Comprehensive transcriptome and WGCNA analysis reveals the potential function of anthocyanins in low-temperature resistance of a red flower mutant tobacco.

The anthocyanin is a protective substance in various plants, and plays important roles in resisting to low-temperature. Here, we explored transcriptome analysis of pink flower (as CK) and the natural mutant red flower (as research objects) under low-temperature conditions, and aimed to reveal the potential functions of anthocyanins and anthocyanin-related regulatory factors in resistance to low-temperature. Our results showed that most of the differentially expressed genes (DEGs) encoding key enzymes in the late stage of anthocyanin metabolism in the mutant were significantly up-regulated. Meanwhile, several genes significantly differentially expressed in CK or mutant were obtained by classification and analysis of transcription factors (TFs), phytohormones and osmoregulators. Additionally, WGCNA was carried out to mine hub genes resistanted to low-temperature stress in flavonoid pathway. Finally, one UFGT family gene, three MYB and one bHLH were obtained as the future hub genes of this study. Combined with the above information, we concluded that the ability of the red flower mutant to grow and develop normally at low-temperatures was the result of a combination of flavonoids and cold resistance genes.

PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco.

The phytochrome-interacting factors (PIFs) function crucially in multiple physiological processes, but the biological functions of some PIFs remain elusive in some species. Here, a PIF transcription factor NtPIF1 was cloned and characterized in tobacco (Nicotiana tabacum L.). The transcript of NtPIF1 was significantly induced by drought stress treatments, and it localized in the nuclear. Knockout of NtPIF1 by CRISPR/Cas9 system led to the improved drought tolerance of tobacco with increased osmotic adjustment, antioxidant activity, photosynthetic efficiency and decreased water loss rate. On the contrary, NtPIF1-overexpression plants displays drought-sensitive phenotypes. In addition, NtPIF1 reduced the biosynthesis of abscisic acid (ABA) and its upstream carotenoids by regulating the expression of genes involved in ABA and carotenoids biosynthetic pathway upon drought stress. Electrophoretic mobility shift and dual-luciferase assays illustrated that, NtPIF1 directly bind to the E-box elements within the promoters of NtNCED3, NtABI5, NtZDS and Ntß-LCY to repress their transcription. Overall, these data suggested that NtPIF1 negatively regulate tobacco adaptive response to drought stress and carotenoids biosynthesis; moreover, NtPIF1 has the potential to develop drought-tolerant tobacco plants using CRISPR/Cas9 system.

Genome-wide analysis of UDP-glycosyltransferases family and identification of UGT genes involved in abiotic stress and flavonol biosynthesis in Nicotiana tabacum.

BACKGROUND: Uridine disphosphate (UDP) glycosyltransferases (UGTs) act upon a huge variety of highly diverse and complex substrates, such as phytohormones and specialized metabolites, to regulate plant growth, development, disease resistance, and environmental interactions. However, a comprehensive investigation of UGT genes in tobacco has not been conducted. RESULTS: In this study, we carried out a genome-wide analysis of family-1 UDP glycosyltransferases in Nicotiana tabacum. We predicted 276 NtUGT genes, which were classified into 18 major phylogenetic subgroups. The NtUGT genes were invariably distributed among all the 24 chromosomes with structural diversity in exon/intron structure, conserved motifs, and cis-acting elements of promoters. Three groups of proteins which involved in flavonoid biosynthesis, plant growth and development, transportation and modification were identified that interact with NtUGT proteins using the PPI analysis. Expression analysis of NtUGT genes in cold stress, drought stress and different flower color using both online RNA-Seq data and the realtime PCR analysis, suggested the distinct role of NtUGT genes in resistance of cold, drought and in flavonoid biosynthesis. The enzymatic activities of seven NtUGT proteins that potentially involved in flavonoid glycosylation were analyzed, and found that all seven exhibited activity on myricetin; six (NtUGT108, NtUGT123, NtUGT141, NtUGT155, NtUGT179, and NtUGT195) showed activity on cyanidin; and three (NtUGT108, NtUGT195, and NtUGT217) were active on the flavonol aglycones kaempferol and quercetin, which catalyzing the substrates (myricetin, cyanidin or flavonol) to form new products. We further investigated the enzymatic products and enzymatic properties of NtUGT108, NtUGT195, and NtUGT217, suggested their diverse enzymatic activity toward flavonol, and NtUGT217 showed the highest catalyzed efficient toward quercetin. Overexpression of NtUGT217 significantly increase the content levels of the quercetin-3-O-glucoside, quercetin-3-O-rutinoside and kaempferol-3-O-rutinoside in transgenic tobacco leaves. CONCLUSION: We identified 276 UGT genes in Nicotiana tabacum. Our study uncovered valuable information about the phylogenetic structure, distribution, genomic characters, expression patterns and enzymatic activity of NtUGT genes in tobacco. We further identified three NtUGT genes involved in flavonoid biosynthesis, and overexpressed NtUGT217 to validate its function in catalyze quercetin. The results provide key candidate NtUGT genes for future breeding of cold and drought resistance and for potential metabolic engineering of flavonoid compounds.

Total value adjustment of Bermudan option valuation under pure jump Lévy fluctuations.

During the COVID-19 pandemic, many institutions have announced that their counterparties are struggling to fulfill contracts. Therefore, it is necessary to consider the counterparty default risk when pricing options. After the 2008 financial crisis, a variety of value adjustments have been emphasized in the financial industry. The total value adjustment (XVA) is the sum of multiple value adjustments, which is also investigated in many stochastic models, such as the Heston [B. Salvador and C. W. Oosterlee, Appl. Math. Comput. 391, 125489 (2020)] and Bates [L. Goudenège et al., Comput. Manag. Sci. 17, 163-178 (2020)] models. In this work, a widely used pure jump Lévy process, the Carr-Geman-Madan-Yor process has been considered for pricing a Bermudan option with various value adjustments. Under a pure jump Lévy process, the value of derivatives satisfies a fractional partial differential equation (FPDE). Therefore, we construct a method that combines Monte Carlo with a finite difference of FPDE to find the numerical approximation of exposure and compare it with the benchmark Monte Carlo simulation and Fourier-cosine series method. We use the discrete energy estimate method, which is different from the existing works, to derive the convergence of the numerical scheme. Based on the numerical results, the XVA is computed by the financial exposure of the derivative value.

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco.

Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. In this study, a MAGIC population derived from eight tobacco parents was developed. Eight parents and 560 homozygous lines were genotyped by a 430K single-nucleotide polymorphism (SNP) chip assay and phenotyped for nicotine content under different conditions. Four QTLs associated with nicotine content were detected by genome-wide association mapping (GWAS), and one major QTL, named qNIC7-1, was mapped repeatedly under different conditions. Furthermore, by combining forward mapping, bioinformatics analysis and gene editing, we identified an ethylene response factor (ERF) transcription factor as a candidate gene underlying the major QTL qNIC7-1 for nicotine content in tobacco. A presence/absence variation (PAV) at qNIC7-1 confers changes in nicotine content. Overall, the large size of this MAGIC population, diverse genetic composition, balanced parental contributions and high levels of recombination all contribute to its value as a genetic and breeding resource. The application of the tobacco MAGIC population for QTL mapping and detecting rare allelic variation was demonstrated using nicotine content as a proof of principle.

Homozygous variants in PANX1 cause human oocyte death and female infertility.

PANX1, one of the members of the pannexin family, is a highly glycosylated channel-forming protein. Recently, we identified heterozygous variants in PANX1 that follow an autosomal dominant inheritance pattern and cause female infertility characterized by oocyte death. In this study, we screened for novel PANX1 variants in patients with the phenotype of oocyte death and discovered a new type of inheritance pattern accompanying PANX1 variants. We identified two novel homozygous missense variants in PANX1 [NM_015368.4 c.712T>C (p.(Ser238Pro) and c.899G>A (p.(Arg300Gln))] associated with the oocyte death phenotype in two families. Both of the homozygous variants altered the PANX1 glycosylation pattern in cultured cells, led to aberrant PANX1 channel activation, and resulted in mouse oocyte death after fertilization in vitro. It is worth noting that the destructive effect of the two homozygous variants on PANX1 function was weaker than that caused by the recently reported heterozygous variants. Our findings enrich the variational spectrum of PANX1 and expand the inheritance pattern of PANX1 variants to an autosomal recessive mode. This highlights the critical role of PANX1 in human oocyte development and helps us to better understand the genetic basis of female infertility due to oocyte death.

NtMYB4 and NtCHS1 Are Critical Factors in the Regulation of Flavonoid Biosynthesis and Are Involved in Salinity Responsiveness.

High levels of salinity induce serious oxidative damage in plants. Flavonoids, as antioxidants, have important roles in reactive oxygen species (ROS) scavenging. In the present study, the tobacco R2R3 MYB type repressor, NtMYB4, was isolated and characterized. The expression of NtMYB4 was suppressed by salinity. Overexpression of NtMYB4 reduced the salt tolerance in transgenic tobacco plants. NtMYB4 repressed the promoter activity of NtCHS1 and negatively regulated its expression. Rutin accumulation was significantly decreased in NtMYB4 overexpressing transgenic plants and NtCHS1 RNAi silenced transgenic plants. Moreover, high H2O2 and O 2 - contents were detected in both types of rutin-reduced transgenic plants under high salt stress. In addition, exogenous rutin supplementation effectively scavenged ROS (H2O2 and O 2 - ) and improved the salt tolerance of the rutin-reduced transgenic plants. In contrast, NtCHS1 overexpressing plants had increased rutin accumulation, lower H2O2 and O 2 - contents, and higher tolerance to salinity. These results suggested that tobacco NtMYB4 acts as a salinity response repressor and negatively regulates NtCHS1 expression, which results in the reduced flavonoid accumulation and weakened ROS-scavenging ability under salt stress.

Simultaneous regulation of F5H in COMT-RNAi transgenic switchgrass alters effects of COMT suppression on syringyl lignin biosynthesis.

Ferulate 5-hydroxylase (F5H) catalyses the hydroxylation of coniferyl alcohol and coniferaldehyde for the biosynthesis of syringyl (S) lignin in angiosperms. However, the coordinated effects of F5H with caffeic acid O-methyltransferase (COMT) on the metabolic flux towards S units are largely unknown. We concomitantly regulated F5H expression in COMT-down-regulated transgenic switchgrass (Panicum virgatum L.) lines and studied the coordination of F5H and COMT in lignin biosynthesis. Down-regulation of F5H in COMT-RNAi transgenic switchgrass plants further impeded S lignin biosynthesis and, consequently, increased guaiacyl (G) units and reduced 5-OH G units. Conversely, overexpression of F5H in COMT-RNAi transgenic plants reduced G units and increased 5-OH units, whereas the deficiency of S lignin biosynthesis was partially compensated or fully restored, depending on the extent of COMT down-regulation in switchgrass. Moreover, simultaneous regulation of F5H and COMT expression had different effects on cell wall digestibility of switchgrass without biomass loss. Our results indicate that up-regulation and down-regulation of F5H expression, respectively, have antagonistic and synergistic effects on the reduction in S lignin resulting from COMT suppression. The coordinated effects between lignin genes should be taken into account in future studies aimed at cell wall bioengineering.

Lévy noise induced transition and enhanced stability in a gene regulatory network.

We investigate a quantitative bistable two-dimensional model (MeKS network) of gene expression dynamics describing the competence development in the Bacillus subtilis under the influence of Lévy as well as Brownian motions. To analyze the transitions between the vegetative and the competence regions therein, two dimensionless deterministic quantities, the mean first exit time (MFET) and the first escape probability, are determined from a microscopic perspective, as well as their averaged versions from a macroscopic perspective. The relative contribution factor λ, the ratio of non-Gaussian and Gaussian noise strengths, is adopted to identify an optimum choice in these transitions. Additionally, we use a recent geometric concept, the stochastic basin of attraction (SBA), to exhibit a pictorial comprehension about the influence of the Lévy motion on the basin stability of the competence state. Our main results indicate that (i) the transitions between the vegetative and the competence regions can be induced by the noise intensities, the relative contribution factor λ and the Lévy motion index α; (ii) a higher noise intensity and a larger α with smaller jump magnitude make the MFET shorter, and the MFET as a function of λ exhibits one maximum value, which is a signature of the noise-enhanced stability phenomenon for the vegetative state; (iii) a larger α makes the transition from the vegetative to the adjacent competence region to occur at the highest probability. The Lévy motion index α0≈0.5 (a larger jump magnitude with a lower frequency) is an ideal choice to implement the transition to the non-adjacent competence region; (iv) there is an expansion in SBA when α decreases.

Molecular docking studies and biological evaluation of 1,3,4-thiadiazole derivatives bearing Schiff base moieties as tyrosinase inhibitors.

1,3,4-Thiadiazole derivatives bearing Schiff base moieties were designed, synthesized, and their tyrosinase inhibitory activities were evaluated. Some compounds displayed potent tyrosinase inhibitory activities, especially, 4-(((5-mercapto-1,3,4-thiadiazol-2-yl)-imino)methyl)-2-methoxy-phenol (14) exhibited superior inhibitory effect to the other compounds with an IC50 value of 0.036µM. The structure-activity relationships (SARs) were preliminarily discussed and docking studies showed compound 14 had strong binding affinity to mushroom tyrosinase. Hydroxy might be the active groups. The inhibition kinetics study revealed that compounds (13 and 14) inhibited tyrosinase by acting as uncompetitive inhibitors. The LD50 value of the compound 14 was 5000mg/kg.

Study on the synthesis and biological activities of α-substituted arylacetates derivatives.

Anisodamine was isolated from the medicinal herb, it was used in the treatment of gastrointestinal smooth muscle spasm, infective toxic shock and organophosphorus intoxication. But there is no report about anisodamine with α-glucosidase inhibitory activity. In order to find novel α-glucosidase inhibitors, a series of α-substituted arylacetates derivatives have been synthesized based on the active unit of anisodamine. In α-glucosidase assay, compound 9 in Schiff base form and compound 22 in ester form show strong inhibition against α-glucosidase with IC50 value of 46.81µM and 83.76µM, respectively. Compounds 9 and 22 exhibit comparable good antidiabetic activities as commercial drug Glimepiride. In addition, Schiff bases of α-substituted arylacetates show antitumor activities against human cancer cell lines, where compound 9 with thiourea moiety performs the best antitumor activity. We anticipate that our research will provide potential candidate scaffolds for antidiabetic drug design.

Design and synthesis of aloe-emodin derivatives as potent anti-tyrosinase, antibacterial and anti-inflammatory agents.

Twenty aloe-emodin derivatives were designed, synthesized, and their biological activities were evaluated. Some compounds displayed potent tyrosinase inhibitory activities, especially, compounds with thiosemicarbazide moiety showed more potent inhibitory effects than the other compounds. The structure-activity relationships (SARs) were preliminarily discussed. The inhibition mechanism of selected compounds 1 and 13 were investigated. The results showed compound 1 was reversible inhibitor, however, compound 13 was irreversible. Kinetic analysis indicated that compound 1 was competitive tyrosinase inhibitor. Furthermore, the antibacterial activities and anti-inflammatory activities of some selected compounds were also screened. The results showed that compound 3 exhibited more potent antibacterial activity than the aloe-emodin, compounds 5 and 6 possessed more potent anti-inflammatory activities than the diacerein.

Microwave-assisted synthesis and tyrosinase inhibitory activity of chalcone derivatives.

A series of chalcones and their derivatives were synthesized, and their inhibitory effects on the diphenolase activity of mushroom tyrosinase were evaluated. The results showed that some of the synthesized compounds exhibited significant inhibitory activity, and four compounds exhibited more potent tyrosinase inhibitory activity than the reference standard inhibitor kojic acid (5-hydroxy-2-(hydroxymethyl)-4H-pyran-4-one). Specifically, 1-(-1-(4-methoxyphen- yl)-3-phenylallylidene)thiosemicarbazide (18) exhibited the most potent tyrosinase inhibitory activity with IC50 value of 0.274 µM. The inhibition mechanism analysis of 1-(-1-(2,4-dihydroxyphenyl)-3-phenylallylidene) thiosemicarbazide (16) and 1-(-1-(4-methoxyphenyl)-3-phenylallylidene) thiosemicarbazide (18) demonstrated that the inhibitory effects of the two compounds on the tyrosinase were irreversible. Preliminary structure activity relationships' analysis suggested that further development of such compounds might be of interest.

Biological evaluation of coumarin derivatives as mushroom tyrosinase inhibitors.

A series of coumarin derivatives were synthesised and their inhibitory effects on the diphenolase activity of mushroom tyrosinase were evaluated. The results showed that some of the synthesised compounds exhibited significant inhibitory activities. Especially, 2-(1-(coumarin-3-yl)ethylidene)hydrazinecarbothioamide bearing thiose-micarbazide group exhibited the most potent tyrosinase inhibitory activity with IC(50) value of 3.44µM. The inhibition mechanism analysis of 2-(1-(coumarin-3-yl)-ethylidene)hydrazinecarbothioamide and 2-(1-(6-chlorocoumarin-3-yl)ethylidene)-hydrazinecarbothioamide demonstrated that the inhibitory effects of the compounds on the tyrosinase were irreversible. Preliminary structure activity relationships' (SARs) analysis suggested that further development of such compounds might be of interest.

Evaluation of dihydropyrimidin-(2H)-one analogues and rhodanine derivatives as tyrosinase inhibitors.

A series of dihydropyrimidin-(2H)-one analogues and rhodanine derivatives were synthesized and their inhibitory effects on the diphenolase activity of mushroom tyrosinase were evaluated. The results showed that some of the synthesized compounds exhibited significant inhibitory activities. Especially, compound 15 bearing a hydroxyethoxyl group at position-4 of phenyl ring exhibited most potent tyrosinase inhibitory activity with IC(50) value of 0.56 mM. The inhibition mechanism analysis of compound 15 demonstrated that the inhibitory effect of the compound on the tyrosinase was irreversible. These results suggested that such compounds might be served as lead compounds for further designing new potential tyrosinase inhibitors.

Design, synthesis and biological evaluation of 3-(4-halophenyl)-3-oxopropanal and their derivatives as novel antibacterial agents.

In continuing our program aimed to search for potent drugs for bacterial infections, a series of 3-(4-halophenyl)-3-oxopropanal and their derivatives were designed, synthesized and their antibacterial activities in vitro against both Gram-positive bacteria Staphylococcus aureus and Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa were evaluated. Compounds 7, 8, 13-16, 21 and 22 had moderate antibacterial activities against Staphylococcus aureus (minimal inhibitory concentration (MIC) <16 microg/ml), suggesting that the introduction of mono-methoxyamine or ethoxyamine moiety might play an important role in determining the potent antibacterial activities. Furthermore, the antibacterial activities of select compounds 7, 15 and 16 against the clinically important pathogenic bacteria-methicillin-resistant Staphylococcus aureus (MRSA) were also investigated. Results showed that these compounds exhibited more potent activities than the well-known antibacterial agents Houttuynin and Levofloxacin.

[Establishment of Saussurea involucrata hairy roots culture and plantlet regeneration].

Hairy root clones of Saussurea involucrata transformed with Agrobacterium rhizogenes strains R1601, R1000, and LBA9402 were established to investigate the flavonoid production. Opine synthesis and PCR analysis confirmed the integration of the T-DNA fragment of Ri plasmid from A. rhizogenes strain R1601 into the transformed root genome. The frequency of hairy root formation from root segments, which were pre-cultured 2 days in N6 solid medium without plant growth regulators, amounted to 100% following infection with R1601 strain of A. rhizogenes. The transformed roots were kept in hormone-free N6 liquid medium in the dark at 25 degrees C, 110r/min and routinely subcultured every 20 - 24 days. One hairy root clone, which grew vigorously with lateral branches, was periodically examined for the ability to produce flavonoid. The maximum of biomass and flavonoid yield achieved 66.7 g/L (fresh weight) and 102.3mg/g dry weight after incubation 20 days. The calli were induced from the hairy root culture in the presence of 0.5mg/L IBA and intact plantlets were regenerated from these calli. The regeneration plantlets from hairy roots, in which the flavonoid content were 53% in that of untransformed plants, weren't different in growth and morphology of the untransformed plantlets. Therefore plant regeneration from hairy roots may be also a means for producing transformed S. involucrata plants. Hairy root cultures of S. involucrata clearly showed higher flavonoid contents compared to the wild plant or the regeneration seedlings. As the wild S. involucrata grows only in special regions with peculiar climate, and cultivation of this species in a normal climate has been unsuccessful so far. The success in obtaining a method for high production of flavonoid might very well be one of the solutions for this problem in the future.