Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides

Direct Cloning and Heterologous Expression of the Dmxorosin Biosynthetic Gene Cluster from Streptomyces thermolilacinus SPC6, a Halotolerant Actinomycete Isolated from the Desert in China

Streptomyces thermolilacinus SPC6 is a halotolerant strain isolated from the Linze Desert in China. It has a very high growth rate and short life cycle compared to other Streptomycetes, including the model organism Streptomyces coelicolor. The one strain-many compounds fermentation approach and global natural products investigation revealed that Streptomyces thermolilacinus SPC6 exhibits impressive productivity of secondary metabolites. Genome mining uncovered 20 typical secondary metabolic biosynthetic gene clusters (BGC), with a BGC dmx identified as completely silent. Subsequently, this cryptic BGC was successfully directly cloned and heterologously expressed in Streptomyces hosts, resulting in the discovery of a new lanthipeptide, dmxorosin. Notably, the proposed biosynthetic pathway indicates its potential as a basis for the synthetic biology of new lanthipeptide.

Chemical Informatics Combined with Kendrick Mass Analysis to Enhance Annotation and Identify Pathways in Soybean Metabolomics

BACKGROUND

Among abiotic stresses to agricultural crops, drought stress is the most prolific and has worldwide detrimental impacts. The soybean (Glycine max) is one of the most important sources of nutrition to both livestock and humans. Different plant introductions (PI) of soybeans have been identified to have different drought tolerance levels.

OBJECTIVES

Here, two soybean lines, Pana (drought sensitive) and PI 567731 (drought tolerant) were selected to identify chemical compounds and pathways which could be targets for metabolomic analysis induced by abiotic stress.

METHODS

Extracts from the two lines are analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The high mass resolution and accuracy of the method allows for identification of ions from hundreds of different compounds in each cultivar. The exact m/z of these species were filtered through SoyCyc and the Human Metabolome Database to identify possible molecular formulas of the ions. Next, the exact m/z values were converted into Kendrick masses and their Kendrick mass defects (KMD) computed, which were then sorted from high to low KMD. This latter process assists in identifying many additional molecular formulas, and is noted to be particularly useful in identifying formulas whose mass difference corresponds to two hydrogen atoms.

RESULTS

In this study, more than 460 ionic formulas were identified in Pana, and more than 340 ionic formulas were identified in PI 567731, with many of these formulas reported from soybean for the first time.

CONCLUSIONS

Using the SoyCyc matches, the metabolic pathways from each cultivar were compared, providing lists of molecular targets available to profile effects of abiotic stress on these soybean cultivars. Key metabolites include chlorophylls, pheophytins, mono- and diacylglycerols, cycloeucalenone, squalene, and plastoquinones and involve pathways which include the anabolism and catabolism of chlorophyll, glycolipid desaturation, and biosynthesis of phytosterols, plant sterols, and carotenoids.

Metabolites rapid-annotation in mice by comprehensive method of virtual polygons and Kendric mass loss filtering: A case study of Dendrobium nobile Lindl

With significant advancements in high-resolution mass spectrometry, there has been a substantial increase in the amount of chemical component data acquired from natural products. Therefore, the rapid and efficient extraction of valuable mass spectral information from large volumes of high-resolution mass spectrometry data holds crucial significance. This study illustrates a targeted annotation of the metabolic products of alkaloid and sesquiterpene components from Dendrobium nobile (D. nobile) aqueous extract in mice serum through the integration of an in-houses database, R programming, a virtual metabolic product library, polygonal mass defect filtering, and Kendrick mass defect strategies. The research process involved initially establishing a library of alkaloids and sesquiterpenes components and simulating 71 potential metabolic reactions within the organism using R programming, thus creating a virtual metabolic product database. Subsequently, employing the virtual metabolic product library allowed for polygonal mass defect filtering, rapidly screening 1705 potential metabolites of alkaloids and 3044 potential metabolites of sesquiterpenes in the serum. Furthermore, based on the chemical composition database of D. nobile and online mass spectrometry databases, 95 compounds, including alkaloids, sesquiterpenes, and endogenous components, were characterized. Finally, utilizing Kendrick mass defect analysis in conjunction with known alkaloids and sesquiterpenes targeted screening of 209 demethylation, methylation, and oxidation products in phase I metabolism, and 146 glucuronidation and glutathione conjugation products in phase II metabolism. This study provides valuable insights for the rapid and accurate annotation of chemical components and their metabolites in vivo within natural products.

Mass spectrometric stochastic dynamic 3D structural analysis of mixture of steroids in solution - Experimental and theoretical study

There is explored, herein, functional relation: Experimental mass spectrometric phenomenon, obeying a certain scientific law ⇔ 3D molecular conformations and electronic structures of analytes obtained for quantum chemical theories. The paper answers to questions: (a) What evidence claims these actual relations among measurable and theoretical parameters, experimental factors and molecular properties; (b) how the provided evidence is collected and used; and (c) how empirical proof relates to assign and explain mass spectrometric phenomena of steroids afforded by our innovative stochastic dynamic mass spectrometric formula, D″_SD = 2.6388.10^-17.(<I²>-<I>²), quantum chemical 3D conformations, electronic structures and energetics of molecules, respectively. The paper address issue concerning empirical evidence at very high-to-exact level of assignment of 3D molecular conformations of steroids to experimental mass spectrometric fragment ions, accounting precisely for (i) effect of protonation; (ii) intramolecular rearrangement for A-D rings of steroidal skeleton and proton transfer effect, if any; in addition to (iii) examination of enantiomers of steroids in mixture with different stereochemistry, (R) and (S), of a set of six atoms of the molecular backbone of hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4), respectively. Results from testosterone (5) are discussed, as well. There are used ultra-high resolution atmospheric pressure chemical ionization mass spectrometric data on analytes (1)-(4) at ng.(mL)^-1 concentration levels in mixtures in solution obtained for positive operation mode. High accuracy static and molecular dynamic quantum chemical computations and chemometrics are also utilized. Experimental 3D structural parameters of steroids obtained for stochastic dynamic diffusion theory are correlated with available crystallographic data.

Pseudomonas sp. COW3 Produces New Bananamide-Type Cyclic Lipopeptides with Antimicrobial Activity against Pythium myriotylum and Pyricularia oryzae

Pseudomonas species are metabolically robust, with capacity to produce secondary metabolites including cyclic lipopeptides (CLPs). Herein we conducted a chemical analysis of a crude CLP extract from the cocoyam rhizosphere-derived biocontrol strain Pseudomonas sp. COW3. We performed in silico analyses on its whole genome, and conducted in vitro antagonistic assay using the strain and purified CLPs. Via LC-MS and NMR, we elucidated the structures of four novel members of the bananamide group, named bananamides D-G. Besides variability in fatty acid length, bananamides D-G differ from previously described bananamides A-C and MD-0066 by the presence of a serine and aspartic acid at position 6 and 2, respectively. In addition, bananamide G has valine instead of isoleucine at position 8. Kendrick mass defect (KMD) allowed the assignment of molecular formulae to bananamides D and E. We unraveled a non-ribosomal peptide synthetase cluster banA, banB and banC which encodes the novel bananamide derivatives. Furthermore, COW3 displayed antagonistic activity and mycophagy against Pythium myriotylum, while it mainly showed mycophagy on Pyricularia oryzae. Purified bananamides D-G inhibited the growth of P. myriotylum and P. oryzae and caused hyphal distortion. Our study shows the complementarity of chemical analyses and genome mining in the discovery and elucidation of novel CLPs. In addition, structurally diverse bananamides differ in their antimicrobial activity.