Biotransformations utilizing β-oxidation cycle reactions in the synthesis of natural compounds and medicines

Biotransformation of ferulic acid into vanillyl alcohol and vanillic acid employing thermophilic bacterium Caldimonas thermodepolymerans

Caldimonas thermodepolymerans, a Gram-negative, moderately thermophilic bacterium, exhibits a remarkable biotechnological potential. Given the presence of genes in its genome dedicated to the metabolization of ferulic acid (FA), this study aimed to explore the bacterium's capability for biotransforming FA into high-value metabolites. The results unequivocally demonstrate the bacterium's proficiency in the efficient and rapid conversion of FA into vanillyl alcohol (VOH) and vanillic acid (VA). By manipulating key cultivation parameters, such as adjusting initial FA doses and varying cultivation periods, the product profile can be tailored. Higher initial doses and shorter cultivation periods favor the production of VOH, while lower FA doses and extended cultivation periods lead to the predominant formation of VA. Furthermore, the process can be operated in a repeated-batch scenario. This underscores the potential of C. thermodepolymerans for industrial biotransformation of FA, presenting a promising avenue for leveraging its capabilities in practical applications.

Altered lipid metabolism as a predisposing factor for liver metastasis in MASLD

Recently, the incidence of metabolic dysfunction-associated steatotic liver disease (MASLD) is increasing due to the high prevalence of metabolic conditions, such as obesity and type 2 diabetes mellitus. Steatotic liver is a hotspot for cancer metastasis in MASLD. Altered lipid metabolism, a hallmark of MASLD, remodels the tissue microenvironment, making it conducive to the growth of metastatic liver cancer. Tumors exacerbate the dysregulation of hepatic metabolism by releasing extracellular vesicles and particles into the liver. Altered lipid metabolism influences the proliferation, differentiation, and functions of immune cells, contributing to the formation of an immunosuppressive and metastasis-prone liver microenvironment in MASLD. This review discusses the mechanisms by which the steatotic liver promotes liver metastasis progression, focusing on its role in fostering an immunosuppressive microenvironment in MASLD. Furthermore, this review highlights lipid metabolism manipulation strategies for the therapeutic management of metastatic liver cancer.

Metabolic and Process Engineering for Producing the Peach-Like Aroma Compound γ-Decalactone in Yarrowia lipolytica

Due to its strong and unique peach-like aroma, γ-decalactone is widely used in dairy products and other foods or beverages. The oleaginous yeast Yarrowia lipolytica, which is generally regarded as safe, has shown great potential in the production of this flavor compound. Recently, the development of metabolic and process engineering has enabled the application of Y. lipolytica for the production of γ-decalactone. This Review summarizes the relevant biosynthesis and degradation pathways of Y. lipolytica, after which the related metabolic engineering strategies to increase the accumulation of γ-decalactone are summarized. In addition, the factors affecting γ-decalactone accumulation in Y. lipolytica are introduced, and corresponding process optimization strategies are discussed. Finally, the current research needs are analyzed to search for remaining challenges and future directions in this field.

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.)

Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.

Human Pharmacokinetics of LYS006, an Oral Leukotriene A4 Hydrolase Inhibitor Displaying Target-Mediated Drug Disposition

LYS006 is a potent leukotriene A4 hydrolase inhibitor currently in clinical development for long-term treatment of various neutrophil-driven inflammatory conditions. Here, we present pharmacokinetics from the first-in-human study with complementary metabolism and transporter profiling data. The randomized first-in-human study included nine cohorts receiving 5-2*100 mg of LYS006 or placebo, a crossover food-effect part, and a multiple-dose part consisting of two fasted (5 mg and 15 mg once daily) and three fed cohorts (20-80 mg twice a day) of LYS006 or placebo. LYS006 and metabolites were assessed in plasma and urine, and transporters involved in LYS006 disposition were analyzed in vitro. Systemic plasma exposure increased with dose; steady-state exposure was dose proportional up to 40 mg twice a day. Steady state was achieved after ∼3 days, with mean accumulation of 2.1-fold for 5 mg once daily and ≤1.4-fold for all higher doses. Despite limited accumulation, a long terminal half-life (T1/2) was observed. The long T1/2 and saturable binding to blood cells, which causes a highly nonlinear blood-to-plasma distribution, reflect a strong impact of target binding on drug distribution at lower concentrations. Skin biopsy and blister fluid concentration data indicated saturable binding in the former but not the latter, suggesting saturable binding in tissues beyond blood. Major excretion of LYS006 (∼90% of dose) through urine at steady state triggered renal transporter investigations that identified LYS006 as a substrate of organic anion transporter (OAT)3, OAT4, breast cancer resistance protein, and multidrug resistance-associated protein 4. Seven metabolites were identified in human plasma and urine, comprising only 4% of the dose recovered in urine at steady state. SIGNIFICANCE STATEMENT: Pharmacokinetic data from a first-in-human study combined with in vitro work support dose and regimen selection for patient studies with LYS006 and provide guidance on drug interaction investigations and other clinical pharmacology work needed for further development. Mass balance information at steady state without the use of a radiolabel, skin concentrations, and identification of the major clearance pathway, as well as the transporters driving elimination, make this a particularly conclusive early study despite nonlinear pharmacokinetics impacted by target binding.

Analyzing macromolecular composition of E. Coli O157:H7 using Raman-stable isotope probing

Metabolic dynamics of bacterial cells is needed for understanding the correlation between changes in environmental conditions and cell metabolic activity. In this study, Raman spectroscopy combined with deuterium labelling was used to analyze the metabolic activity of a single Escherichia coli O157:H7 cell. The incorporation of deuterium from heavy water into cellular biomolecules resulted in the formation of carbon-deuterium (CD) peaks in the Raman spectra, indicating the cell metabolic activity. The broad vibrational peaks corresponding to CD and CH peaks encompassed different specific shifts of macromolecules such as protein, lipids, and nucleic acid. The utilization of tryptophan and oleic acid by the cell as the sole carbon source led to changes in cell lipid composition, as indicated by new peaks in the second derivative spectra. Thus, the proposed method could semi-quantitatively determine total metabolic activity, macromolecule specific identification, and lipid and protein metabolism in a single cell.

Production of lactones for flavoring and pharmacological purposes from unsaturated lipids: an industrial perspective

The enantiomeric pure and natural (+)-Lactones (C ≤ 14) with aromas obtained from fruits and milk are considered flavoring compounds. The flavoring value is related to the lactones' ring size and chain length, which blend in varying concentrations to produce different stone-fruit flavors. The nature-identical and enantiomeric pure (+)-lactones are only produced through whole-cell biotransformation of yeast. The industrially important γ-decalactone and δ-decalactone are produced by a four-step aerobic-oxidation of ricinoleic acid (RA) following the lactonization mechanism. Recently, metabolic engineering strategies have opened up new possibilities for increasing productivity. Another strategy for increasing yield is to immobilize the RA and remove lactones from the broth regularly. Besides flavor impact, γ-, δ-, ε-, ω-lactones of the carbon chain (C8-C12), the macro-lactones and their derivatives are vital in pharmaceuticals and healthcare. These analogues are isolated from natural sources or commercially produced via biotransformation and chemical synthesis processes for medicinal use or as active pharmaceutical ingredients. The various approaches to biotransformation have been discussed in this review to generate more prospects from a commercial point of view. Finally, this work will be regarded as a magical brick capable of containing both traditional and genetic engineering technology while contributing to a wide range of commercial applications.

Identification of Microorganisms Dwelling on the 19th Century Lanna Mural Paintings from Northern Thailand Using Culture-Dependent and -Independent Approaches

Simple Summary

In this study, we compared microbial communities in Lanna mural paintings in temples with different numbers of visitors using culture-dependent and culture independent approaches. The results showed that microorganisms could damage the colors that are used on murals. The process of degradation involved the production of organic acids and formation of the calcium crystal. Furthermore, we found that the site with higher number of visitors is associated with microbial contamination from humans while the site with lower number of visitors had higher saprotroph population. Further research into these microorganisms, their activities and functional roles may provide crucial information to aid the preservation of mural paintings.

Abstract

Lanna painting is a unique type of painting in many temples in the Northern Thai region. Similar to most mural paintings, they usually decay over time partly due to the activity of microbes. This study aimed to investigate the microorganisms from two Lanna masterpiece paintings in two temples that differ in the numbers of visitors using both culture-dependent and -independent approaches. The microorganisms isolated from the murals were also tested for the biodeterioration activities including discoloration, acid production and calcium precipitation. Most microorganisms extracted from the paintings were able to discolor the paints, but only fungi were able to discolor, produce acids and precipitate calcium. The microorganism communities, diversity and functional prediction were also investigated using the culture-independent method. The diversity of microorganisms and functional prediction were different between the two temples. Gammaproteobacteria was the predominant group of bacteria in both temples. However, the fungal communities were different between the two temples as Aspergillus was the most abundant genus in the site with higher number of visitors [Buak Krok Luang temple (BK)]. Conversely, mural paintings at Tha Kham temple (TK) were dominated by the Neodevriesia genera. We noticed that a high number of visitors (Buak Krok Luang) was correlated with microbial contamination from humans while the microbial community at Tha Kham temple had a higher proportion of saprotrophs. These results could be applied to formulate a strategy to mitigate the amount of tourists as well as manage microorganism to slow down the biodeterioration process.

Stereoselective synthesis of chiral δ-lactones via an engineered carbonyl reductase

A carbonyl reductase variant, SmCR_M5, from Serratia marcescens was obtained through structure-guided directed evolution. The variant showed improved specific activity (U mg^-1) towards most of the 16 tested substrates and gave high stereoselectivities of up to 99% in the asymmetric synthesis of 13 γ-/δ-lactones. In particular, SmCR_M5 showed a 13.8-fold higher specific activity towards the model substrate, i.e., 5-oxodecanoic acid, and gave (R)-δ-decalactone in 99% ee with a space-time yield (STY) of 301 g L^-1 d^-1. The preparative synthesis of six δ-lactones in high yields and with high enantiopurities showed the feasibility of the biocatalytic synthesis of these high-value-added chemicals, providing a cost-effective and green alternative to noble-metal catalysis.

Fatty Acid Composition of Meat Animals as Flavor Precursors

This article provides an overview of fatty acids in meat, their variation among animal species, and the roles of fatty acids as flavor precursors. Animal fat mostly consists of triglycerides and phospholipids. Fats from ruminant (cattle, sheep, and goats) and monogastric (pigs and horses) animals have similar fatty acids with more saturated fatty acids and monounsaturated fatty acids than polyunsaturated fatty acids. In monogastric animals, fatty acids in the muscle reflect the composition of diets, whereas ruminant fatty acids are more saturated because of biohydrogenation in the rumen. Lipid- derived flavor compounds are formed from the thermal oxidation of fatty acids during cooking, producing more desirable aromatic compounds than autoxidation. Monounsaturated fatty acids such as oleic acid and polyunsaturated fatty acids such as linoleic acid in meat produce various volatile compounds contributing to cooked meat aromas. Under most cooking conditions, lipid-derived flavor compounds are usually predominant. However, these compounds have greater thresholds than those derived from water-soluble compounds, such as the Maillard reaction products. The interactions between lipid oxidation products and Maillard compounds are more important for the development of meat flavor than originally thought. Moreover, fat-derived volatile compounds provide flavor notes indicative of species identification.

Double-Edged Metabolic Effects from Short-Term Feeding of Functionalized Wheat Bran to Mouse Revealed by Metabolomic Profiling

Health-promoting activities of wheat bran are limited by the high-degree crosslinking of its dietary fiber and the low bioavailability of its phenolics. In this study, functionalized wheat bran (FWB) was prepared through a combination of milling, alkaline hydrolysis, high-shear mixing, and high-pressure homogenization treatments. Feasibility and metabolic effects of feeding FWB were investigated by a short-term mouse feeding trial and liquid chromatography-mass spectrometry-based metabolomic analysis. The combinatorial processing dramatically enhanced the function-associated physicochemical properties of wheat bran, including viscosity, fiber compositions, free ferulic acid, and antioxidant capacity. FWB feeding led to diverse positive metabolic effects, including fecal sequestration of bile acids and cholesterol, reduced serum triacylglycerols and cholesterol, elevated fermentation for short-chain fatty acids, increased bioavailability of ferulic acid and its microbial metabolites, and improved redox balance. However, FWB feeding also negatively affected the nutritional status by decreasing the bioavailability of essential amino acids through the excessive loss of amino acids in feces and disrupting lipid homeostasis by reducing choline supply in the liver. These double-edged metabolic effects warrant further investigations on how to achieve the balance between the functionalization of wheat bran bioactives and the disruption of nutrient bioavailability.

Bioconversion of ferulic acid into aroma compounds by newly isolated yeast strains of the Latin American biodiversity

Nine yeast strains isolated from Latin American biodiversity were screened for ferulic acid (FA) consumption and conversion into aroma compounds such as vanillin, vanillic acid (VA), and 4-vinylguaiacol (VG). Selected strains (Rhodotorula mucilaginosa UFMG-CM-Y3647, UFMG-CM-Y2190, UFMG-CM-Y665) were evaluated in flask experiments to investigate the influence of the pH media on bioconversion and a two-step process was conducted to maximize the metabolites production. The effect of pH was found to be significantly important for FA bioconversion, as acidic conditions (pH < 6.0) improved VA accumulation, with highest production of 1.14 ± 0.02 and 1.25 ± 0.03 g/L shown by UFMG-CM-Y3647 and UFMG-CM-Y2190, respectively. The two-step process favored 4-VG production for most strains, being UFMG-CM-Y2190 the best producer, its cultures reaching 1.63 ± 0.09 g/L after 55 hr, showing a productivity of 29.59 ± 1.55 mg/(L·hr), as glucose affected the metabolites pool and redirected yeast metabolism. R mucilaginosa UFMG-CM-Y3647 was selected for scaled-up cultivations in a 2-L bioreactor, where pH-controlled pH 5.5 and aeration of 2.5 vvm was found to be the best condition to improve VA productivity, attaining final concentrations of 1.20 ± 0.02 g/L^-1 (78% molar yield) and a productivity of 40.82 ± 0.57 mg/(L·hr).

Fatty Acid Hydratases: Versatile Catalysts to Access Hydroxy Fatty Acids in Efficient Syntheses of Industrial Interest

The utilization of hydroxy fatty acids has gained more and more attention due to its applicability in many industrial building blocks that require it, for example, polymers or fragrances. Furthermore, hydroxy fatty acids are accessible from biorenewables, thus contributing to a more sustainable raw material basis for industrial chemicals. Therefore, a range of investigations were done on fatty acid hydratases (FAHs), since these enzymes catalyze the addition of water to an unsaturated fatty acid, thus providing an elegant route towards hydroxy-substituted fatty acids. Besides the discovery and characterization of fatty acid hydratases (FAHs), the design and optimization of syntheses with these enzymes, the implementation in elaborate cascades, and the improvement of these biocatalysts, by way of mutation in terms of the substrate scope, has been investigated. This mini-review focuses on the research done on process development using fatty acid hydratases as a catalyst. It is notable that biotransformations, running at impressive substrate loadings of up to 280 g L−1, have been realized. A further topic of this mini-review is the implementation of fatty acid hydratases in cascade reactions. In such cascades, fatty acid hydratases were, in particular, combined with alcohol dehydrogenases (ADH), Baeyer-Villiger monooxygenases (BVMO), transaminases (TA) and hydrolases, thus enabling access to a broad variety of molecules that are of industrial interest.

Vanilla bahiana, a contribution from the Atlantic Forest biodiversity for the production of vanilla: A proteomic approach through high-definition nanoLC/MS

Only a few cultivated species of Vanilla are used to produce vanilla, despite the high demand, predatory exploitation, and low genetic variability that threaten the production of natural vanilla. Vanilla bahiana pods from the Atlantic Forest may be an alternative source of natural vanilla. This study applied bottom-up and shotgun proteomics analysis to identify proteins related to flowering, fruiting, and vanilla-flavor production. Extraction solutions, including Tris-HCl buffer, β-mercaptoethanol and SDS, were assayed. SDS proved to be feasible for extraction of Vanilla fruit proteins and could be an alternative to the phenol method of protein extraction. Progenesis QI for Proteomics (QIP) software loaded with an Orchidaceae database identified 2326 proteins in our samples. Among these, 75 were highlighted as useful for the synthesis of compounds related to vanilla flavor, such as vanillin synthase, which was successfully extracted with 1% SDS, which also improved the variety of the extracted proteins. The proteins identified in V. bahiana pods indicate the enzymatic potential of this species, as further validated by quantifying the vanilla in the samples.

Comprehensive Comparative Analysis of Cholesterol Catabolic Genes/Proteins in Mycobacterial Species

In dealing with Mycobacterium tuberculosis, the causative agent of the deadliest human disease—tuberculosis (TB)—utilization of cholesterol as a carbon source indicates the possibility of using cholesterol catabolic genes/proteins as novel drug targets. However, studies on cholesterol catabolism in mycobacterial species are scarce, and the number of mycobacterial species utilizing cholesterol as a carbon source is unknown. The availability of a large number of mycobacterial species’ genomic data affords an opportunity to explore and predict mycobacterial species’ ability to utilize cholesterol employing in silico methods. In this study, comprehensive comparative analysis of cholesterol catabolic genes/proteins in 93 mycobacterial species was achieved by deducing a comprehensive cholesterol catabolic pathway, developing a software tool for extracting homologous protein data and using protein structure and functional data. Based on the presence of cholesterol catabolic homologous proteins proven or predicted to be either essential or specifically required for the growth of M. tuberculosis H37Rv on cholesterol, we predict that among 93 mycobacterial species, 51 species will be able to utilize cholesterol as a carbon source. This study’s predictions need further experimental validation and the results should be taken as a source of information on cholesterol catabolism and genes/proteins involved in this process among mycobacterial species.

Development of a promising microbial platform for the production of dicarboxylic acids from biorenewable resources

BACKGROUND

As a sustainable industrial process, the production of dicarboxylic acids (DCAs), used as precursors of polyamides, polyesters, perfumes, plasticizers, lubricants, and adhesives, from vegetable oil has continuously garnered interest. Although the yeast Candida tropicalis has been used as a host for DCA production, additional strains are continually investigated to meet productivity thresholds and industrial needs. In this regard, the yeast Wickerhamiella sorbophila, a potential candidate strain, has been screened. However, the lack of genetic and physiological information for this uncommon strain is an obstacle that merits further research. To overcome this limitation, we attempted to develop a method to facilitate genetic recombination in this strain and produce high amounts of DCAs from methyl laurate using engineered W. sorbophila.

RESULTS

In the current study, we first developed efficient genetic engineering tools for the industrial application of W. sorbophila. To increase homologous recombination (HR) efficiency during transformation, the cell cycle of the yeast was synchronized to the S/G2 phase using hydroxyurea. The HR efficiency at POX1 and POX2 loci increased from 56.3% and 41.7%, respectively, to 97.9% in both cases. The original HR efficiency at URA3 and ADE2 loci was nearly 0% during the early stationary and logarithmic phases of growth, and increased to 4.8% and 25.6%, respectively. We used the developed tools to construct W. sorbophila UHP4, in which β-oxidation was completely blocked. The strain produced 92.5 g/l of dodecanedioic acid (DDDA) from methyl laurate over 126 h in 5-l fed-batch fermentation, with a productivity of 0.83 g/l/h.

CONCLUSIONS

Wickerhamiella sorbophila UHP4 produced more DDDA methyl laurate than C. tropicalis. Hence, we demonstrated that W. sorbophila is a powerful microbial platform for vegetable oil-based DCA production. In addition, by using the developed genetic engineering tools, this emerging yeast could be used for the production of a variety of fatty acid derivatives, such as fatty alcohols, fatty aldehydes, and ω-hydroxy fatty acids.

Pharmacokinetic, Antiproliferative and Apoptotic Effects of Phenolic Acids in Human Colon Adenocarcinoma Cells Using In Vitro and In Silico Approaches

Colon cancer is the second most common cause of cancer deaths in the USA and Europe. Despite aggressive therapies, many tumors are resistant to current treatment protocols and epidemiological data suggest that diet is a major factor in the etiology of colon cancer. This study aimed to evaluate the antioxidant activity and the influence of 3,4-dihydroxyphenylacetic (3,4-DHPAA), p-coumaric (p-CoA), vanillic (VA) and ferulic (FA) acids on cell viability, cell cycle progression, and rate of apoptosis in human colon adenocarcinoma cells (HT-29). The results showed that all compounds tested reduce cell viability in human colon cancer cells. 3,4-DHPAA promoted the highest effect antiproliferative with an increase in the percentage of cells in G₀/G₁ phase, accompanied by a reduction of cells in G₂/M phase. Cell cycle analysis of VA and FA showed a decrease in the proportion of cells in G_0/G₁ phase (10.0 µM and 100.0 µM). p-CoA and FA acids increased the percentage of apoptotic cells and non-apoptotic cells. 3,4-DHPAA seems to be the substance with the greatest potential for in vivo studies, opening thus a series of perspectives on the use of these compounds in the prevention and treatment of colon cancer.

Theoretical Studies of Intracellular Concentration of Micro-organisms' Metabolites

With the rapid growth of micro-organism metabolic networks, acquiring the intracellular concentration of microorganisms’ metabolites accurately in large-batch is critical to the development of metabolic engineering and synthetic biology. Complementary to the experimental methods, computational methods were used as effective assessing tools for the studies of intracellular concentrations of metabolites. In this study, the dataset of 130 metabolites from E. coli and S. cerevisiae with available experimental concentrations were utilized to develop a SVM model of the negative logarithm of the concentration (-logC). In this statistic model, in addition to common descriptors of molecular properties, two special types of descriptors including metabolic network topologic descriptors and metabolic pathway descriptors were included. All 1997 descriptors were finally reduced into 14 by variable selections including genetic algorithm (GA). The model was evaluated through internal validations by 10-fold and leave-one-out (LOO) cross-validation, as well as external validations by predicting -logC values of the test set. The developed SVM model is robust and has a strong predictive potential (n = 91, m = 14, R² = 0.744, RMSE = 0.730, Q² = 0.57; R²_p = 0.59, RMSE_p = 0.702, Q²_p = 0.58). An effective tool could be provided by this analysis for the large-batch prediction of the intracellular concentrations of the micro-organisms’ metabolites.

Characterization of the newly isolated ω-oxidizing yeast Candida sorbophila DS02 and its potential applications in long-chain dicarboxylic acid production

α, ω-Dicarboxylic acids (DCAs) are multipurpose chemicals widely used in polymers, perfumes, plasticizers, lubricants, and adhesives. The biotransformation of DCAs from alkanes and fatty acids by microorganisms has attracted recent interest, since synthesis via chemical oxidation causes problems in terms of the environment and safety. We isolated an ω-oxidizing yeast from a wastewater disposal facility of a petrochemical factory by chemostat enrichment culture. The haploid strain identified as Candida sorbophila DS02 grew on glucose and dodecane, exhibiting greater cell shrinkage on the latter. In flask cultures with mixed alkanes (C10-16) and fatty acid methyl esters (C10-16), DS02 used mixed alkanes simultaneously unlike Candida tropicalis and Yarrowia lipolytica and showed high substrate resistance. In flask cultures with acrylic acid-a known inhibitor of β-oxidation-DS02 produced 0.28 g/l dodecanedioic acid (DDDA) from dodecane, similar to wild-type C. tropicalis ATCC 20336. In fed-batch fermentation, DS02 produced 9.87 g/l DDDA, which was 5.7-fold higher than wild-type C. tropicalis. These results suggest that C. sorbophila strain DS02 has potential applications for the large-scale production of DCA.

Toward the stereochemical identification of prohibited characterizing flavors in tobacco products: the case of strawberry flavor

With the revision of the European Tobacco Products Directive (2014/40/EU), characterizing flavors such as strawberry, candy, vanillin or chocolate will be prohibited in cigarettes and fine-cut tobacco. Product surveillance will therefore require analytical means to define and subsequently detect selected characterizing flavors that are formed by supplemented flavors within the complex matrix tobacco. We have analyzed strawberry-flavored tobacco products as an example for characterizing fruit-like aroma. Using this approach, we looked into aroma components to find indicative patterns or features that can be used to satisfy obligatory product information as requested by the European Directive. Accordingly, a headspace solid-phase microextraction (HS-SPME) technique was developed and coupled to subsequent gas chromatography-mass spectrometry (GC/MS) to characterize different strawberry-flavored tobacco products (cigarettes, fine-cut tobacco, liquids for electronic cigarettes, snus, shisha tobacco) for their volatile additives. The results were compared with non-flavored, blend characteristic flavored and other fruity-flavored cigarettes, as well as fresh and dried strawberries. Besides different esters and aldehydes, the terpenes linalool, α-terpineol, nerolidol and limonene as well as the lactones γ-decalactone, γ-dodecalactone and γ-undecalactone could be verified as compounds sufficient to convey some sort of strawberry flavor to tobacco. Selected flavors, i.e., limonene, linalool, α-terpineol, citronellol, carvone and γ-decalactone, were analyzed further with respect to their stereoisomeric composition by using enantioselective HS-SPME-GC/MS. These experiments confirmed that individual enantiomers that differ in taste or physiological properties can be distinguished within the tobacco matrix. By comparing the enantiomeric composition of these compounds in the tobacco with that of fresh and dried strawberries, it can be concluded that non-natural strawberry aroma is usually used to produce strawberry-flavored tobacco products. Such authenticity control can become of interest particularly when manufacturers claim that natural sources were used for flavoring of products. Although the definition of characterizing flavors by analytical means remains challenging, specific compounds or features are required to be defined for routine screening of reported information. Clarifications by sensory testing might still be necessary, but could be limited to a few preselected samples.

Can Ocimum basilicum L. and Ocimum tenuiflorum L. in vitro culture be a potential source of secondary metabolites?

In this study Ocimum basilicum L. (OB) and Ocimum tenuiflorum L. (OT) in vitro culture standardisation for increasing eugenol distribution, in comparison to their respective field grown parts was carried out. Eugenol was quantified using an optimised HPLC method and its relation with the total phenolic content (TPC) was measured. In vitro grown leaves and somatic embryos, of both OB and OT were found to contain similar quantities of eugenol (85μg/g approximately), higher than OB and OT field-grown leaves (30.2μg/g and 25.1μg/g respectively). It was also determined that in vitro grown leaves were richer in TPC than the field-grown intact organs. Results demonstrated the prominence of in vitro cultures for eugenol extraction. This study underlines that important food flavouring metabolites (e.g. vanillin, vanillic acids) might be produced, via the eugenol pathway, in Ocimum species that may be a good potential source of eugenol.

Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium

p-Hydroxycinnamates, such as ferulate and p-coumarate, are components of plant cell walls and have a number of commercial applications. Rhodococcus jostii RHA1 (RHA1) catabolizes ferulate via vanillate and the β-ketoadipate pathway. Here, we used transcriptomics to identify genes in RHA1 that are upregulated during growth on ferulate versus benzoate. The upregulated genes included three transcriptional units predicted to encode the uptake and β-oxidative deacetylation of p-hydroxycinnamates: couHTL, couNOM, and couR. Neither ΔcouL mutants nor ΔcouO mutants grew on p-hydroxycinnamates, but they did grow on vanillate. Among several p-hydroxycinnamates, CouL catalyzed the thioesterification of p-coumarate and caffeate most efficiently (k(cat)/K(m) = ∼ 400 mM(-1) s(-1)). p-Coumarate was also RHA1's preferred growth substrate, suggesting that CouL is a determinant of the pathway's specificity. CouL did not catalyze the activation of sinapate, in similarity to two p-coumaric acid:coenzyme A (CoA) ligases from plants, and contains the same bulged loop that helps determine substrate specificity in the plant homologues. The couO mutant accumulated 4-hydroxy-3-methoxyphenyl-β-ketopropionate in the culture supernatant when incubated with ferulate, supporting β-oxidative deacetylation. This phenotype was not complemented with a D257N variant of CouO, consistent with the predicted role of Asp257 as a metal ligand in this amidohydrolase superfamily member. These data suggest that CouO functionally replaces the β-ketothiolase and acyl-CoA thioesterase that occur in canonical β-oxidative pathways. Finally, the transcriptomics data suggest the involvement of two distinct formaldehyde detoxification pathways in vanillate catabolism and identify a eugenol catabolic pathway. The results of this study augment our understanding of the bacterial catabolism of aromatics from renewable feedstocks.

Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, beta-oxidative deacetylation pathway

The soil- and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl-CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl-CoA, vanillic acid, and protocatechuic acid. The genes atu1416, atu1417, and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)-CoA β-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform p-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

Anoxic androgen degradation by the denitrifying bacterium Sterolibacterium denitrificans via the 2,3-seco pathway

The biodegradation of steroids is a crucial biochemical process mediated exclusively by bacteria. So far, information concerning the anoxic catabolic pathways of androgens is largely unknown, which has prevented many environmental investigations. In this work, we show that Sterolibacterium denitrificans DSMZ 13999 can anaerobically mineralize testosterone and some C19 androgens. By using a (13)C-metabolomics approach and monitoring the sequential appearance of the intermediates, we demonstrated that S. denitrificans uses the 2,3-seco pathway to degrade testosterone under anoxic conditions. Furthermore, based on the identification of a C17 intermediate, we propose that the A-ring cleavage may be followed by the removal of a C2 side chain at C-5 of 17-hydroxy-1-oxo-2,3-seco-androstan-3-oic acid (the A-ring cleavage product) via retro-aldol reaction. The androgenic activities of the bacterial culture and the identified intermediates were assessed using the lacZ-based yeast androgen assay. The androgenic activity in the testosterone-grown S. denitrificans culture decreased significantly over time, indicating its ability to eliminate androgens. The A-ring cleavage intermediate (≤ 500 μM) did not exhibit androgenic activity, whereas the sterane-containing intermediates did. So far, only two androgen-degrading anaerobes (Sterolibacterium denitrificans DSMZ 13999 [a betaproteobacterium] and Steroidobacter denitrificans DSMZ 18526 [a gammaproteobacterium]) have been isolated and characterized, and both of them use the 2,3-seco pathway to anaerobically degrade androgens. The key intermediate 2,3-seco-androstan-3-oic acid can be used as a signature intermediate for culture-independent environmental investigations of anaerobic degradation of C19 androgens.

The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems

The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.