion chromatography before utilizing a traditional bottom-up proteomics approach to unravel the composition of the venom proteome. As expected by its clinical presentation, N. nivea venom was found to consist mainly of neurotoxins, with three-finger toxins (3FTx), making up 76.01% of the total venom proteome. Additionally, cysteine-rich secretory proteins (CRISPs), vespryns (VESPs), cobra venom factors (CVFs), 5′-nucleotidases (5′NUCs), nerve growth factors (NGFs), phospholipase A2s (PLA₂), acetylcholinesterases (AChEs), Kunitz-type serine protease inhibitor (KUN), phosphodiesterases (PDEs), L-amino acid oxidases (LAAOs), hydrolases (HYDs), snake venom metalloproteinases (SVMPs), and snake venom serine protease (SVSP) toxins were also identified in decreasing order of abundance. Interestingly, contrary to previous reports, we find PLA₂ toxins in N. nivea venom. This highlights the importance of repeatedly profiling the venom of the same species to account for intra-species variation. Additionally, we report the first evidence of covalent protein complexes in N. nivea venom, which likely contribute to the potency of this venom. Full article

Soluble epoxide hydrolase (sEH) is an enzyme involved in the metabolism of bioactive lipid signaling molecules. sEH converts epoxyeicosatrienoic acids (EET) to virtually inactive dihydroxyeicosatrienoic acids (DHET). The first acids are “medicinal” molecules, the second increase the inflammatory infiltration of cells. Mitogen-activated protein kinases (p38 MAPKs) are key protein kinases involved in the production of inflammatory mediators, including tumor necrosis factor-α (TNF-α) and cyclooxygenase-2 (COX-2). p38 MAPK signaling plays an important role in the regulation of cellular processes, especially inflammation. The proto-oncogenic serine/threonine protein kinase Raf (c-Raf) is a major component of the mitogen-activated protein kinase (MAPK) pathway: ERK1/2 signaling. Normal cellular Raf genes can also mutate and become oncogenes, overloading the activity of MEK1/2 and ERK1/2. The development of multitarget inhibitors is a promising strategy for the treatment of socially dangerous diseases. We synthesized 1,3-disubstituted ureas and diureas containing a dichloroadamantyl moiety. The results of computational methods show that soluble epoxide hydrolase inhibitors can act on two more targets in different signaling pathways of mitogen-activated protein kinases p38 MAPK and c-Raf. The two chlorine atoms in the adamantyl moiety may provide additional Cl-π interactions in the active site of human sEH. Molecular dynamics studies have shown that the stability of ligand–protein complexes largely depends on the “spacer effect.” The compound containing a bridge between the chloroadamantyl fragment and the ureide group forms more stable ligand–protein complexes with sEH and p38 MAPK, which indicates a better conformational ability of the molecule in the active sites of these targets. In turn, a compound containing two chlorine atoms forms a more stable complex with c-Raf, probably due to the presence of additional halogen bonds of chlorine atoms with amino acid residues. Full article

Neuropathy target esterase (NTE) is a serine hydrolase with phospholipase B activity, which is involved in maintaining the homeostasis of phospholipids. It can be inhibited by aging inhibitors such as some organophosphorus (OP) compounds, which leads to delayed neurotoxicity with distal degeneration of axons. However, the detailed binding conformation of aging and non-aging inhibitors with NTE is not known. In this study, new computational models were constructed by using MODELLER 10.3 and AlphaFold2 to further investigate the inhibition mechanism of aging and non-aging compounds using molecular docking. The results show that the non-aging compounds bind the hydrophobic pocket much deeper than aging compounds and form the hydrophobic interaction with Phe1066. Therefore, the unique binding conformation of non-aging compounds may prevent the aging reaction. These important differences of the binding conformations of aging and non-aging inhibitors with NTE may help explain their different inhibition mechanism and the protection of non-aging NTE inhibitors against delayed neuropathy. Full article

Traumatic brain injury (TBI) affects millions of people of all ages around the globe. TBI is notoriously hard to diagnose at the point of care, resulting in incorrect patient management, avoidable death and disability, long-term neurodegenerative complications, and increased costs. It is vital to develop timely, alternative diagnostics for TBI to assist triage and clinical decision-making, complementary to current techniques such as neuroimaging and cognitive assessment. These could deliver rapid, quantitative TBI detection, by obtaining information on biochemical changes from patient’s biofluids. If available, this would reduce mis-triage, save healthcare providers costs (both over- and under-triage are expensive) and improve outcomes by guiding early management. Herein, we utilize Raman spectroscopy-based detection to profile a panel of 18 raw (human, animal, and synthetically derived) TBI-indicative biomarkers (N-acetyl-aspartic acid (NAA), Ganglioside, Glutathione (GSH), Neuron Specific Enolase (NSE), Glial Fibrillary Acidic Protein (GFAP), Ubiquitin C-terminal Hydrolase L1 (UCHL1), Cholesterol, D-Serine, Sphingomyelin, Sulfatides, Cardiolipin, Interleukin-6 (IL-6), S100B, Galactocerebroside, Beta-D-(+)-Glucose, Myo-Inositol, Interleukin-18 (IL-18), Neurofilament Light Chain (NFL)) and their aqueous solution. The subsequently derived unique spectral reference library, exploiting four excitation lasers of 514, 633, 785, and 830 nm, will aid the development of rapid, non-destructive, and label-free spectroscopy-based neuro-diagnostic technologies. These biomolecules, released during cellular damage, provide additional means of diagnosing TBI and assessing the severity of injury. The spectroscopic temporal profiles of the studied biofluid neuro-markers are classed according to their acute, sub-acute, and chronic temporal injury phases and we have further generated detailed peak assignment tables for each brain-specific biomolecule within each injury phase. The intensity ratios of significant peaks, yielding the combined unique spectroscopic barcode for each brain-injury marker, are compared to assess variance between lasers, with the smallest variance found for UCHL1 (σ² = 0.000164) and the highest for sulfatide (σ² = 0.158). Overall, this work paves the way for defining and setting the most appropriate diagnostic time window for detection following brain injury. Further rapid and specific detection of these biomarkers, from easily accessible biofluids, would not only enable the triage of TBI, predict outcomes, indicate the progress of recovery, and save healthcare providers costs, but also cement the potential of Raman-based spectroscopy as a powerful tool for neurodiagnostics. Full article

Camellia oleifera (C. oleifera), one of the world’s four major edible woody oil crops, has been widely planted in southern China’s subtropical region for the extremely high nutritional and health benefits of its seed oil. Timing and synchronization of fruit dehiscence are critical factors influencing the oil output and quality, as well as the efficiency and cost of harvesting C. oleifera, yet they extremely lack attention. To gain an understanding of the molecular basis underlying the dehiscence of C. oleifera fruit, we sampled pericarp–replum tissues containing dehiscence zones from fruits at different developmental stages and performed time-series transcriptomic sequencing and analysis for the first time. Statistical and GO enrichment analysis of differentially expressed genes revealed that drastic transcriptional changes occurred over the last short sampling interval (4 days, 18th–22nd October), which directed functional classifications link to cell wall and cell wall macromolecule activity. WGCNA further showed that factors controlling cell wall modification, including endo-1,3;1,4-beta-D-glucanase, WAT1-like protein 37, LRR receptor-like serine/threonine-protein kinase, and cellulose synthase A catalytic subunit, were identified as core members of the co-expression network of the last stage highly related modules. Furthermore, in these modules, we also noted genes that were annotated as coding for polygalacturonase and pectinesterase, two pectinases that were expected to be major players in cell separation during dehiscence. qRT-PCR further confirmed the expression profiles of these cell wall modification relating factors, which possessed a special high transcriptional abundance at the final stage. These results suggested the cell wall associated cell separation, one of the essential processes downstream of fruit dehiscence, happened in dehiscing fruit of C. oleifera during ripening. Hydrolases acting on cell wall components are good candidates for signal mediating dehiscence of C. oleifera fruit. In conclusion, our analysis provided insights into the cell wall macromolecule-mediated fruit dehiscence during ripening in C. oleifera. Full article