In silico biotechnological potential of Bacillus sp. strain MHSD_37 bacterial endophyte

BACKGROUND

Endophytic bacteria possess a range of unique characteristics that enable them to successfully interact with their host and survive in adverse environments. This study employed in silico analysis to identify genes, from Bacillus sp. strain MHSD_37, with potential biotechnological applications.

RESULTS

The strain presented several endophytic lifestyle genes which encode for motility, quorum sensing, stress response, desiccation tolerance and root colonisation. The presence of plant growth promoting genes such as those involved in nitrogen fixation, nitrate assimilation, siderophores synthesis, seed germination and promotion of root nodule symbionts, was detected. Strain MHSD_37 also possessed genes involved in insect virulence and evasion of defence system. The genome analysis also identified the presence of genes involved in heavy metal tolerance, xenobiotic resistance, and the synthesis of siderophores involved in heavy metal tolerance. Furthermore, LC-MS analysis of the excretome identified secondary metabolites with biological activities such as anti-cancer, antimicrobial and applications as surfactants.

CONCLUSIONS

Strain MHSD_37 thereby demonstrated potential biotechnological application in bioremediation, biofertilisation and biocontrol. Moreover, the strain presented genes encoding products with potential novel application in bio-nanotechnology and pharmaceuticals.

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

An Integrated Molecular Networking and Docking Approach to Characterize the Metabolome of Helichrysum splendidum and Its Pharmaceutical Potentials

South Africa is rich in diverse medicinal plants, and it is reported to have over 35% of the global Helichrysum species, many of which are utilized in traditional medicine. Various phytochemical studies have offered valuable insights into the chemistry of Helichrysum plants, hinting at bioactive components that define the medicinal properties of the plant. However, there are still knowledge gaps regarding the size and diversity of the Helichrysum chemical space. As such, continuous efforts are needed to comprehensively characterize the phytochemistry of Helichrysum, which will subsequently contribute to the discovery and exploration of Helichrysum-derived natural products for drug discovery. Thus, reported herein is a computational metabolomics work to comprehensively characterize the metabolic landscape of the medicinal herb Helichrysum splendidum, which is less studied. Metabolites were methanol-extracted and analyzed on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. Spectral data were mined using molecular networking (MN) strategies. The results revealed that the metabolic map of H. splendidum is chemically diverse, with chemical superclasses that include organic polymers, benzenoids, lipid and lipid-like molecules, alkaloids, and derivatives, phenylpropanoids and polyketides. These results point to a vastly rich chemistry with potential bioactivities, and the latter was demonstrated through computationally assessing the binding of selected metabolites with CDK-2 and CCNB1 anti-cancer targets. Molecular docking results showed that flavonoids (luteolin, dihydroquercetin, and isorhamnetin) and terpenoids (tiliroside and silybin) interact strongly with the CDK-2 and CCNB1 targets. Thus, this work suggests that these flavonoid and terpenoid compounds from H. splendidum are potentially anti-cancer agents through their ability to interact with these proteins involved in cancer pathways and progression. As such, these actionable insights are a necessary step for further exploration and translational studies for H. splendidum-derived compounds for drug discovery.

A Relook into the Flavonoid Chemical Space of Moringa oleifera Lam. Leaves through a Combination of LC-MS and Molecular Networking

Moringa oleifera Lam. is a functional tree that is known to produce a variety of metabolites with purported pharmacological activities. It is frequently called the "miracle tree" due to its utilization in numerous nutraceutical and pharmacological contexts. This study was aimed at studying the chemical space of M. oleifera leaf extracts through molecular networking (MN), a tool that identifies metabolites by classifying them based on their MS-based fragmentation pattern similarities and signals. In this case, a special emphasis was placed on the flavonoid composition. The MN unraveled different molecular families such as flavonoids, carboxylic acids and derivatives, lignin glycosides, fatty acyls, and macrolactams that are found within the plant. In silico annotation tools such as network annotation propagation (NAP) and DEREPLICATOR, an unsupervised substructure identification tool (MS2LDA), and MolNet enhancer were also explored to further compliment the classic molecular networking output within the Global Natural Product Social (GNPS) site. In this study, common flavonoids found within Moringa oleifera were further annotated using MS2LDA. Utilizing computational tools allowed for the discovery of a wide range of structurally diverse flavonoid molecules within M. oleifera leaf extracts. The expansion of the flavonoid chemical repertoire in this plant arises from intricate glycosylation modifications, leading to the creation of structural isomers that manifest as isobaric ions during mass spectrometry (MS) analyses.

Rationalising the retro-Diels-Alder fragmentation pattern of viscutins using electrospray interface-tandem mass spectrometry coupled to theoretical modelling

RATIONALE

Although mass spectrometry (MS) is a powerful tool in structural elucidation of unknown flavonoids based on their unique fragmentation patterns, proposing the correct fragmentation mechanism is still a challenge from tandem mass spectrometry data only. In recent years, computational tools such as molecular networking and MS2LDA have played a major role in the identification of structurally related compounds through an in-depth survey of their fragmentation patterns.

METHODS

Therefore, in this study, three viscutin molecules in Viscum combreticola Engl. crude extracts were characterised using ultra-high-performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry and MS2LDA, a computational tool. Ion-trap mass spectrometry and density functional theoretical modelling were used as confirmatory tools to rationalise the unique fragmentation patterns observed for these molecules.

RESULTS

Here, MS2LDA revealed the presence of a unique Mass2Motif in all the three viscutin molecules at m/z 137, which was confirmed to be a ^1,3 A^- RDA (retro-Diels-Alder) fragmentation product using liquid chromatography-ion-trap mass spectrometry and density functional theoretical modelling. Moreover, MS2LDA proved to be useful in differentiating this spectral feature that was specific to viscutin molecules in the presence of other isobaric ions at m/z 137 occurring in compounds in other molecular families.

CONCLUSION

Therefore, the results of the current study showed that computational tools such as MS2LDA are essential in uncovering some gas-phase fragmentation reactions of molecules in MS and that theoretical modelling is a powerful tool in rationalising these reactions in metabolite identification.

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.

Eco-physiological response of secondary metabolites of teas: Review of quality attributes of herbal tea

Herbal tea is a rich source of secondary metabolites which are reputed to have medicinal and nutritional efficacy. These secondary metabolites are influenced by the abiotic and biotic stresses that improve the production of herbal teas in terms of biomass production, accumulation and partitioning of assimilates of compounds. In this study, various examples of herbal teas have been shown to respond differently to secondary metabolites affected by environmental factors. Thus, the meta-analysis of this study confirms that different herbal teas' response to environmental factors depends on the type of species, cultivar, and the degree of shade that the plant is exposed. It is also evident that the metabolic processes are also known to optimize the production of secondary metabolites which can thus be achieved by manipulating agronomic practices on herbal teas. The different phenolic compound in herbal teas possesses the antioxidant, antimicrobial, antiatherosclerosis, anti-inflammatory, antimutagenic, antitumor, antidiabetic and antiviral activities that are important in managing chronic diseases associated with lifestyle. It can be precluded that more studies should be conducted to establish interactive responses of biotic and abiotic environmental factors on quality attributes of herbal teas.

Evaluation of a Chaotrope and Kosmotrope in the Multivariate Optimization of PHW-ATPE of Solasodine from Leaves of Solanum mauritianum

A hyphenated pressurized hot water—aqueous two-phase extraction (PHW-ATPE) method was applied to extract solasodine from Solanum mauritianum (S. mauritianum). A central composite design (CCD) was applied to determine the optimal conditions for the extraction of solasodine. The parameters evaluated included the percentage concentration of salt (NaCl or Na2CO3) and temperature. The fit of the central composite design response surface model for PHW-ATPE to the data generated a model with a good quadratic fit (R2 = 0.901). The statistically significant (p < 0.05) parameters, such as the linear and quadratic effects of the concentration of salt (%) powder, had a significant impact on the extraction of solasodine. The application of multiply charged salts such as Na2CO3 (kosmotrope) was shown to be a comparably better extractant of solasodine than NaCl (chaotrope) due to the salting-out effect. The optimized conditions for extraction of solasodine with NaCl or Na2CO3 were a temperature of 80 °C at a salt concentration of 20%. The maximum extraction of solasodine was 300.79 mg kg−1 and 162.34 mg kg−1 for Na2CO3 and NaCl, respectively.

Diverse chemical modifications of the chlorogenic acid composition of Viscum combreticola Engl.: A premise for the state of readiness against excessive sunlight exposure

Mistletoe plants that are positioned on the canopy of their hosts are more susceptible to UV radiation exposure. These aerial plants are resistant to damage by UV radiation due the presence of epidermal constituents such as the cuticle, cork layer, trichomes and antioxidant secondary metabolites. In response to the photo-oxidative stress associated with UV exposure, plants generally deploy photo-protective responsive mechanisms that involve the biosynthesis of UV absorbing phenolic compounds such as chlorogenic acids (CGAs). The hydroxycinnamic acid moieties of these CGAs are predominantly in the trans configuration, naturally. However, excessive sunlight exposure of plants containing these compounds can result in geometrical isomerisation, characterized by the formation of cis isomers. Therefore, in this study, the effect of UV light radiation on the CGA composition of Viscum combreticola Engl. (Santalacaeae) plants using an in vitro model was unravelled through UHPLC-q-TOF-MS-based metabolic profiling. Interestingly, the findings of this study revealed that this plant has a diverse chemical composition of CGAs that is characterized by epimerization, monoacylation, homodiacylation and heterodiacylation of the quinic acid (QA), thereby, contributing to the state of readiness in these plants against sunlight or UV exposure. In addition to the commonly reported cinnamoyl containing heterodiacylated CGAs, hydroxybenzoyl containing heterodiacylated CGAs were also reported in this study. Moreover, cis isomers (24 in total) of some CGAs were identified in the non-irradiated samples and the formation of these compounds has been reported to help plants in the mitigation of photo-oxidative stress. An additional 28 cis isomers of CGAs and HCA derivatives were observed in the UV-irradiated samples, hence, further increasing the complexity of the metabolome of this plant, with a total of 108 compounds identified in this study. The presence of epimers, positional and geometrical isomers of these compounds could be a biochemical strategy to maximize the chemical arsenal of this plant to withstand the photo-oxidative stress posed by UV radiation from the sunlight. Due to purported pharmacological properties associated with the identified compounds these parasitic plants can be a rich source of prospective therapeutic compounds that can be employed as drug discovery leads. Moreover, UV radiation might be essential in future to produce potent drugs since plants naturally produce these compounds in low quantities.

Parallel validation of a green-solvent extraction method and quantitative estimation of multi-mycotoxins in staple cereals using LC-MS/MS

In this study, 15 different mycotoxins were estimated in three staple cereals from selected agro-ecological regions in Nigeria using a 'novel' green extraction method, pressurized hot water extraction (PHWE) in comparison to a conventional solvent extraction method. Discrimination of the results of PHWE and solvent extraction using principal component analysis (PCA) and orthogonal projection to latent structures discriminate analysis (OPLS-DA) did not yield any differential clustering patterns. All maize samples (n = 16), 32% (n = 38) of sorghum and 35% (n = 37) of millet samples were positive for at least one of the 15 tested mycotoxins. Contamination levels for the cereals were higher in the warm humid rain forest region and gradually decreased towards the hot and arid region in the north of the country. The results demonstrate the applicability of PHWE as a possible alternative extraction method to conventional methods of extraction, which are solvent based.

Scribbling the Cat: A Case of the "Miracle" Plant, Moringa oleifera

This paper reviews the properties of the most cultivated species of the Moringaceae family, Moringa oleifera Lam. The paper takes a critical look at the positive and the associated negative properties of the plant, with particular emphasis on its chemistry, selected medicinal and nutritional properties, as well as some ecological implications of the plant. The review highlights the importance of glucosinolates (GS) compounds which are relatively unique to the Moringa species family, with glucomoriginin and its acylated derivative being the most abundant. We highlight some new research findings revealing that not all M. oleifera cultivars contain an important flavonoid, rutin. The review also focuses on phenolic acids, tannin, minerals and vitamins, which are in high amounts when compared to most vegetables and fruits. Although there are numerous benefits of using M. oleifera for medicinal purposes, there are reports of contraindications. Nonetheless, we note that there are no major harmful effects of M. oleifera that have been reported by the scientific community. M. oleifera is suspected to be potentially invasive and moderately invasive in some regions of the world because of its ability to grow in a wide range of environmental conditions. However, the plant is currently classified as a low potential invasive species and thus there is a need to constantly monitor the species. Despite the numerous benefits associated with the plant, there is still a paucity of data on clinical trials proving both the positive and negative effects of the plant. We recommend further clinical trials to ascertain the properties associated with the plant, especially regarding long term use.

Development, chemometric-assisted optimization and in-house validation of a modified pressurized hot water extraction methodology for multi-mycotoxins in maize

Effective management of mycotoxins rely on stringent regulation and routine surveillance of food/feed commodities via efficient analysis, hence the continuous need for improved methods. The present study developed, optimized and validated a modified pressurized hot water extraction (PHWE) method for the simultaneous extraction of multi-mycotoxins from maize and subsequent quantification on LC-MS/MS. The PHWE system was modified using ethanol (EtOH) as a cosolvent, while a numerical modelling approach, the central composite design (CCD), was adopted for the optimization of the extraction conditions. Using the optimized method, it was possible to effectively extract and quantify 15 different mycotoxins from maize in a single step with satisfactory linearities (0.986-0.999), recoveries (14-124%) and other associated method validation parameters. Further efficacious application of the method to real samples re-affirmed the prospects of PHWE as a suitable, cost-effective and greener alternative to traditional methods of mycotoxin extraction.

Metabolomics-guided investigations of unintended effects of the expression of the hydroxycinnamoyl quinate hydroxycinnamoyltransferase (hqt1) gene from Cynara cardunculus var. scolymus in Nicotiana tabacum cell cultures

Chlorogenic acids (CGAs) are phenolic compounds biosynthesized in the phenylpropanoid pathway, with hydroxycinnamoyl quinate hydroxycinnamoyltransferase (HQT) as the key enzyme. Variation of CGAs has been noted in different plants, with globe artichoke (Cynara cardunculus var. scolymus L.) producing high amounts and a diverse spectrum of CGAs in its leaves. In the current study, the effect of overexpression of the hqt1 transgene from globe artichoke in tobacco was evaluated at the metabolome level. Here, metabolomic approaches based on ultra-high performance liquid chromatography coupled to mass spectrometry, together with chemometric models such as principal component analysis and orthogonal partial least square discriminant analysis, were employed to evaluate altered metabolic changes due to hqt1 overexpression. CGA profiles (caffeoylquinic acids: 3-CQA, 4-CQA and 5-CQA; p-coumaroylquinic acids: 4-pCoQA and 5-pCoQA; and 4,5-di-caffeoylquinic acid) of transgenic tobacco cell cultures were detected at lower concentrations than in the wild type. Interestingly, the cells were found to rather accumulate, as an unintended effect, abscisic acid - and benzoic acid derivatives. The results suggest that insertion of hqt1 in tobacco, and overexpression in undifferentiated cells, led to rechannelling of the phenylpropanoid pathway to accumulate benzoic acids. These findings proved to be contrary to the results shown elsewhere in leaf tissues, thus indicating differential metabolic control and regulation in the undifferentiated cell culture system.

Untargeted metabolomics analysis reveals dynamic changes in azelaic acid- and salicylic acid derivatives in LPS-treated Nicotiana tabacum cells

To counteract biotic stress factors, plants employ multilayered defense mechanisms responsive to pathogen-derived elicitor molecules, and regulated by different phytohormones and signaling molecules. Here, lipopolysaccharide (LPS), a microbe-associated molecular pattern (MAMP) molecule, was used to induce defense responses in Nicotiana tabacum cell suspensions. Intracellular metabolites were extracted with methanol and analyzed using a liquid chromatography-mass spectrometry (UHPLC-qTOF-MS/MS) platform. The generated data were processed and examined with multivariate and univariate statistical tools. The results show time-dependent dynamic changes and accumulation of glycosylated signaling molecules, specifically those of azelaic acid, salicylic acid and methyl-salicylate as contributors to the altered metabolomic state in LPS-treated cells.

Chlorogenic Acids Biosynthesis in Centella asiatica Cells Is not Stimulated by Salicylic Acid Manipulation

Exogenous application of synthetic and natural elicitors of plant defence has been shown to result in mass production of secondary metabolites with nutraceuticals properties in cultured cells. In particular, salicylic acid (SA) treatment has been reported to induce the production of phenylpropanoids, including cinnamic acid derivatives bound to quinic acid (chlorogenic acids). Centella asiatica is an important medicinal plant with several therapeutic properties owing to its wide spectrum of secondary metabolites. We investigated the effect of SA on C. asiatica cells by monitoring perturbation of chlorogenic acids in particular. Different concentrations of SA were used to treat C. asiatica cells, and extracts from both treated and untreated cells were analysed using an optimised UHPLC-QTOF-MS/MS method. Semi-targeted multivariate data analyses with the aid of principal component analysis (PCA) and orthogonal projection to latent structures-discriminant analysis (OPLS-DA) revealed a concentration-dependent metabolic response. Surprisingly, a range of chlorogenic acid derivatives were found to be downregulated as a consequence of SA treatment. Moreover, irbic acid (3,5-O-dicaffeoyl-4-O-malonilquinic acid) was found to be a dominant CGA in C. asiatica cells, although the SA treatment also had a negative effect on its concentration. Overall SA treatment was found to be an ineffective elicitor of CGA production in cultured C. asiatica cells.

Secondary metabolite perturbations in Phaseolus vulgaris leaves due to gamma radiation

Oxidative stress is a condition in which the balance between the production and elimination of reactive oxygen species (ROS) is disturbed. However, plants have developed a very sophisticated mechanism to mitigate the effect of ROS by constantly adjusting the concentration thereof to acceptable levels. Electromagnetic radiation is one of the factors which results in oxidative stress. In the current study, ionizing gamma radiation generated from a Cobalt-60 source was used to induce oxidative stress in Phaseolus vulgaris seedlings. Plants were irradiated with several radiation doses, with 2 kGy found to be the optimal, non-lethal dose. Metabolite distribution patterns from irradiated and non-irradiated plants were analyzed using UHPLC-qTOF-MS and multivariate data models such as principal component analysis (PCA) and orthogonal projection to latent structures discriminate analysis (OPLS-DA). Metabolites such as hydroxycinnamic phenolic acids, flavonoids, terpenes, and a novel chalcone were found to be perturbed in P. vulgaris seedlings treated with the aforementioned conditions. The results suggest that there is a compensatory link between constitutive protectants and inducible responses to injury as well as defense against oxidative stress induced by ionizing radiation. The current study is also the first to illustrate the power of a metabolomics approach to decipher the effect of gamma radiation on crop plants.

Metabolomic fingerprinting of primed tobacco cells provide the first evidence for the biological origin of cis-chlorogenic acid

Previous studies suggest that only trans-isomers of chlorogenic acid (CGA) are naturally produced. Cis-isomers have been noted in some plant tissues exposed to different mechanical processes as well as untreated tobacco leaves exposed to sunlight. Very little, however, is known about the biological significance and origin of cis-isomers. Here we show for the first time the accumulation of cis-5-caffeoylquinic acid in cultured tobacco cells treated with different inducers of plant defence (lipopolysaccharides, flagellin peptide-22, chitosan, acibenzolar-S-methyl and isonitrosoacetophenone), without exposure to UV light and with a 2-fold (on average) increase in the concentration of the pool in comparison to non-stimulated cells. Our UHPLC-Q-TOF-MS and multivariate statistical results suggest the presence of a possible biological pathway responsible for the production of cis-CGAs in tobacco plants.

Activation of camalexin biosynthesis in Arabidopsis thaliana in response to perception of bacterial lipopolysaccharides: a gene-to-metabolite study

Lipopolysaccharides (LPS), as lipoglycan microbe-associated molecular pattern molecules, trigger activation of signal transduction pathways involved in defence that generate an enhanced defensive capacity in plants. The transcriptional regulation of the genes for tryptophan synthase B, TSB1, and the cytochrome P450 monooxygenases CYP79B2 and CYP71B15, involved in the camalexin biosynthetic pathway, were investigated in response to LPS treatment. GUS-reporter assays for CYP71B15 and CYP79B2 gene promoter activation were performed on transgenic plants and showed positive histochemical staining in response to LPS treatment, indicating activation of the promoters. Quantitative PCR revealed that transcripts of TSB1, CYP79B2 and CYP71B15 exhibited differential, transient up-regulation. TSB1 transcript levels were up-regulated between 6 and 9 h after LPS-induction, while CYP71B15 and CYP79B2 both exhibited maxima at 12 h. To obtain information on the gene-to-metabolite network, the effect of the transcriptome changes on the metabolome was correlated to camalexin production. Increases in camalexin concentration were quantified by ultra pressure liquid chromatography-mass spectrometry and both absorbance spectra and elemental composition confirmed its identity. The concentrations increased from 0.03 to 3.7 μg g(-1) fresh weight over a 24-h time period, thus indicating that the up-regulation of the biosynthetic pathway in response to LPS was accompanied by a time-dependent increase in camalexin concentration. Metabolomic analysis through principal component analysis-derived scores plots revealed clusters of sample replicates for 0, 6, 12, 18 and 24 h while loadings plots for LPS data identified camalexin as a biomarker that clearly demonstrated the variability between samples.