Search Results (962)

Gymnosperms represent an ancient lineage with diverse chemical profiles. Their terpenoids constitute a major class notable for substantial structural diversity. Terpene synthases (TPSs) are the driving force of terpene diversity. TPS-d is a gymnosperm-specific TPS subfamily, yet the evolution and functional diversity of TPS-d are still understudied. In this review, we analyze 134 functionally characterized gymnosperm TPSs to elucidate the evolutionary history and functional diversity of the predominant TPS-d subfamily. Phylogenetic analysis revealed substantial lineage-specific expansion and divergence within the TPS-d subfamily post-speciation. Crucially, we highlight the shifts in domain architecture during TPS-d evolution, providing structural evidence for the progressive attrition and eventual loss of the ancestral γ domain in TPS-d2 and TPS-d1 clades. Furthermore, we summarize the functional diversity of TPS-d enzymes in specialized metabolites, emphasizing their ecological roles in plant defense. Overall, this review provides a comprehensive overview of the evolutionary and functional landscape of the gymnosperm-specific TPS-d subfamily, serving as a valuable reference for future studies on TPSs in gymnosperms. Full article

Coprinellus comprises mushroom-forming saprotrophic fungi that colonize decomposing plant-derived substrates, yet chromosome-complete genomic resources for this genus remain limited. To resolve chromosome architecture and lineage-specific evolution in this fungal group, we generated chromosome-complete assemblies of Coprinellus xanthothrix and C. saccharinus by integrating Oxford Nanopore Technologies (ONT) long reads, DNA nanoball sequencing (DNBSEQ) short reads, Hi-C, and RNA-seq data. Each genome comprised 13 gapless chromosomes with all 26 telomeres recovered; assembly sizes were 46.92 and 54.81 Mb, with BUSCO completeness of 99.20% and 99.10%, respectively. The larger C. saccharinus genome was primarily associated with greater retroelement content, whereas functional annotation profiles and CAZyme repertoires were broadly comparable between species. Phylogenomic analyses grouped C. xanthothrix with C. radians and C. saccharinus with C. micaceus, with estimated divergence times of 54.4 and 32.8 Ma, respectively. Both divergence events occurred within the Paleogene. Gene family analyses identified lineage-specific expansions enriched in nucleotide metabolism, DNA replication and repair, glutathione metabolism, redox regulation, endocytosis, cytoskeletal organization, and cell-cycle processes. Synteny and Ks analyses further revealed chromosome-level rearrangements and lineage-specific small-scale duplication but no strong evidence of recent whole-genome duplication. Together, the temporal placement of these divergences and the associated genomic patterns raise a testable hypothesis that long-term climatic and vegetation reorganization, together with changes in plant-derived substrates and microhabitats, may have contributed to lineage establishment and ecological differentiation. However, because direct paleoecological evidence and functional validation are currently lacking, this proposed relationship should not be interpreted as causal. These chromosome-complete assemblies provide important resources for comparative genomics in Coprinellus and future experimental studies of saprotrophic adaptation. Full article

The phosphotransferase activity of the protein kinase known as the mechanistic Target of Rapamycin (mTOR) is arguably one of the most studied biochemical events in biomedical sciences because of its importance to human health and evolution. Despite progress being made in understanding the structure, biochemical characteristics, and function of the enzyme, tremendous knowledge gaps remain unfilled. Altered mTOR activity occurs in numerous neurological disorders, including those that present with seizures and neoplasms. Advances in cancer biology have identified that neuron activity is a critical driver of neoplastic growth. Here, we discuss mTOR, examples of neoplasms with altered neuron activity, and the potential utility of using mTOR inhibitors to modulate tumor-associated neurons. Full article

Resistant hypertension (RH) is a high-risk phenotype associated with increased cardiovascular and renal morbidity despite multidrug therapy. Dysregulation of the renin–angiotensin–aldosterone system (RAAS), particularly excess aldosterone activity, plays a central role in the pathophysiology of RH. Although conventional RAAS-targeted therapies including angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and mineralocorticoid receptor antagonists improve outcomes, their effectiveness is limited by aldosterone breakthrough, persistent non-genomic aldosterone effects, hyperkalaemia, and off-target adverse effects. Aldosterone synthase inhibitors (ASIs) have emerged as a novel therapeutic strategy targeting CYP11B2, the terminal enzyme responsible for aldosterone biosynthesis. This review summarises the physiological basis of aldosterone synthesis, the pathological consequences of aldosterone excess, and the pharmacological evolution of ASIs. Early-generation agents were limited by inadequate selectivity between CYP11B2 and the closely related CYP11B1 enzyme, resulting in cortisol suppression and deoxycorticosterone accumulation. Advances in structural biology and medicinal chemistry enabled the development of second-generation ASIs with markedly improved selectivity and preserved cortisol biosynthesis. Recent clinical trials of baxdrostat, lorundrostat, vicadrostat, and dexfadrostat have demonstrated clinically meaningful reductions in blood pressure and albuminuria with acceptable safety profiles. Based on the positive trial data, baxdrostat has become the first in class ASI to be approved by regulatory authorities for management of uncontrolled hypertension. Full article

It has been suggested that hypoxia-inducible factor 1α (HIF1α) serves as a key regulatory factor in insect metabolism remodelling under hypoxia, in which lipid metabolism appears to play an important role. However, the underlying mechanism remains incompletely understood. In this paper, the function of HIF1α in regulating lipid metabolism under hypoxia in Callosobruchus chinensis (Coleoptera: Bruchidae), a typical stored-product insect, was investigated. Based on the amplification and cloning, the sequence of the CcHIF1α gene was analysed and found to be highly conserved throughout evolution. Then HIF1α expression in the adult C. chinensis was knocked down using RNA interference (RNAi) via feeding methods. After HIF1α knockdown, insects under hypoxic conditions exhibited higher mortality, along with decreased activities of four typical antioxidant enzymes (CAT, POD, GST, and SOD) and increased levels of two peroxide products (ROS and LPO), compared to those of the control. Moreover, comprehensive lipidomic analysis using UHPLC-QE–MS/MS revealed that lipid metabolism was reprogrammed, with significant changes in the levels of lipids such as SM, LPC, PI, SQDG, MAG, PE, ACar, and TAG. In particular, the increase in ceramide (Cer) or Cer-related lipids was observed to be associated with the production of peroxides. ELISA assays further verified the effect of HIF1α on changes in these characteristic lipids, such as the increase in PA and Cer and a decrease in TAG, PC and SM. Correspondingly, the expressions of the key genes (i.e., SPTLC₁, KDSR, SMPD₃, SGPL₁, DGAT) involved in sphingolipid metabolism changed following HIF1α knockdown. These results are consistent with the possibility that HIF1α-mediated regulation of lipid metabolism may be important for insects facing hypoxic environments, and these findings could provide an in-depth understanding of insect hypoxia adaptation, thereby potentially contributing to the development of innovative pest management strategies. Full article

Tropane alkaloids (TA) constitute a class of plant specialized metabolites with important pharmaceutical applications, including the anticholinergic agents hyoscyamine and scopolamine and the local anesthetic cocaine. Over the past decade, advances in genomics, structural biology, and synthetic biology have substantially revised our understanding of TA biosynthesis, leading to the identification of numerous key biosynthetic enzymes and evolutionary mechanisms. This review comprehensively summarizes current knowledge of TA biosynthesis from precursor formation to structurally diverse end products. We describe the pathway from putrescine to tropinone, the stereoselective metabolic branching mediated by Tropinone Reductases, and the downstream biosynthesis of medicinal tropane alkaloids, calystegines, and cocaine. Particular emphasis is placed on recent discoveries concerning catalytic mechanisms, structural determinants of substrate specificity, metabolic compartmentalization, and the convergent evolution of TA biosynthesis in Solanaceae and Erythroxylaceae. We further integrate advances in genomics, evolutionary biology, and metabolic engineering to highlight emerging strategies for microbial production and pathway redesign. By providing a comprehensive synthesis of recent progress and critical perspectives on unresolved questions, this review offers an updated framework for understanding TA biosynthesis and supports future research in plant specialized metabolism, synthetic biology, and natural product engineering. Full article

Alkaloid biosynthesis is a central topic in plant specialized metabolism because many alkaloids have ecological, pharmacological, and biotechnological relevance. Isoquinoline alkaloids (IAs) and Amaryllidaceae alkaloids (AAs) are both connected to aromatic amino acid metabolism, but they differ in taxonomic distribution, scaffold-forming chemistry, pathway resolution, and biotechnological development. This review compares the historical and methodological trajectories that have shaped IA and AA pathway elucidation, from compound isolation, radiotracer experiments, and biochemical inference to transcriptomics, metabolomics, functional enzymology, isotope-guided active-tissue identification, regulatory studies, and heterologous pathway reconstruction. In IAs, especially benzylisoquinoline alkaloids, broad genomic and transcriptomic resources have supported candidate gene discovery and functional characterization of several branches, including morphinan, protoberberine, benzophenanthridine, and aporphine-related pathways. In contrast, AA biosynthesis has advanced more recently through function-driven approaches that clarified key steps such as N4OMT-mediated 4′-O-methylation, NBS/NR-mediated norbelladine formation, CYP96T-dependent regioselective oxidative coupling, and transient reconstruction of major scaffold-forming branches. Remaining gaps include the unresolved enzymatic formation of 3,4-dihydroxybenzaldehyde in AAs and incomplete functional validation across less-studied IA scaffold classes. By integrating biochemical logic, omics-guided discovery, enzyme evolution, tissue specificity, regulation, and synthetic biology, this review identifies priorities for future alkaloid pathway discovery and sustainable production. Full article

Plant cell walls play a crucial role in plant development and evolution. This structure is primarily composed of proteins and polysaccharides, including cellulose, hemicellulose, and pectins. Homogalacturonan (HG), the most abundant pectin in the primary cell wall, is synthesized by α -1,4-D-GALACTURONOSYLTRANSFERASE (GAUT) enzymes, methylesterified, and subsequently secreted into the apoplast. The dynamics of pectin methylesterification is regulated by enzymes such as PECTIN METHYLESTERASES (PMEs) and PECTIN METHYLESTERASE INHIBITORS (PMEIs). Across plant evolution and development, different cell types display distinct domains of pectin methylesterification. The binding of de-methylesterified pectins to the Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) proteins and RAPID ALKALINIZATION FACTOR (RALF) peptides is involved in pectin signaling and cell wall integrity maintenance during developmental processes. While phylogenetic studies highlight molecular innovations in pectin metabolism, functional studies remain scarce outside of angiosperms. Furthermore, the explicit role of de-methylesterified pectin in coupling cell wall structure to intracellular signaling has only been demonstrated in angiosperms. Comparative functional studies addressing key evolutionary transitions will ultimately reveal how pectin metabolism has contributed to morphological innovations across plant evolution. Full article

Cuticular wax is a critical component of the plant cuticle, playing an indispensable role in plant growth, development, and defense against environmental stresses. ECERIFERUM3 (CER3), a very-long-chain fatty acyl-CoA reductase, serves as a pivotal hub channeling carbon resources into the alkane- and alcohol-forming pathways respectively. Here, we systematically characterized the protein structural features and evolutionary patterns of CER3. We also comprehensively reviewed the multiple regulatory mechanisms governing CER3, encompassing transcriptional, post-transcriptional, translational, and epigenetic modifications, with particular emphasis on the definitive finding that CER3 modulates cuticular wax biosynthetic flux by assembling distinct protein complexes. Finally, existing knowledge gaps and future research directions are also discussed. Full article

Melatonin is an important stress-protective agent in plant growth. Methyltransferase (ASMT) is an important enzyme in the concluding phase of melatonin production in plants. In this study, we performed the genome-wide identification and functional investigation of the ASMT gene family in hexaploid wheat and 14 other plants. ASMT genes in 15 plants were identified by using HMM scanning against the proteomes derived from a single representative reference genome for each species. They were classified into three subfamilies I-III by constructing four types of phylogenetic trees (Neighbour-joining with p-distance model, Neighbour-joining with JTT model, Maximum likelihood, and Bayesian inference). Based on exon–intron structure and domain diagrams, a conserved structural pattern characterized by successive intron phases 1 and 0 (the “1-0” pattern) was found in ASMT genes during evolution. Collinear events analysis indicated that polyploidization and tandem duplication synergistically promote the expansion of T. aestivum ASMT members. Cis-acting element analysis revealed that numerous stress- and hormone-responsive motifs (such as ABRE and LTR) were present in ASMTs of wheat, suggesting a role for ASMTs in adaptive signal transduction. Transcriptome analysis revealed that specific T. aestivum ASMT genes were strongly responsive to stress; for instance, II_TraesCS2B02G041200 and II_TraesCS2B02G606200 were strongly upregulated under drought and salt stress, respectively. To independently confirm the stress responsiveness of these candidates in a different genetic background, we performed quantitative real-time PCR (qRT-PCR) on selected genes under drought and salt treatments. The result showed that the expression trends of transcriptome and qRT-PCR were almost the same, identifying these ASMT genes as strong stress-responsive candidates under drought and salt treatments. In this study, we performed identification, classification, evolution analysis and expression pattern analysis of ASMTs in wheat and 14 other plants. Our study will provide a framework for the targeted genetic improvement of melatonin-mediated stress resistance. Full article

The long-term accumulation of polyethylene terephthalate (PET) in marine environments may drive the evolution of microbial degradation capabilities, positioning the ocean as a valuable reservoir for discovering novel PET-degrading microorganisms. In this study, we isolated 305 marine-derived microorganisms with potential PET-degrading capability from samples collected from mangrove areas of Zhanjiang and the intertidal zones of Daya Bay, Shenzhen, China, using PET powder as a major carbon source. Subsequent evaluation of degradation performance via scanning electron microscopy and Fourier-transform infrared spectroscopy analysis identified 14 isolates capable of degrading PET film. These 14 strains belonged to 14 distinct species, none of which, to the best of our knowledge, has been previously documented as PET degraders. Among them, Microbacterium aurum SCSIO 85700 exhibited the most potent PET-degrading activity, achieving a weight loss of 2.1 mg (2.1%) and a 6.5% increase in relative crystallinity over 30 days. Genome analysis revealed the genetic basis underlying PET degradation and associated metabolic pathways in strain SCSIO 85700. Notably, genome mining and structural modeling identified two candidate polyester hydrolases, MA2267 and MA2443, possessing conserved His–Asp–Ser catalytic triads and exposed substrate-binding clefts resembling those of characterized PET-degrading enzymes, suggesting their potential involvement in PET depolymerization. Collectively, this study expands the recognized diversity of marine PET-degrading microorganisms and provides microbial resources for sustainable PET bioremediation. Full article

Tremella sanguinea is a morphologically distinctive gelatinous mycoparasite of Stereum within Tremellales whose generic placement has remained unresolved for lack of high-quality genomic resources. We combined Oxford Nanopore long-read sequencing, short-read whole-genome sequencing and Hi-C chromatin conformation capture to assemble the first telomere-to-telomere (T2T) genome of this species: 21.44 Mb in nine gap-free chromosomes, with telomeric repeats recovered at all 18 chromosome ends. Phylogenomic analysis of nine Tremellales genomes, including the type species of Phaeotremella, placed T. sanguinea within Phaeotremella as sister to P. skinneri (divergence 24.50 Ma; 95% HPD 22.14–26.89) rather than within Tremella sensu stricto, corroborating at genome scale a placement previously indicated by multi-locus data, providing the first divergence-time estimates for the lineage, and reconciling its position with its dark, foliose basidiocarp morphology. Gene family evolution was contraction-biased, most strongly at the Phaeotremella crown node (92 expansions vs. 855 contractions). The carbohydrate-active enzyme repertoire of T. sanguinea (185 genes) fell within the range reported for Tremellales, whereas families that expanded on its branch were significantly enriched for transport functions, including dipeptide and allantoate transport. These results indicate that T. sanguinea acquires host-derived nutrients through uptake of small molecules rather than through an expanded hydrolytic repertoire, and provide genomic evidence for revising its generic placement within the segregate genera of Tremella sensu lato. Full article

DNA polymerases are crucial for the replication and repair of genetic material. Advances in recombinant DNA technology and protein engineering have enabled the production of enzymes with specific catalytic properties tailored to the requirements of molecular diagnostics, next-generation sequencing, and synthetic biology. This review discusses the classification and structural–functional organization of DNA polymerases, with an emphasis on the thermostable members of Families A and B, which are of great practical importance. The main systems for heterologous expression and methods for purifying recombinant polymerases are summarized. Molecular engineering approaches, including rational design, site-directed mutagenesis, directed evolution, and domain engineering, are also discussed, highlighting how enzymes with improved synthesis fidelity, processivity, inhibitor resistance, and broadened substrate specificity are created. Technologies for developing hot-start polymerases along with the creation of chimeric and multifunctional polymerases are reviewed. Information on commercial polymerases utilized in scientific research and molecular diagnostics is also provided. Furthermore, the current applications of recombinant DNA polymerases in conventional, quantitative, and digital PCR; isothermal amplification; sequencing; synthetic biology; and molecular diagnosis of infectious and hereditary diseases are summarized. Finally, we discuss how the integration of structural biology, computational modeling, and high-throughput screening creates new prospects for engineering next-generation specialized enzymes. Full article

The calcium ion-transporting ATPase (Ca²⁺-ATPase) gene family maintains plant intracellular Ca²⁺ homeostasis and regulates growth, development and stress immunity; however, its functions remain poorly characterized in Malus domestica. Here, we performed a genome-wide identification of apple Ca²⁺-ATPase genes and obtained 45 members, which were classified into MdACA (39) and MdECA (6) subfamilies and unevenly distributed on 14 chromosomes. Phylogenetic analysis of Ca²⁺-ATPase genes from Malus domestica, Arabidopsis thaliana, and Oryza sativa classified these proteins into five subgroups. The ACA and ECA subfamilies were highly conserved across species, whereas Group D was apple-specific. Collinearity and Ka/Ks analyses indicated that segmental duplication and purifying selection dominated the evolution of apple Ca²⁺-ATPase genes. Promoter cis-element prediction uncovered numerous regulatory elements related to phytohormone signaling, growth, development and stress defense. Codon usage bias analysis indicated that AUG (methionine) was the dominant codon. Tissue expression profiles showed differential expression of apple Ca²⁺-ATPase genes in various organs. Quantitative real-time PCR (qRT-PCR) assays demonstrated widespread responses of Ca²⁺-ATPase genes to Alternaria alternata infection, exogenous CaCl₂, salicylic acid (SA) and methyl jasmonate (MeJA), among which MdACA39 was strongly induced under all treatments. Subcellular localization verified that MdACA39 resides on the plasma membrane. Moreover, transient overexpression of MdACA39 significantly enhanced apple resistance to A. alternata, likely due to the activation of SA, MeJA and Ca²⁺ signaling-mediated immune pathways, the induction of disease resistance-related genes, and elevated antioxidant enzyme activity. Collectively, this study systematically characterizes the apple Ca²⁺-ATPase family and identifies MdACA39 as a key regulator of fungal resistance, providing valuable gene resources for dissecting Ca²⁺ signaling-mediated disease resistance in apple. Full article

The accumulation and persistence of plastic waste have made microbial plastic biodegradation an important topic in pollution control, environmental remediation, and sustainable materials management. This study combines a mini-review with bibliometric analysis to link mechanistic understanding with global research trends in microbial plastic biodegradation from 2000 to 2025. The mini-review summarizes polymer weathering and fragmentation, microbial colonization and biofilm formation, extracellular depolymerization or oxidative chain cleavage, uptake and intracellular catabolism of plastic-derived intermediates, physiological regulation, ecological interactions, and potential applications in bioremediation and upcycling. Bibliographic records were retrieved from the Web of Science Core Collection and analyzed using bibliometrix, VOSviewer, CiteSpace, and SCImago Graphica. A total of 2959 publications were identified. Publication output increased markedly, especially after 2018, reaching 617 publications in 2025; cumulative citations reached 31,373. China, India, and the United States were the leading contributors. Journal and keyword analyses showed strong links among environmental science, polymer science, microbiology, biotechnology, and engineering. Highly cited publications mainly focused on plastic biodegradability, biodegradable polymers, engineered PET depolymerization, polyethylene degradation, and microbial or enzymatic degradation mechanisms. Keyword evolution revealed a shift from material-oriented topics, including polymer blends, poly(vinyl alcohol), polyesters, morphology, mechanical properties, composites, and polyhydroxyalkanoates, toward degrading enzymes, cutinase-like enzymes, plastic-degrading strains, microbial colonization, fungi, and marine environmental degradation. Overall, microbial plastic biodegradation has evolved from material-centered biodegradability evaluation toward a mechanism-oriented and environment-oriented interdisciplinary field. Full article