Levels Of Secondary Metabolites Research Articles

Proanthocyanidins Alleviate Cadmium Stress in Industrial Hemp (Cannabis sativa L.).

Industrial hemp (Cannabis sativa L.), an annual herbaceous cash crop, is widely used for the remediation of heavy metal-contaminated soils due to its short growth cycle, high tolerance, high biomass, and lack of susceptibility to transfer heavy metals into the human food chain. In this study, a significant increase in proanthocyanidins was found in Yunnan hemp no. 1 after cadmium stress. Proanthocyanidins are presumed to be a key secondary metabolite for cadmium stress mitigation. Therefore, to investigate the effect of proanthocyanidins on industrial hemp under cadmium stress, four experimental treatments were set up: normal environment, cadmium stress, proanthocyanidin treatment, and cadmium stress after pretreatment with proanthocyanidins. The phenotypes from the different treatments were compared. The experimental results showed that pretreatment with proanthocyanidins significantly alleviated cadmium toxicity in industrial hemp. The transcriptome and metabolome of industrial hemp were evaluated in the different treatments. Proanthocyanidin treatment and cadmium stress in industrial hemp mainly affected gene expression in metabolic pathways associated with glutathione metabolism, phenylpropanoids, and photosynthesis, which in turn altered the metabolite content in metabolic pathways of phenylalanine, vitamin metabolism, and carotenoid synthesis. The combined transcriptomic and metabolomic analysis revealed that proanthocyanidins mitigated cadmium toxicity by enhancing photosynthesis, secondary metabolite synthesis, and antioxidant synthesis. In addition, exogenous proanthocyanidins and cadmium ions acted simultaneously on EDS1 to induce the production of large amounts of salicylic acid in the plant. Finally, overexpression of CsANR and CsLAR, key genes for proanthocyanidins synthesis in industrial hemp, was established in Arabidopsis plants. The corresponding plants were subjected to cadmium stress, and the results showed that CsLAR transgenic plants were more tolerant to cadmium than the CsANR transgenic and wild-type Arabidopsis plants. The results showed that salicylic acid and jasmonic acid were increased in Arabidopsis overexpressing CsLAR compared to AT wild-type Arabidopsis, and levels of secondary metabolites were significantly higher in Arabidopsis overexpressing CsLAR than in AT wild-type Arabidopsis. These results revealed how proanthocyanidins alleviated cadmium stress and laid the foundation for breeding industrial hemp varieties with higher levels of proanthocyanidins and greater tolerance.

The interplays between epigallocatechin-3-gallate (EGCG) and Aspergillus niger RAF106 based on metabolism

Epigallocatechin-3-gallate (EGCG) is a vital kind of catechin with high bioactive activities, however, limited research has been conducted to elucidate the molecular basis of EGCG biotransformation by Aspergillus niger and the underlying regulatory mechanisms. In this study, A. niger RAF106, isolated from Pu-erh tea, was applied to conduct the EGCG fermentation process, and the samples were collected at different fermentation times to determine the intermediary metabolites of EGCG and the metabolome as well as physiological activity changes of A. niger RAF106. The results demonstrated that EGCG enhances the growth of A. niger RAF106 by promoting conidial germination and hyphae branching. Meanwhile, metabolomic analyses indicated that EGCG significantly regulates the amino acid metabolism of A. niger RAF106. Furthermore, metabolomic analyses also revealed that the levels of original secondary metabolites in the supernatant of the cultures changed significantly from the fermentation stage M2 to M3, in which the main differentially changed metabolites (DCMs) were flavonoids. Most of these flavonoids exhibited antioxidant properties and thus increased the radical scavenging activity of the supernatant of the cultures. In addition, we also found several intermediary metabolites of EGCG, GA, and EGC, including oolonghomobisflavan A, (−)-Epigallocatechin 3, 5-di-gallate, (−)-Epigallocatechin 3-(3-methyl-gallate) (−)-Catechin 3-O-gallate, 4′-Methyl-(−)-epigallocatechin 3-(4-methyl-gallate), myricetin, prodelphinidin B, 7-galloylcatechin, and 3-hydroxyphenylacetic acid. These findings contribute to improving the bioavailability of EGCG and help mine highly active metabolites, which can be used as raw materials for the development of pharmaceutical intermediates or functional foods. In addition, the results also provide a theoretical basis for better control of the risk of A. niger origin and the regulatory mechanisms of the biotransformation process mediated by A. niger.

Genomic DNA Extraction: The Critical Stage in Plant Molecular Analysis Activities

<p>DNA extraction is a crucial stage in plant molecular analysis activities that determine the success of further downstream analysis stages. Molecular analysis activities, including Polymerase Chain Reaction (PCR), restriction digestion, DNA hybridisation, genomic library construction, and DNA sequencing, mostly require DNA with high quality and enough quantity. Some plants contain high levels of polysaccharides, proteins, and secondary metabolites, such as polyphenols, tannins, and alkaloids, which can affect the purity of the isolated DNA. The presence of these contaminants can inhibit the activity of several enzymes, such as DNA polymerase and restriction enzymes, so that DNA could not be amplified or digested. Various DNA extraction methods have been developed, ranging from manual method, manual commercial kits, and robotic techniques. Each method has its advantages and disadvantages since the selection of the right method needs to be determined carefully in order to obtain the best results. Some modifications at certain stages in DNA extraction process need to be conducted to minimize the number of DNA contaminants. Several rapid DNA extraction methods nowadays have also been developed to save times, labors, and costs. In addition, the rapid DNA extraction method could also reduce the use of some hazardous chemical compounds, so that the method is not only giving economic benefits, but also good for human health.</p>

Corn Starch in Pharmaceuticals Isolation, Characterization, and Applications

>MOvergrowth of Candida tends to produce high levels of secondary metabolites affecting the immersion of infectious and degenerative diseases. Biofilm’s existence as a virulence factor of Candida makes it challenging to overcome causing multidrugresistant issues. Studies on the effectiveness of Candida antibiofilm drug candidates should be supported by data related to model structure and molecular interaction within the eradication process of biofilm through homology modeling and in-silico docking. This study aims to determine molecular interactions between 1,3-β-glucanase Achatina fulica in which the substrate is, through homology modeling and docking studies within the biofilm matrix eradication process. The alignment results show that mkafGlu1 is a new representative of the Glycoside Hydrolase 16 family (GH16) with EC 3.2.1.39. MKAFGlu1 enzymes are 1,3-1,6-β-glucanase able to cleave 1,3-β- dan 1,6-β-glycosidic bonds. This in-silico docking study also shows that mkafGlu1 has high specificity towards laminarin (substrate 1,3-1,6-β-glucanase) and that the enzyme of MKAFGlu1 works based on a retention mechanism in its reaction to the substrate. The result of the recombinant enzyme of 1,3-β-glucanase novel genes can hydrolyze the substrate of 1,3-β-glucan as one of the biofilm matrix components, opening up an opportunity for new medicine as an antibiofilm candidate.

The Effect of Butterfly Pea (Clitoria ternatea) Against Fish Pathogens: A Mini-review

Butterfly pea (Clitoria ternatea) is a plant with the potentiality to inhibit the fish pathogens because its rich of bioactive compounds. Leaves, stems, roots and flowers contain diverse substances among which there are alkaloids, tannins, glycosides, terpenoids, phenols, reducing sugars, flavonoids etc. The secondary metabolites in leaves reported can inhibit the pathogens such as Aeromonas formicans, Aeromonas hydrophilia, Streptococcus agalactiae, Escherichia coli, Klebsiella pneumoniae, Bacillus subtilis. The roots can inhibit Pseudomonas aeruginosa and K. pneumoniae. The bioactive compounds in flowers and seeds can inhibit B. subtilis, E. coli, P. aeruginosa, Klebsiella spp. Different part of plant give different effect to inhibit the growth of pathogens because it contains different types and levels of secondary metabolites. In addition, the different solvent used in extraction process give difference result to prevent the growth of disease microorganism in fish with the inhibition zone ranged 7-28 mm.

Optimised germination protocol for jackfruit seeds and evaluation of methods for extraction of DNA suitable for genetic analysis

Jackfruit (Artocarpus heterophyllus) is an underutilised plant that is promising in curbing food and nutritional security in sub-Saharan Africa. However, high level of secondary metabolites in its tissues significantly hampers its genetic characterisation for breeding purposes. Primarily, the compounds react with DNA during the extraction process, thus reducing its yield and quality. The utilisation of leaves from jackfruit seedlings is a potentially effective approach of addressing the challenge, however, limited information is available on efficient jackfruit seed germination procedures. Elucidating effective methods of jackfruit seed germination, and optimising protocols for DNA extraction is crucial in promoting its genetic characterisation studies for identification of superior varieties for propagation. The objective of this study was to evaluate methods of jackfruit seed germination, and DNA extraction procedures using jackfruit leaves. Pre-treatment of seeds with 3% hydrogen peroxide was effective in enhancing seed germination within a short time, compared to distilled water and 3% hydrochloric acid. We optimised a DNA extraction technique by combining CTAB-SDS based approach with an enhanced solvent extraction method. The technique yielded high quantity and quality of DNA from jackfruit leaves, which was appropriate for downstream polymerase chain reaction analysis. The sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) amplifications confirmed the effectiveness of the optimised CTAB-SDS based protocol for extraction of high quality DNA.

Combined Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Flavonoid Biosynthesis in Handroanthus chrysanthus (Jacq.) S.O.Grose

Handroanthus and Tabebuia are known for their ornamental and medicinal value, which are attributed to metabolites. However, the mechanisms underlying the synthesis of these metabolites are poorly understood. In this study, the expression levels of secondary metabolites and the mechanism of flavonoid biosynthesis in the bark and leaves of Handroanthus chrysantha (Jaq.) were examined using transcriptomic and metabolomic techniques. Metabolic analysis identified several differentially accumulated metabolites (DAMs), most of which were flavonoids, isoprenoids, and sterols. Additionally, 30 flavonoids were identified in the bark and leaves of H. chrysantha. Transcriptomic analysis identified 69 genes involved in flavonoid biosynthesis, among which 49 were significantly different between the bark and leaves. qRT-PCR analysis of eight genes involved in flavonoid biosynthesis showed that the expression patterns of the genes were consistent with the transcriptome sequencing data. Integrative transcriptomic and metabolomic analysis showed that 20 differentially expressed genes (DEGs) associated with flavonoid biosynthesis were strongly correlated with seven DAMs, confirming the involvement of the DEGs in flavonoid biosynthesis. These findings considerably contribute to the understanding of the biosynthesis of secondary metabolites in H. chrysantha and serve as a reference for further pharmacological studies.

Nitrogen addition modifies the relative gene expression level and accumulation of carbon-based bioactive substances in Cyclocarya paliurus

In China, lots of Cyclocarya paliurus plantations have been established for tea and functional food production on nitrogen (N)-limited land. The optimum N levels require for biosynthesis and accumulation of carbon-based bioactive substances vary among plant species. This study integrated field trial with hydroponic culture to assess impact of nitrogen addition on accumulation and relative gene expression level of carbon-based secondary metabolites in C. paliurus. N addition significantly influenced not only contents of polyphenols, flavonoids and triterpenoids and relative gene expression levels of their biosynthetic pathway in C. paliurus leaves but also leaf biomass production and the bioactive substance accumulations. An intermediate N addition induced the highest contents of polyphenols, flavonoids and triterpenoids in leaves, but the optimized accumulation of these bioactive substances in the leaves was the trade-off between their contents and leaf biomass production. Correlation analysis showed that related gene expression levels were closely correlated with contents of their leaf corresponding secondary metabolites. Compared with ratios of carbon/N (C/N) and carbon/phosphorus (C/P) in the soil, ratios of C/N and C/P in the leaves were more strongly related to the contents and accumulations of polyphenols, flavonoids and triterpenoids. To obtain higher yields of targeted phytochemicals, the threshold ratios of C/N and C/P in the leaves are recommended for N and P fertilization at similar sites. Overall, our findings would provide the theoretical basis and technical support for manipulating N fertilization in C. paliurus plantations to obtain higher accumulations of targeted bioactive substances.

Extracellular vesicles of cannabis with high CBD content induce anticancer signaling in human hepatocellular carcinoma.

Plant-derived extracellular vesicles (EVs) have been the topic of interest in recent years due to their proven therapeutic properties. Intact or manipulated plant EVs have shown antioxidant, anti-inflammatory, and anti-cancerous activities as a result of containing bioactive metabolites and other endogenous molecules. Less is known about the EV efficacy with high levels of bioactive secondary metabolites derived from medicinal or non-edible plants. Numerous data suggest the functionality of Cannabis sativa extract and its phytocannabinoids in cancer treatment. Here, two chemotypes of cannabis with different levels of D-9-tetrahydrocannabinol (THC) and cannabidiol (CBD) were selected. EVs were isolated from each chemotype via differential ultracentrifugation. HPLC analysis was illustrative of the absence of THC in EVs derived from both plants. Therefore, two types of EVs were classified according to their CBD content into high- (H.C-EVs) and low-CBD EVs (L.C-EVs). Electron microscopy and DLS showed both cannabis-derived EVs (CDEVs) can be considered as exosome-like nanovesicles. Cytotoxicity assay showed that H.C-EVs strongly decreased the viability of two hepatocellular carcinoma (HCC) cell lines, HepG2 and Huh-7, in a dose and time-dependent manner compared with L.C-EVs. H.C-EVs had no significant effect on HUVECs normal cell growth. The finding showed that the H.C-EVs arrested the G0/G1 phase in the cell cycle and significantly induced cell death by activating mitochondrial-dependent apoptosis signaling pathways in both HCC cell lines. Altogether, the current study highlights that CDEVs can be an ideal natural vehicle for bioactive phytocannabinoids and a promising strategy in cancer management.

A Comparative Study of The Secondary Metabolite from Talinum triangulare (jacq.) Willd. Methanolic Extract From Malang and Kediri, East Java

Talinum triangulare is a medicinal plant that has been used broadly by the Indonesia community because of its properties. Several studies have proven the components of secondary metabolites in T. triangulare. However, the content of secondary metabolites in each part of T. triangulare is not clearly understood. Therefore, this study aimed to analyse the types of secondary metabolites of leaf, stems, and roots of T. triangulare. The plant from Malang was chosen as the sample source because it is a highland suitable for the life of T. triangulare. The plant from Kediri was chosen as a lowland location. Samples of leaves, stems, and roots of T. triangulare were extracted by maceration method. Phytochemical analyses include phenolics, flavonoids, alkaloids, tannins, saponins, and terpenoids. The absorbance values were measured at different wavelengths. The leaf and stems of T. triangulare contain flavonoid compounds, tannins, phenolics, alkaloids, saponins, and terpenoids with higher levels of secondary metabolites in the leaf. While the roots have the lowest secondary metabolite was only containing steroids. The differential levels and types of secondary metabolites samples obtained from Kediri tend to be lower than samples obtained from Malang. These results indicate that the leaf metabolite secondary of T. triangulare has high potential health benefits for regulating molecular and cellular metabolism.

HPLC-DAD profiling, enzyme inhibitory, antihemolytic, and photoprotective activities of Limonium delicatulum leaf extract

Limonium delicatulum is a halophyte that synthesizes high levels of various secondary metabolites in response to abiotic stress and therefore can be a valuable source of different bio-active compounds. The leaf extract of L. delicatulum was analyzed for its phenolic compounds by HPLC-DAD and evaluated for its inhibitory effects on acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-glucosidase, α-amylase, urease, and lipase. The protective effect on oxidative hemolysis of rabbit erythrocytes as well as its photoprotective action have also been investigated. HPLC analysis led to the identification of five phenolic compounds including salvianolic acid B (14.8 mg/g of extract) followed by polydatin (extract 4.0 mg/g of extract). The extract showed strong inhibitory actions on AChE, BChE, α-glucosidase, α-amylase and urease close to or even better than those shown by the standards with IC50 values of 5.94 ± 0.54, 11.68 ± 0.35, 30.17 ± 0.65, 22.74 ± 0.54, and 10.23 ± 087 μg/mL, respectively, while it was inactive against lipase. In addition, an important reduction in the rate of lysis of erythrocytes was observed (with a percentage of 89.18 ± 0.95%) after treatment with leaf extract at the concentration of 200 μg/mL. Finally, an SPF value of 35.5 ± 0.90 was recorded with the leaf extract. These results confirm that L. delicatulum can be of great importance in food, pharmaceutical, and cosmetics.

Flavonoid Accumulation Varies in Medicago truncatula in Response to Mercury Stress.

Mercury (Hg) contamination is increasing worldwide in both wild ecosystems and agricultural soils due to natural processes, but mostly to anthropic activities. The molecular mechanisms involved in Hg toxicity and tolerance in plants have been extensively studied; however, the role of flavonoids in response to Hg stress remains to be investigated. We conducted a metabolomic study to analyze the changes induced at the secondary metabolite level in three Hg-tolerant and one Hg-sensitive Medicago truncatula cultivars. A total of 46 flavonoid compounds, classified into five different flavonoid families: anthocyanidins, flavones, isoflavones, pterocarpan flavonoids, and flavanones, along with their respective glycoconjugate derivatives, were identified in leaf and root tissues. The synthesis of free isoflavones, followed by monoglycosylation and further malonylation was shown to be characteristic of root samples, whereas higher glycosylation, followed by further acylation with coumaric and ferulic acid was characteristic of leaf tissues. While minor changes were observed in leaves, significant quantitative changes could be observed in roots upon Hg treatment. Some flavonoids were strongly upregulated in roots, including malonylglucosides of biochanin A, formononetin and medicarpin, and aglycones biochanin, daidzein, and irisolidone. Hg tolerance appeared to be mainly associated to the accumulation of formononetin MalGlc, tricin GlcAGlcA, and afrormosin Glc II in leaves, whereas aglycone accumulation was associated with tolerance to Hg stress in roots. The results evidence the alteration of the flavonoid metabolic profile and their glycosylation processes in response to Hg stress. However, notable differences existed between varieties, both in the basal metabolic profile and in the response to treatment with Hg. Overall, we observed an increase in flavonoid production in response to Hg stress, and Hg tolerance appeared to be associated to a characteristic glycosylation pattern in roots, associated with the accumulation of aglycones and monoglycosylated flavonoids. The findings are discussed in the context of the flavonoid biosynthetic pathway to provide a better understanding of the role of these secondary metabolites in the response and tolerance to Hg stress in M. truncatula.

Analysis of Molecular Modeling and Molecular Docking of Beta-glucanase from Metagenomic Expression Library as Candida Antibiofilm Candidate

MOvergrowth of Candida tends to produce high levels of secondary metabolites affecting the immersion of infectious and degenerative diseases. Biofilm’s existence as a virulence factor of Candida makes it challenging to overcome causing multidrugresistant issues. Studies on the effectiveness of Candida antibiofilm drug candidates should be supported by data related to model structure and molecular interaction within the eradication process of biofilm through homology modeling and in-silico docking. This study aims to determine molecular interactions between 1,3-β-glucanase Achatina fulica in which the substrate is, through homology modeling and docking studies within the biofilm matrix eradication process.

Uji Aktivitas Antikolesterol Kombinasi Ekstrak Teh Oolong, Buncis Dan Kayu Manis

Hyperlipidemia has an important role in the occurrence of cardiovascular, cerebrovascular, and peripheral vascular diseases. High cholesterol and LDL levels in the blood are at risk of causing various diseases such as atherosclerosis, pancreatic dysfunction and kidney disorders. Meanwhile, high triglyceride levels can cause impaired liver, pancreas and kidney function. Green bean, oolong tea and cinnamon are plants that can lower cholesterol levels. Oolong tea contains catechins, Green Bean contain phytosterols and cinnamon contains cinnamaldehyde. Determination of secondary metabolite levels of extracts was carried out using the Liquid Chromatography – Mass Spectroscopy (LC-MS) method. The activity test was carried out with 30 Wistar white rats which were divided into 6 test groups. The normal control group was treated with CMC-Na without feeding hypercholesterolemia, the positive control group was treated with simvastatin 0.4 mg/KgBW, the negative control group was treated with CMC-Na, the test groups 1, 2 and 3 were treated with cinnamon extract, oolong tea and green bean, respectively (150:50:50 mg/KgBW), (50:150:50 mg/KgBW) and (50:50:150 mg/KgBW). The detected metabolite content was cinnamaldehyde in cinnamon up to 10%, catechins in oolong tea up to 12% and stigmasterol in beans as much as 3.4%.The results obtained by test group 1 and test group 2 can reduce cholesterol and triglyceride levels (p0.05). All test groups had no significant effect on HDL and LDL levels.

Exploring the impacts of traditional crafts on microbial community succession in Jiang-flavored Daqu

The usage of traditional crafts during the fermentation process has a great influence on the quality of Jiang-flavored Daqu. This study focused on exploring the impacts of traditional crafts on Daqu microecology through high-throughput sequencing and statistical analyses. These results show that traditional crafts modulated microbial community succession through the regulation of temperature, moisture, and acidity. High temperatures (66 ± 1 °C) were conducive to the growth of microbes that produced flavor compounds, such as Bacillus and Thermoactinomyces. Low moisture content (correlated with 22 genera) and high acidity (8 genera) were mainly responsible for the decreased microbial diversity. Two flipping processes showed significant effects on the internal microecology and microbial metabolism. The first flip of Daqu may assist in regulating the microbial community structure and promoting the enrichment of flavor-functional microorganisms. The second flipping was reasonable for the enrichment of esterifying functional microorganisms, thus enhancing the esterifying power of Daqu with reduced acidity. Furthermore, analysis of the metabolic pathways at different stages of the process showed that the levels of flavor precursors and secondary metabolites within Jiang-flavored Daqu significantly increased during fermentation.

Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins

As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome-scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads and high-throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50=30.9Mb; contig N50=6.34 Mb) with 95.71% of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to have diverged from the Leguminosae lineage at ~72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analysed and offers new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponin biosynthesis. As the first high-quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.

A physiological and metabolomic analysis reveals the effect of shading intensity on blueberry fruit quality.

With the advancement of blueberry industrialization, cultivation measures for obtaining high-quality fruits and technologies for obtaining high levels of the main secondary metabolites have become inevitable requirements for further development of the blueberry industry. This study applied different shading treatments and found that the FT1 shading treatment yielded the largest values for the single fruit weight, solid longitudinal diameter and transverse diameter of blueberry fruit as well as the highest solidity-acid ratio and total phenol and vitamin C contents. Moreover, 470 known metabolites were obtained from blueberry fruits. Interestingly, the differentially abundant metabolites related to ABC transporters, pyrimidine metabolism, and purine metabolism pathways were commonly identified from the three comparisons, which indicated that these three metabolic pathways in blueberry fruits are vulnerable to shading treatment. This study provides a theoretical basis for the application of summer shading to improve the quality and antioxidant substances of small berries.

Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families.

Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION® platform, with and without the use of a short fragment depletion kit.

Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria.

For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the ‘Secondary Metabolite Transcriptomic Pipeline’ (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest.

Effects of Host Plants on Bacterial Community Structure in Larvae Midgut of Spodoptera frugiperda.

Simple SummaryThe gut microbiota plays an important role in insect physiology and behavior. The interaction among the different structures of gut bacterial community in the fall armyworm (FAW), Spodoptera frugiperda, and different host plants, and whether these different gut bacteria are responsible for the rapid spread of FAW to a variety of host plants after invasion are largely unexplored. In the present paper, we used a culture-independent approach targeting the bacterial 16S rRNA gene of gut bacteria of the 5th instar larvae of FAW fed on four different host plants. It aimed to analyze the effects of host plants on gut bacteria abundance, community structure and metabolic function. We found that host plants exerted considerable effects on the structure and composition of the gut bacteria in FAW and the differences among the four groups identified were significant. They were related to the detoxification and adaptation of FAW to toxic secondary metabolites of the host plant. These differences enabled the gut microbiome to perform different functions. This study lays a foundation for further studies on the function of intestinal bacteria in FAW and the adaptive mechanism to the host.The fall armyworm (FAW), Spodoptera frugiperda, is one of the most important invasive species and causes great damage to various host crops in China. In this study, the diversity and function of gut bacteria in the 5th instar larvae of FAW fed on maize, wheat, potato and tobacco leaves were analyzed through 16S rRNA sequencing. A total of 1324.25 ± 199.73, 1313.5 ± 74.87, 1873.00 ± 190.66 and 1435.25 ± 139.87 operational taxonomic units (OTUs) from the gut of FAW fed on these four different host plants were detected, respectively. Firmicutes, Proteobacteria and Bacteroidetes were the most abundant bacterial phyla. Beta diversity analysis showed that the gut bacterial community structure of larvae fed on different host plants was significantly differentiated. At the genus level, the abundance of Enterococcus in larvae fed on wheat was significantly lower than those fed on the other three host plants. Enterobacter and ZOR0006 were dominant in FAW fed on tobacco leaves, and in low abundance in larvae fed on wheat. Interestingly, when fed on Solanaceae (tobacco and potato) leaves which contained relative higher levels of toxic secondary metabolites than Gramineae (wheat and maize), the genera Enterococcus, Enterobacter and Acinetobacter were significantly enriched. The results indicated that gut bacteria were related to the detoxification and adaptation of toxic secondary metabolites of host plants in FAW. Further analysis showed that replication, repair and nucleotide metabolism functions were enriched in the gut bacteria of larvae fed on tobacco and potato. In conclusion, the gut bacterial diversity and community composition in FAW larvae fed on different host plants showed significant differences, and the insect is likely to regulate their gut bacteria for adaptation to different host plants.