Role In Biosynthesis Research Articles

Genome-wide identification of the phenylalanine ammonia-lyase gene from Epimedium Pubescens Maxim. (Berberidaceae): novel insight into the evolution of the PAL gene family

BackgroundPhenylalanine ammonia-lyase (PAL) serves as a key gateway enzyme, bridging primary metabolism and the phenylpropanoid pathway, and thus playing an indispensable role in flavonoid, anthocyanin and lignin biosynthesis. PAL gene families have been extensively studied across species using public genomes. However, a comprehensive exploration of PAL genes in Epimedium species, especially those involved in prenylated flavonol glycoside, anthocyanin, or lignin biosynthesis, is still lacking. Moreover, an in-depth investigation into PAL gene family evolution is warranted.ResultsSeven PAL genes (EpPAL1-EpPAL7) were identified. EpPAL2 and EpPAL3 exhibit low sequence identity to other EpPALs (ranging from 61.09 to 64.38%) and contain two unique introns, indicating distinct evolutionary origins. They evolve at a rate ~ 10 to ~ 54 times slower compared to EpPAL1 and EpPAL4-7, suggesting strong purifying selection. EpPAL1 evolved independently and is another ancestral gene. EpPAL1 formed EpPAL4 through segmental duplication, which lead to EpPAL5 and EpPAL6 through tandem duplications, and EpPAL7 through transposed duplication, shaping modern EpPALs. Correlation analysis suggests EpPAL1, EpPAL2 and EpPAL3 play important roles in prenylated flavonol glycosides biosynthesis, with EpPAL2 and EpPAL3 strongly correlated with both Epimedin C and total prenylated flavonol glycosides. EpPAL1, EpPAL2 and EpPAL3 may play a role in anthocyanin biosynthesis in leaves. EpPAL2, EpPAL3, EpPAL6, and EpPAL7 might be engaged in anthocyanin production in petals, and EpPAL2 and EpPAL3 might also contribute to anthocyanin synthesis in sepals. Further experiments are needed to confirm these hypotheses. Novel insights into the evolution of PAL gene family suggest that it might have evolved from a monophyletic group in bryophytes to large-scale sequence differentiation in gymnosperms, basal angiosperms, and Magnoliidae. Ancestral gene duplications and vertical inheritance from gymnosperms to angiosperms likely occurred during PAL evolution. Most early-diverging eudicotyledons and monocotyledons have distinct histories, while modern angiosperm PAL gene families share similar patterns and lack distant gene types.ConclusionsEpPAL2 and EpPAL3 may play crucial roles in biosynthesis of prenylated flavonol glycosides and anthocyanins in leaves and flowers. This study provides novel insights into PAL gene family evolution. The findings on PAL genes in E. pubescens will aid in synthetic biology research on prenylated flavonol glycosides production.

An integrative metabolomics and metagenomics analysis of functional microbiota examines the extraction of bioactive products using longan pericarp

Longan (Dimocarpus longan Lour.) is a nutrient-rich fruit, widely cultivated in China. However, its seeds and pericarp, often discarded as waste, are rich in bioactive components, particularly polyphenolics. In this research, we develop microbiota-assisted extraction technique, which is efficient and environmentally friendly for extracting these valuable components. These results showcased superior efficiency in the diversity and richness of extracted bioactive components, although yielding slightly lower TP content than ethanol extraction. The active components extracted by microbiota-assisted extraction technique increased to 2.45 mg/g, which was higher 2.13 times and 3.10 times compared to optimized ethanol and water extraction, respectively. The numbers of active components extracted by these three methods were 39, 24 and 30, separately, and Quercetin 3-D-xyloside and Kaempferol 3-O-alpha-L-rhamnopyranosyl were identified in longan pericarp extracts by microbiota-assisted extraction. Metagenomics analysis revealed stable and diverse microbiota with functional capabilities for enhancing extraction efficiency. Functional annotations indicated significant roles in biosynthesis, carbohydrate degradation, and fatty acid metabolism. Microbiota-assisted extracts exhibited a broad spectrum of bioactive compounds with potential health benefits, including antioxidant and anti-inflammatory properties. These results provide a theoretical foundation for developing sustainable extraction technologies.

Role of Biosynthesis and Catabolism of Neurotransmitters in Drug Discovery for Anxiety and Depression.

The purpose of this review is to correlate the probable causes of anxiety disorders with the imbalance of neurotransmitters in the brain and also highlight the drugs for these mental disorders that have been discovered based on the biosynthesis and catabolism of these brain chemicals. Peer-reviewed journal's articles, news and books published in English between 1997 and 2023 describing the role of neurotransmitters in anxiety disorders were searched in Google Scholar, Research Gate and PubMed databases. The contents were carefully analyzed by the authors and understood and compiled to build a concise perspective on the role of biosynthesis and catabolism of neurotransmitters in anxiety and depression. Anxiety disorders are reported to be common patterns of psychological symptoms that impact multiple areas of life. Anxiety and depression are prevalent worldwide and are significantly contributing towards the global health burden. Genetic determinants are believed to play an important role in these disorders. According to modern medicine, one of the most important aspects that is known to be crucial for these disorders is the imbalance of neurotransmitters in the brain. The biosynthesis and catabolism of neurotransmitters have been extensively targeted for innovative drug discovery approaches at various steps that have led to the discovery of many drugs for these psychological disorders. The biosynthetic and catabolic reaction cycles of neurotransmitters and the discovery of drugs based on these hypotheses are discussed. To the best of the authors' knowledge, this review compiles already known descriptive knowledge on "relation of neurotransmitter imbalance with anxiety disorders" in a precise way that will provide readers with an overview of the vast literature.

Three Arabidopsis UMP kinases have different roles in pyrimidine nucleotide biosynthesis and (deoxy)CMP salvage.

Pyrimidine nucleotide monophosphate biosynthesis ends in the cytosol with uridine monophosphate (UMP). UMP phosphorylation to uridine diphosphate (UDP) by UMP KINASEs (UMKs) is required for the generation of all pyrimidine (deoxy)nucleoside triphosphates as building blocks for nucleic acids and central metabolites like UDP-glucose. The Arabidopsis (Arabidopsis thaliana) genome encodes five UMKs and three belong to the AMP KINASE (AMK)-like UMKs, which were characterized to elucidate their contribution to pyrimidine metabolism. Mitochondrial UMK2 and cytosolic UMK3 are evolutionarily conserved, whereas cytosolic UMK1 is specific to the Brassicaceae. In vitro, all UMKs can phosphorylate UMP, cytidine monophosphate (CMP) and deoxycytidine monophosphate (dCMP), but with different efficiencies. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-induced null mutants were generated for UMK1 and UMK2, but not for UMK3, since frameshift alleles were lethal for germline cells. However, a mutant with diminished UMK3 activity showing reduced growth was obtained. Metabolome analyses of germinating seeds and adult plants of single- and higher-order mutants revealed that UMK3 plays an indispensable role in the biosynthesis of all pyrimidine (deoxy)nucleotides and UDP-sugars, while UMK2 is important for dCMP recycling that contributes to mitochondrial DNA stability. UMK1 is primarily involved in CMP recycling. We discuss the specific roles of these UMKs referring also to the regulation of pyrimidine nucleoside triphosphate synthesis.

Characterization and Functional Analysis of PmCMK: A Gene Involved in Terpenoid Synthesis in Pinus massoniana

In Pinus massoniana, the methyl-D-erythritol-4-phosphate (MEP) pathway plays a crucial role in the biosynthesis of terpenoids. The fourth step of this pathway is specifically regulated by 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase (CMK). In this study, PmCMK (MW892445.1) was isolated. As a member of the GHMP kinase family, PmCMK exhibits homology with CMK genes across diverse species. The examination of relative expression patterns revealed that PmCMK exhibited higher expression levels in tissues of P. massoniana that are rich in resin. We successfully cloned the PmCMK promoter (1654 bp) and integrated it into a GUS reporter vector. This construct was then transformed into the leaves of tobacco (Nicotiana × sanderae) to assess transient expression patterns. The results demonstrated that the promoter was active not only in the roots, leaves, and stems of the tobacco plants but also exhibited varying expression levels in response to treatments with IAA, SA, MeJA, and PEG6000. This suggested that PmCMK expression was modulated by a variety of signals. It revealed that the expression of PmCMK was affected by different treatments. Further allogeneic expression studies showed that tobacco overexpressing PmCMK exhibited increased levels of chlorophyll and carotene compared to the wild type. This enhancement in content indicates that PmCMK has a significant role in isoprene biosynthesis. These findings provide valuable insights for future research aimed at elucidating the biosynthetic pathways of terpenoids and developing breeding strategies to enhance resin production in P. massoniana.

Glycosyltransferases: Unraveling Molecular Insights and Biotechnological Implications

Glycosyltransferases (GTs) are present in almost all living organisms; plants, animals and microorganisms. GTs transfer sugar molecule from nucleotide sugars to a wide range of molecules including hormones, secondary metabolites, biotic and abiotic chemicals. When glycosyltransferases add a sugar moiety in any molecule, the hydrophilicity of that molecule changes and thus alter the chemical properties of the molecule. This phenomenon is vital for appropriate working of living organisms. For the first time, X-ray structure of bacteriophage T4-glucosyltransferase was reported in 1994. In bacteria, GTs play essential roles in various biological processes such as cell wall biosynthesis, surface glycosylation and virulence factor production. The point mutation as well as the domain-swapping has been reported in Bacteria. The sequence change as well as the whole cells has been engineered in bacteria too. GTs play very important role in survival, growth, development, metabolism, detoxification, insecticide resistance, chitin formation, chemosensation, defense and immunity, involved in various signaling pathways, etc. In plants, glycosyltransferase enzymes play essential role in biosynthesis of cell wall components, secondary metabolites, and signaling molecules. GTs are involved in the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, leading to the formation of glycosidic bonds. GTs modify flavonoids, alkaloids and terpenoids, etc. with sugar residues and alter the solubility, stability, and bioactivity of these compounds and regulate the plant defense mechanism and interaction with insects, microorganisms and other organisms. GTs have direct impact on plant homeostasis. Site directed mutagenesis (SDM) in UGTs or GTs cause a change in substrate specificity and produce increased or total loss in the catalytic activity GTs. This kind of change demonstrated that a change in substrate specificity could cause better glycosylation and perked up anticancer activity of UGTs. GTs are also involved in glycosylaton of phytohormones and regulate their metabolism and signaling pathways. GTs are involved in the activity, stability, and transport of these hormones and influence the plant growth, development, and responses to various environmental stimuli. Four UGT families encoding 200 genes are reported in humans which regulate cell signaling, protein folding, immune response, growth and development, detoxification, metabolism and elimination of drugs, DNA methylation and histone modifications, transcriptional regulation, post-transcriptional regulation and post-translational regulation, synthesis of human blood group antigens A and B and recently GTs are also reported as linked with COVID-19-related loss of smell or taste. Various bioinformatics tools have been developed which would help analyse in silico, the structure of the GTs using any reference enzyme. The activity and the ordered structures along with various stability assays can be performed before to conduct in vitro analyses such as mutagenesis. Targeted mutagenesis have been reported through site directed mutagenesis (SDM) or domain-swapping. Standard protocols of molecular biology i.e. transformation, protein expression, extraction and purification followed by mass spectrometric analysis has been described. This molecular technique would direct future endeavours to engineer more glycosyltransferases to augment their activity with different substrates and provide a basis for more exploration of GTs as an active compound for potential anti-cancer therapeutics. Additionally, the role of GTs in medicine, food industry, pharmaceutical industry and agriculture is discussed. More research work is needed for the better understanding of the biological processes and the mechanisms of glycosyltransferases involved in cancer, tumor, drug metabolism etc. New era of engineering is awaited to engineer these GT enzymes in vitro to get them boost in industry as well as to help cure cancer and other diseases as well.

Stored alcohol and fatty acid intermediates and the biosynthesis of sex pheromone aldehyde in the moth Chloridea virescens.

In most species of moths, the female produces and releases a volatile sex pheromone from a specific gland to attract a mate. Biosynthesis of the most common type of moth sex pheromone component (Type 1) involves de novo synthesis of hexadecanoate (16:Acyl), followed by modification to various fatty acyl intermediates, then reduction to a primary alcohol, which may be acetylated or oxidized to produce an acetate ester or aldehyde, respectively. Our previous work on the moth Chloridea virescens (Noctuidae) showed that females produce 90% of the major pheromone component, (Z)-11-hexadecenal (Z11-16:Ald), via a direct and rapid route of de novo biosynthesis with highly labile intermediates, and ca. 10% from an indirect route that likely mobilizes a pre-synthesized 16-carbon skeleton, possibly, (Z)-11-hexadecenoate (Z11-16:Acyl) or hexadecanoate (16:Acyl). In this paper, we use stable isotope tracer/tracee techniques to study the dynamics of the precursor alcohol (Z)-11-hexadecenol (Z11-16:OH) and stores of Z11-16:Acyl and 16:Acyl to determine their roles in biosynthesis of Z11-16:Ald. We found: (i) that intracellular Z11-16:OH is synthesized at roughly the same rate as Z11-16:Ald, indicating that translocation and oxidation of this moiety does not rate limit biosynthesis of Z11-16:Ald, (ii) intracellular Z11-16:OH consists of two pools, a highly labile one rapidly translocated out of the cell and converted to Z11-16:Ald, and a less labile one that mostly remains in gland cells, (iii) during pheromone biosynthesis, net stores of Z11-16:Acyl increase, suggesting it is not the source of Z11-16:Ald produced by the indirect route, and (iv) no evidence for the gland synthesizing stored 16:Acyl prior to (up to 2days before eclosion), or after, synthesis of pheromone commenced, suggesting the bulk of this stored moiety is synthesized elsewhere and transported to the gland prior to gland maturation. Thus, the pheromone gland of C. virescens produces very little stored fat over its functional lifetime, being optimized to produce sex pheromone.

Class II terpene cyclases: structures, mechanisms, and engineering.

Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.

Identification of novel flavin-dependent monooxygenase from Strobilanthes Cusia reveals molecular basis of indoles’ biosynthetic logic

BackgroundStrobilanthes cusia (Nees) Kuntze is a traditional medical plant distributed widely in south China. The indole compounds that originated from the plant are responsible for its pharmacological activities. However, the reason why indole ingredients are accumulated in this herb and how it is biosynthesized has remained largely unknown.ResultsIn this study, metabolic and transcriptional profiling measurement experiments of different S. cusia organs were carried out to understand the underlying molecular basis of indoles’ biosynthetic logic. A metabolic investigation demonstrated that the indoles are primarily accumulated mainly in aerial parts, particularly in leaves. RNA-seq was employed to reveal the organ specific accumulation of indoles in different S. cusia organs. Meanwhile, a flavin-dependent monooxygenase gene (ScFMO1) was found in S. cusia, and it has capacity to produce indoxyl from indole by the fermentation assay. Finally, we assessed the outcomes of transient expression experiment in tobacco and confirmed that ScFMO1 localizes in cytoplasm.ConclusionsOur results suggest that ScFMO1 plays a key role in biosynthesis of indoles (Indigo, indirubin, indican, etc.), it will be useful for illuminating the molecular basis of the medicinal indoles’ biosynthesis and developing strategies for improving their yields.

Functional characterization of a naphthalene-O-methyltransferase from Nocardia sp. CS682

Methylation plays important roles in biosynthesis, metabolism, signal transduction, detoxification, protein sorting and repair, and nucleic acid processing. Generally the methyltransferases transfer methyl groups in various natural products using S-adenosyl methionine (SAM) as a cofactor. In this study, we examined and functionally characterized ThnM3 (enzyme), by testing various substrates with different chemical structures. Among the tested substrates, 1,8-dihydroxynaphthalene was the best substrate for methylation. Whole-cell biotransformation was performed using the enzyme in engineered Escherichia coli to produce 8-methoxynaphthalene-1-ol, and 1,8-dimethoxynaphthalene derivatives of 1,8-dihydroxynaphthalene. The products were confirmed using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopic analyses. Therefore, this study is the first to amplify, express the thnM3 (gene), and functionally characterize theThnM3, which exhibits the regioselective modifications of 1,8-dihydroxynaphthalene.

TetR and OmpR family regulators in natural product biosynthesis and resistance.

This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.

Phenolic Compounds of the Medicinal Plants in an Anthropogenically Transformed Environment.

In this article, the impact of an anthropogenically transformed environment on the content of pharmaceutically valuable biologically active compounds in medicinal plants is analyzed. The studied biologically active substances included phenolic compounds (flavonoids, anthocyanins, tannins, and phenolic acids). The number of transmissible forms of heavy metals (HMs), including cadmium, lead, and mercury, were discharged from factories that are present in the soil. Plants uptake these toxic metals from the soil. HM causes changes in the activity of the several enzymes such as phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI) and other enzymes. These enzymes play an important role in biosynthesis of phenolic compounds in medicinal plants. It has been demonstrated that plant materials possess high antioxidant potential due to their high phenolic content. As a result, the present review discusses a thorough investigation of anthropogenically transformed environment effects on the quantity of pharmaceutically valuable phenolic compounds in medicinal plants.

Overexpression of geranyl diphosphate synthase 1 (NnGGPPS1) from Nelumbo nucifera enhances carotenoid and chlorophyll content and biomass

As the traditional herb with pharmacological compounds in China, the key genes related with terpenoid biosynthesis are still unveiled in Nelumbo nucifera. Geranylgeranyl pyrophosphate synthase (GGPPS) is one of the key enzymes in terpenoids biosynthesis, synthesizing the common precursor of GGPP for downstream enzymes for generating various terpenoids. In this study, four NnGGPPS genes were isolated from N. nucifera. Sequence and phylogenetic analyses indicate that NnGGPPS1 and NnGGPPS2 belong to large subunit (LSU). Whereas NnGGPPS3 and NnGGPPS4 are classified as small subunit (SSU) of SSU Ⅱ and SSU I, respectively. Among four NnGGPPSs, only NnGGPPS1 and NnGGPPS2 can produce GGPP in bacterial pigment complementation assay. Combination analysis of subcellular localization and gene co-expression analysis (GCN) illustrates that NnGGPPS1 is the main transcript related with methylerythritol phosphate (MEP) pathway, abscisic acid (ABA) biosynthesis, carotenoid and chlorophyll biosynthesis and degradation. Overexpression of NnGGPPS1 improves the growth of transgenic tobacco, and increases carotenoids and chlorophyll contents. Moreover, NnGGPPS1 transgenic tobacco exhibits improved photosynthesis efficiency and ROS scavenging ability. The up-regulated expression of the key genes in MEP pathway, carotenoid biosynthesis and chlorophyll biosynthesis, result in the increase of metabolic flux in NnGGPPS1 transgenic lines. Furthermore, the elevated MEP-derived primary metabolites of carotenoid and chlorophyll was attributed to enhancement of plant biomass of NnGGPPS1 transgenic lines. Therefore, NnGGPPS1 plays a vital role in biosynthesis of carotenoid and chlorophyll.

Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin.

Patulin synthase (PatE) from Penicillium expansum is a flavin-dependent enzyme that catalyses the last step in the biosynthesis of the mycotoxin patulin. This secondary metabolite is often present in fruit and fruit-derived products, causing postharvest losses. The patE gene was expressed in Aspergillus niger allowing purification and characterization of PatE. Thisconfirmed that PatE is active not only on the proposed patulin precursorascladiol but also on several aromatic alcohols including 5-hydroxymethylfurfural. By elucidating its crystal structure, details on its catalytic mechanism were revealed. Several aspects of the active site architecture are reminiscent of that of fungal aryl-alcohol oxidases. Yet, PatE is most efficient with ascladiol as substrate confirming its dedicated role in biosynthesis of patulin.

Genome-wide analysis of bHLH gene family in Coptis chinensis provides insights into the regulatory role in benzylisoquinoline alkaloid biosynthesis

Coptis chinensis Franch is a perennial species with high medical value. The rhizome of C. chinensis is a traditional Chinese medicine widely used for more than 2000 years in China. Its principal active ingredients are benzylisoquinoline alkaloids (BIAs). The basic helix-loop-helix (bHLH) transcription factors play an important regulatory role in the biosynthesis of plant secondary metabolites. However, the bHLH genes in C. chinensis have not been described, and little is known about their roles in alkaloid biosynthesis. In this study, a total of 143 CcbHLH genes (CcbHLHs) were identified and unevenly distributed on nine chromosomes. Phylogenetic analysis divided the 143 CcbHLH proteins into 26 subfamilies by comparison with Arabidopsis thaliana bHLH proteins. The majority CcbHLHs in each subgroup had similar gene structures and conserved motifs. Furthermore, the physicochemical properties, conserved motif, intron/exon composition, and cis-acting elements of CcbHLHs were analyzed. Transcriptome analysis revealed that 30 CcbHLHs were significantly expressed in the rhizomes of C. chinensis. Co-expression analysis revealed that 11 CcbHLHs were highly positively correlated with contents of various alkaloids of C. chinensis. Moreover, yeast one-hybrid experiments verified that CcbHLH001 and CcbHLH0002 could interact with the promoters of berberine biosynthesis pathway genes CcBBE and CcCAS, suggesting their regulatory roles in BIA biosynthesis. This study provides comprehensive insights into the bHLH gene family in C. chinensis and will support in-depth functional characterization of CcbHLHs involved in the regulation of protoberberine-type alkaloid biosynthesis.

Acceptors and Effectors Alter Substrate Inhibition Kinetics of a Plant Glucosyltransferase NbUGT72AY1 and Its Mutants.

One of the main obstacles in biocatalysis is the substrate inhibition (SI) of enzymes that play important roles in biosynthesis and metabolic regulation in organisms. The promiscuous glycosyltransferase UGT72AY1 from Nicotiana benthamiana is strongly substrate-inhibited by hydroxycoumarins (inhibitory constant Ki < 20 µM), but only weakly inhibited when monolignols are glucosylated (Ki > 1000 µM). Apocarotenoid effectors reduce the inherent UDP-glucose glucohydrolase activity of the enzyme and attenuate the SI by scopoletin derivatives, which could also be achieved by mutations. Here, we studied the kinetic profiles of different phenols and used the substrate analog vanillin, which has shown atypical Michaelis-Menten kinetics in previous studies, to examine the effects of different ligands and mutations on the SI of NbUGT72AY1. Coumarins had no effect on enzymatic activity, whereas apocarotenoids and fatty acids strongly affected SI kinetics by increasing the inhibition constant Ki. Only the F87I mutant and a chimeric version of the enzyme showed weak SI with the substrate vanillin, but all mutants exhibited mild SI when sinapaldehyde was used as an acceptor. In contrast, stearic acid reduced the transferase activity of the mutants to varying degrees. The results not only confirm the multi-substrate functionality of NbUGT72AY1, but also reveal that the enzymatic activity of this protein can be fine-tuned by external metabolites such as apocarotenoids and fatty acids that affect SI. Since these signals are generated during plant cell destruction, NbUGT72AY1 likely plays an important role in plant defense by participating in the production of lignin in the cell wall and providing direct protection through the formation of toxic phytoalexins.

Positive regulatory role of R2R3 MYBs in terpene biosynthesis in Lilium ‘Siberia’

Terpenoids are the main components contributing to the fragrance of Lilium ‘Siberia’, and LiTPS2 plays a critical role in the biosynthesis of monoterpenoids. Although the major terpene synthases in Lilium ‘Siberia’ have been identified, how these TPS genes are transcriptionally regulated remains elusive in this distinguished flower. This study aimed to identify transcription factors that regulate the terpene synthesis in Lilium, and disclose the related underlying transcriptional regulation mechanism. In this study, we identified three R2R3-MYB TFs—LiMYB1, LiMYB305 and LiMYB330, which were involved in regulating the biosynthesis of terpenes in Lilium ‘Siberia’. Quantitative real-time PCR showed spatial and temporal expression patterns consistent with the emission patterns of terpene compounds. When LiMYB1, LiMYB305 and LiMYB330 were overexpressed in flowers, the release of some main monoterpenes, such as linalool and ocimene, as well as the expression of TPS genes, especially for LiTPS2, were enhanced. A virus-induced gene silencing (VIGS) assay showed that silencing these three LiMYBs decreased the level of monoterpenes by down-regulating the expression of the TPS genes. The yeast one-hybrid and transient expression assays indicated that all three LiMYBs could bind to and activate the promoter of LiTPS2. Moreover, the yeast two-hybrid assay verified that LiMYB1 could interact with LiMYB308 and LiMYB330, indicating their synergistic roles in the regulation of floral terpene biosynthesis. In general, these results indicated that LiMYB1, LiMYB305, and LiMYB330 might play essential roles in terpene biosynthesis in Lilium and would provide a new perspective for the transcriptional regulation of volatile terpenes in flowers.

MoaB1 Homologs Contribute to Biofilm Formation and Motility by Pseudomonas aeruginosa and Escherichia coli.

moaB homologs, encoding the molybdopterin biosynthetic protein B1, have been reported to be expressed under anoxic conditions and during biofilm growth in various microorganisms; however, little is known about MoaB's function. Here, we demonstrate that in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes. Specifically, moaB1 expression is induced in biofilms, and insertional inactivation of moaB1 reduced biofilm biomass accumulation and pyocyanin production while enhancing swarming motility, and pyoverdine abundance without affecting attachment, swimming motility, or c-di-GMP levels. Inactivation of the highly conserved E. coli homolog of moaB1, moaBEc, likewise coincided with reduced biofilm biomass accumulation. In turn, heterologous expression of moaBEc restored biofilm formation and swarming motility by the P. aeruginosa moaB1 mutant to wild-type levels. Moreover, MoaB1 was found to interact with other conserved biofilm-associated proteins, PA2184 and PA2146, as well as the sensor-kinase SagS. However, despite the interaction, MoaB1 failed to restore SagS-dependent expression of brlR encoding the transcriptional regulator BrlR, and inactivation of moaB1 or moaBEc had no effect on the antibiotic susceptibility phenotype of biofilms formed by P. aeruginosa and E. coli, respectively. While our findings did not establish a link between MoaB1 and molybdenum cofactor biosynthesis, they suggest that MoaB1 homologs contribute to biofilm-associated phenotypes across species boundaries, possibly hinting at the existence of a previously undescribed conserved biofilm pathway. IMPORTANCE Proteins contributing to the biogenesis of molybdenum cofactors have been characterized; however, the role of the molybdopterin biosynthetic protein B1 (MoaB1) has remained elusive, and solid evidence to support its role in biosynthesis of molybdenum cofactor is lacking. Here, we demonstrate that, in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes in a manner that does not support a role of MoaB1 in the biosynthesis of molybdenum cofactors.

Regioselectivity of the Thunbergia alata Δ6-16:0-acyl carrier protein desaturase by molecular dynamics.

The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty-acyl ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of mono-unsaturated fatty acids in plants. The archetype of this group is the Δ9-18:0-ACP desaturase that introduces a cis double bond between carbons 9 and 10 to produce oleoyl-ACP. Several variants expressing distinct regioselectivity have been described including a Δ6-16:0-ACP desaturase from black-eyed Susan vine (Thunbergia alata). ACPs are central proteins in the fatty acid biosynthesis that deliver the substrate to the desaturase. They have been reported to show a varying degree of local dynamics and structural variability depending on the substrate length. It has been suggested that the substrate specific change in structure and dynamics is crucial for the decreasing enzymatic activity in the case of the Δ9-Desaturase for chains length shorter than 18. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position carbons 6 and 7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ6 desaturase to Δ9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

Anthrol reductases: discovery, role in biosynthesis and applications in natural product syntheses.

Covering: up to 2023Short-chain dehydrogenase/reductases (SDR) are known to catalyze the regio- and stereoselective reduction of a variety of substrate types. Investigations of the deoxygenation of emodin to chrysophanol has led to the discovery of the anthrol reductase activity of an SDR, MdpC involved in monodictyphenone biosynthesis of Aspergillus nidulans and provided access to (R)-dihydroanthracenone, a putative biosynthetic intermediate. This facilitated the identification of several MdpC-related enzymes involved in the biosynthesis of aflatoxins B1, cladofulvin, neosartorin, agnestins and bisanthraquinones. Because of their ability to catalyze the reduction of hydroanthraquinone (anthrols) using NADPH, they were named anthrol reductases. This review provides a comprehensive summary of all the anthrol reductases that have been identified and characterized in the last decade along with their role in the biosynthesis of natural products. In addition, the applications of these enzymes towards the chemoenzymatic synthesis of flavoskyrins, modified bisanthraquinones, 3-deoxy anthraquinones, chiral cycloketones and β-halohydrins have been discussed.