Target Metabolites Research Articles

Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis

Rheum emodi is a perennial herb and an important medicinal plant, with anthraquinones and flavonoids as its main bioactive compounds. However, there is little knowledge about the biosynthetic pathway of anthraquinones in rhubarbs. In this study, we qualitatively and quantitatively assessed 62 pharmacological metabolites in rhubarb using dynamic multiple reaction monitoring (dMRM) of triple-quadrupole mass spectrometry (QqQ-MS), including 21 anthraquinones, 17 flavonoids, 6 stilbenes, 12 gallate esters, 3 tannins, and 3 others. Besides, the metabolomics results showed significant differences among all the 60 metabolites, except for gallic acid and piceatannol-O-β-glucoside. The combined transcriptome data of R. palmatum L. (RPL) and R. officinale Baill. (ROB) showed that 21,691 unigenes were annotated in the metabolic pathways. Taken together, 17 differentially expressed genes (DEGs) were associated with the anthraquinone biosynthetic pathway. Additionally, a significant correlation between anthraquinone peak intensity and DEG expression level existed, validating that DEGs contribute to the anthraquinone biosynthetic pathway. RT-qPCR results showed that the cluster-14354.38156 gene may catalyze the O-methylation of emodin to produce physcion. This study provides a useful resource for further studies on secondary metabolism in rhubarb and the combination analysis of transcriptome and metabolome, which can help with the discovery of enzyme genes involved in metabolite biosynthesis.

Serum Metabolomic Indicates Potential Biomarkers and Metabolic Pathways of Pediatric Kashin-Beck Disease

ObjectiveTo explore potential serum biomarkers of children with Kashin-Beck Disease (KBD) and the metabolic pathways to which the biomarkers belong. MethodsA two-stage metabolomic study was employed. The discovery cohort included 56 patients, 51 internal controls, and 50 external controls. The metabolites were determined by HPLC-(Q-TOF)-MS and confirmed by Human Metabolome Databases (HMDB) and Metlin databases. MetaboAnalyst 3.0 and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to analyze the metabolic pathways of the candidate metabolites. The use of HPLC-(Q-TRAP)-MS enabled quantitative detection of the target metabolites which were chosen using the discovery study and verified in another independent verification cohort of 31 patients, 41 internal controls, and 50 external controls. ResultsEight candidate metabolites were identified out in the discovery study, namely kynurenic acid, N-α-acetylarginine, 6-hydroxymelatonin, sphinganine, ceramide, sphingosine-1P, spermidine, and glycine. These metabolites exist in sphingolipid, glutathione, and tryptophan metabolic pathways. In the second-stage study, five candidate metabolites were validated, including kynurenic acid, N-α-acetylarginine, sphinganine, spermidine, and sphingosine-1P. Except for spermidine, all substances exhibited low expression in the case group compared with the external control group, and the difference in levels of sphinganine, spermidine, and sphingosine-1P was statistically significant. ConclusionThe direction of change of levels of sphinganine, spermidine, and sphingosine-1P in the two-stage study cohorts was completely consistent, and the differences were statistically significant. Therefore, these substances can be used as potential biomarkers of KBD. Furthermore, these results raise the possibility that sphingolipid metabolic pathways may be closely related to KBD.

Targeted metabolomics study of early pathological features in hippocampus of triple transgenic Alzheimer's disease male mice.

Alzheimer's disease (AD) is a serious neurodegenerative disease in people of age 65 or above. The detailed etiology and pathogenesis of AD have not been elucidated yet. In this study, the hippocampi of 2- and 6-month-old triple transgenic Alzheimer's disease male mice and age-sex-matched wild-type (WT) mice were analyzed by using targeted metabolomics approach. Compared with WT mice, 24 and 60 metabolites were found with significant differences in 2- and 6-month-old AD mice. Among these, 14 metabolites were found common while 10 metabolites showed consistent variable trends in both groups. These differential metabolites are found associated with amino acid, lipid, vitamin, nucleotide-related base, neurotransmitter and energy metabolisms, and oxidative stress. The results suggest that these differential metabolites might play a critical role in AD pathophysiology, and may serve as potential biomarkers for AD. Moreover, the results highlight the involvement of abnormal purine, pyrimidine, arginine, and proline metabolism, along with glycerophospholipid metabolism in early pathology of AD. For the first time, several differential metabolites are found to be associated with AD in this study. Targeted metabolomics can be used for rapid and accurate quantitative analysis of specific target metabolites associated with AD.

Integrative Biosynthetic Gene Cluster Mining to Optimize a Metabolic Pathway to Efficiently Produce l-Homophenylalanine in Escherichia coli.

Mining biosynthetic genes for the exploration of hybrid metabolic pathways is a promising approach in heterologous production of natural and unnatural products. Here, we developed an integrative biosynthetic gene cluster (BGC) mining strategy to engineer the biosynthesis of l-homophenylalanine (l-Hph), an important intermediate for the synthesis of angiotensin-converting enzyme inhibitors. We assembled the putative l-Hph BGCs and integrated phylogenetic analysis with target metabolite abundance mapping to prioritize candidate BGCs. To obtain an effective l-Hph pathway, various combinations of candidate genes from different species were screened in an iterative design-build-test stepwise manner. After the pathway was strength balanced and the metabolic flux was enhanced, engineered Escherichia coli produced 1.41 g/L of l-Hph from glucose in feeding shake-flask fermentation. Our cluster mining strategy enabled optimization of the target metabolic pathway, and it would be promising for production of other valuable products in the postgenomic era.

Fluorescence-activated droplet sorting for enhanced pyruvic acid accumulation by Candida glabrata

One of the goals of metabolic engineering is to engineer strains that can optimally produce target metabolites. However, the current workflow for rational engineering of the metabolic pathway is sometimes time-consuming and labor-intensive. Here, we have established a cost-effective approach for screening for variants secreting metabolites. Different surface display systems were adopted and verified, which anchored pHluorin to the Candida glabrata cell surface to associate pyruvic acid detection with the read out of this reporter. A generalizable simulation approach based on computational fluid dynamics and regularity of generated droplet dimension was presented, which was found to be an efficient design tool to explore microfluidic characteristics or optimization. Finally, a microfluidic platform based on simulation coupled with surface display system was constructed. A mutant exhibiting a 73.6% increase in pyruvic acid production was identified. This ultrahigh-throughput screening pattern offers a practical guide for identifying microbial strains with many traits of interest.

Изучение физико-химических свойств и биологической активности экстрактов из высушенной биомассы каллусных, суспензионных клеток и корневых культур in vitro

Introduction. One of the urgent problems of medicine and biology is the use of plant objects as industrial producers of target metabolites in vitro. In vitro cells can be used as pharmaceutical preparations. Study objects and methods. The present research featured medicinal plants that grow in the Siberian Federal district and are a popular source of medicinal raw materials. The physicochemical properties, e.g. total ash content in extracts, the content of heavy metals, the content of organic solvents in the extracts, and the mass loss upon drying was determined by standard methods. The antimicrobial properties of in vitro extracts were determined by the diffusion method and the method based on optical density measurement. The list of opportunistic and pathogenic test strains included the following microorganisms: E. coli ATCC 25922, S. aureus ATCC 25923, P. vulgaris ATCC 63, P. aeruginosa ATCC 9027, and C. albicans EMTC 34. The number of viable cancer cells was determined using the MTT colorimetric method. Results and discussion. The paper describes the physicochemical properties, safety indicators, antioxidant activity, antimicrobial activity, and antitumor properties of extracts of a complex of biologically active substances obtained in vitro from the dried biomass of callus and suspension cell cultures and root cultures. The root extracts proved to have the maximum antimicrobial and cytotoxic properties. They could reduce the survival rate of cancer cells to 24.8–36.8 %. Conclusion. The research featured extracts obtained from the dried biomass of callus and suspension cell cultures and root cultures in vitro of safflower leuzea (Leuzea carthamoides L.), Rhodiola rosea (Rhodiola rosea L.), various sorts of skullcap (Scutellaria baicalensis L., Scutellaria andrachnoides L., Scutellaria galericulata L.), Potentilla alba (Potentilla alba L.) and ginseng (Panax L.). The results showed that the extracts can be used for the production of pharmaceuticals and biologically active additives with antitumor, antimicrobial, and antioxidant properties.

Development of an LC-MS Targeted Metabolomics Methodology to Study Proline Metabolism in Mammalian Cell Cultures.

A growing interest in metabolomics studies of cultured cells requires development not only untargeted methods capable of fingerprinting the complete metabolite profile but also targeted methods enabling the precise and accurate determination of a selected group of metabolites. Proline metabolism affects many crucial processes at the cellular level, including collagen biosynthesis, redox balance, energetic processes as well as intracellular signaling. The study aimed to develop a robust and easy-to-use targeted metabolomics method for the determination of the intracellular level of proline and the other two amino acids closely related to proline metabolism: glutamic acid and arginine. The method employs hydrophilic interaction liquid chromatography followed by high-resolution, accurate-mass mass spectrometry for reliable detection and quantification of the target metabolites in cell lysates. The sample preparation consisted of quenching by the addition of ice-cold methanol and subsequent cell scraping into a quenching solution. The method validation showed acceptable linearity (r > 0.995), precision (%RSD < 15%), and accuracy (88.5–108.5%). Pilot research using HaCaT spontaneously immortalized human keratinocytes in a model for wound healing was performed, indicating the usefulness of the method in studies of disturbances in proline metabolism. The developed method addresses the need to determine the intracellular concentration of three key amino acids and can be used routinely in targeted mammalian cell culture metabolomics research.

Simultaneous determination of 24,25- and 25,26-dihydroxyvitamin D3 in serum samples with liquid-chromatography mass spectrometry – A useful tool for the assessment of vitamin D metabolism

Vitamin D status is typically assessed by the measurement of 25-hydroxyvitamin D (25(OH)D). However, in selected patient groups the sole determination of 25(OH)D has been proven insufficient for this purpose. The simultaneous measurement of additional vitamin D metabolites may provide useful information for a better evaluation of the vitamin D status. Therefore, we developed and validated a liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the simultaneous determination of 25(OH)D3, 25(OH)D2, 24,25(OH)2D3 and additionally 25,26(OH)2D3, which was identified with a synthesized pure substance.Pure and deuterated substances were used to prepare calibrators and internal standards for all target metabolites. Pre-analytical sample preparation comprised protein precipitation followed by liquid-liquid-extraction and derivatization with 4-Phenyl-1,2,4-triazole-3,5-dione (PTAD) using 50 µL sample volume. Samples were analyzed on an Agilent HPLC 1260 system equipped with a silica-based Kinetex® 5 µm F5 100 Å core-shell column (150 × 4.6 mm) coupled to a Sciex 4500 mass spectrometer.For all four metabolites, limit of detection (LoD) and limit of quantification (LoQ) ranged from 0.3 to 1.5 nmol/L and 1.0 to 3.1 nmol/L, respectively. Recovery varied between 76.1 % and 84.3 %. Intra- and inter-assay imprecision were <8.6 % and <11.5 %, respectively. The analysis of external and internal quality control samples showed good accuracy for 25(OH)D3, 25(OH)D2, 24(R),25(OH)2D3 and 25,26(OH)2D3. Method comparison studies with human samples that were also analyzed with two other LC-MS/MS methods showed close agreement. Finally, the present method has been shown capable of identifying patients with 24-hydroxylase deficiency, which proves its clinical utility.

Modular engineering of Shiraia bambusicola for hypocrellin production through an efficient CRISPR system

Shiraia bambusicola exhibits an excellent capability to produce high-value pharmacological drugs, such as hypocrellin. However, less effective molecular tools hamper the processes to discover or exploit these metabolites. To address this issue, the more effective CRISPR/Cas9 system was constructed by optimizing the sgRNA transcription elements and disrupting the endogenous non-homologous end-joining pathway. These tactics prompted the gene-targeting frequency of 100% and simultaneously multiplex genome editing in S. bambusicola. This optimal CRISPR system encouraged us to rewire the entire hypocrellin flux and improve the yield by orchestrating the substrate pool supply, the central hypocrellin pathway, and the antioxidant system. Thus, 8632 mg/L hypocrellin was obtained, resulting in a 12-fold increase than that of the wild-type strain. This engineered S. bambusicola can still endure oxidative stresses from higher target metabolites and sustain an excellent biological activity. This study provides a whole conception to establish the more efficient genome-editing system. Higher conserved transcription elements for sgRNA expressions inspire us to adopt this system for gene modifications of other filamentous fungi. The rational and global biosystems outline will offer guidance to modulate metabolite productivity in other filamentous fungi.

Directed evolution of the transcription factor Gal4 for development of an improved transcriptional regulation system in Saccharomyces cerevisiae

As a well-characterized eukaryotic DNA binding transcription factor, Gal4 has been extensively employed to construct controllable gene expression systems in Saccharomyces cerevisiae. The problem of insufficient inducibility arises in the constructs with multiples genes under control of GAL promoters due to the low expression level and activity of the native Gal4. In order to obtain improved transcriptional regulation systems for multi-gene pathways, Gal4 mutants with improved activity were created by directed evolution. During the preliminary screening, five positive Gal4 variants were isolated based on the lycopene-indicated high-throughput screening method. Analysis of the mutation sites revealed that the majority of positive mutations are localized in the middle homology region with unspecified function, suggesting an important role of this domain in transactivation of Gal4. Through combinatorial site-directed mutagenesis, the best variant Gal4T406A/V413A was obtained, which successfully increased the transcription of PGAL-driven lycopene pathway genes and led to 48 % higher lycopene accumulation relative to the wild-type Gal4. This study demonstrates the viability of modifying Gal4 activity by directed evolution for elevated expression of PGAL-driven genes and therefore enhanced production of the target metabolite.

Lyophilization as pre-processing for sample storage in the determination of vitamin D3 and metabolites in serum and plasma

Determination of vitamin D levels in human biological specimens has gained a high relevance over the last decades, essentially because low levels have been associated with several biological disorders. In fact, vitamin D deficiency has become a worldwide health concern covering all ages and genders. The storage of biofluids has to be considered for determination of vitamin D and metabolites in order to fully preserve matrices status. This study attempts to evaluate lyophilization of serum and plasma as a pre-processing step for sample storage prior to quantitative analysis of vitamin D3 and its main hydroxylated metabolites −25(OH)D3, 24,25(OH)2D3 and 1,25(OH)2D3. The protocol including sample lyophilization was characterized in terms of analytical features and compared to the same method, based on SPE–LC–MS/MS, without lyophilization. Sensitivity, precision and accuracy were not affected when we operated with lyophilized serum and plasma and results provided by a set of twenty-four serum samples from DEQAS (Vitamin D External Quality Assessment Scheme) were in agreement with reported concentrations for 25(OH)D3 and 1,25(OH)2D3. A stability study programmed for 9 months allowed ensuring that the concentration of vitamin D3 and metabolites in lyophilized serum and plasma stored at room temperature was not affected during this period. This research has demonstrated that the quantitation of target metabolites is not under the influence of lyophilization. Therefore, including lyophilization prior to analysis could reduce shipment and storage costs, avoid delays of sample processing, and increase the stability of the target analytes due to an effective quenching process.

Novel Polyketide-Terpenoid Hybrid Metabolites from a Potent Nematicidal Arthrobotrys oligospora Mutant ΔAOL_s00215g278.

Here, we reported that detailed investigation on trace targeted metabolites from nematode-trapping fungus Arthrobotrys oligospora mutant with deletion of P450 gene AOL_s00215g278 led to isolation of 9 new polyketide-terpenoid hybrid derivatives, including four new glycosides of the key precursor farnesyl hydrotoluquinol (1) and, surprisingly, four new sesquiterpenyl epoxy-cyclohexenoids (SECs) analogues. Among them, two major target metabolites 1 and 14 displayed moderate nematode inhibitory ability. Moreover, the mutant lacking AOL_s00215g278 could form far more nematode-capturing traps within 6 h in contact with nematodes and show rapid potent nematicidal activity with killing 93.7% preys, though deletion of the P450 gene resulted in dramatic decrease in fungal colony growth and failure to produce fungal conidia. The results unequivocally revealed that gene AOL_s00215g278 should be involved in not only the SEC biosynthetic pathway in the nematode-trapping fungus A. oligospora but also fungal conidiation and nematicidal activity.

Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery from Salmonella enterica subsp. enterica Serovar Typhimurium Infection in Neonatal Chickens.

Enrofloxacin is an important antibiotic used for prevention and treatment of Salmonella infection in poultry in many countries. However, oral administration of enrofloxacin may lead to the alterations in the microbiota and metabolome in the chicken intestine, thereby reducing colonization resistance to the Salmonella infection. To study the effect of enrofloxacin on Salmonella in the chicken cecum, we used different concentrations of enrofloxacin to feed 1-day-old chickens, followed by oral challenge with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). We then explored the distribution pattern of S. Typhimurium in cecum contents in vivo and analyzed the microbial community structure of cecum contents using microbial 16S amplicon sequencing. Untargeted metabolomics was used to explore the gut metabolome on day 14. Faecalibacterium and Anaerostipes, which are closely related to the chicken intestinal metabolome, were screened using a multi-omics technique. The abundance of S. Typhimurium was significantly higher in the enrofloxacin-treated group than in the untreated group, and S. Typhimurium persisted longer. Moreover, the cecal colony structures of the three groups exhibited different characteristics, with Lactobacillus reaching its highest abundance on day 21. Notably, S. Typhimurium infection is known to affect the fecal metabolome of chickens differently. Thus, our results suggested that enrofloxacin and Salmonella infections completely altered the intestinal microbiota and metabolism of chickens.IMPORTANCE In this study, we examined the effects of S. Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote S. Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent S. Typhimurium infection.

Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics.

Global change scenarios in the Mediterranean basin predict a precipitation reduction within the coming hundred years. Therefore, increased drought will affect forests both in terms of adaptive ecology and ecosystemic services. However, how vegetation might adapt to drought is poorly understood. In this report, four years of climate change was simulated by excluding 35% of precipitation above a downy oak forest. RNASeq data allowed us to assemble a genome-guided transcriptome. This led to the identification of differentially expressed features, which was supported by the characterization of target metabolites using a metabolomics approach. We provided 2.5 Tb of RNASeq data and the assembly of the first genome guided transcriptome of Quercus pubescens. Up to 5724 differentially expressed transcripts were obtained; 42 involved in plant response to drought. Transcript set enrichment analysis showed that drought induces an increase in oxidative pressure that is mitigated by the upregulation of ubiquitin-like protein protease, ferrochelatase, oxaloacetate decarboxylase and oxo-acid-lyase activities. Furthermore, the downregulation of auxin biosynthesis and transport, carbohydrate storage metabolism were observed as well as the concomitant accumulation of metabolites, such as oxalic acid, malate and isocitrate. Our data suggest that early metabolic changes in the resistance of Q. pubescens to drought involve a tricarboxylic acid (TCA) cycle shunt through the glyoxylate pathway, galactose metabolism by reducing carbohydrate storage and increased proteolytic activity.

Determination of Aromatic Compounds Metabolites in Human Urine by Solid Phase Extraction-liquid Chromatography-Tandem Mass Spectrometry

To establish the method based on high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) with solid phase extraction (SPE) for simultaneous determination of the biological metabolites of aromatic compounds, including N-acetyl-S-phenyl-L-cysteine (SPMA), N-acetyl-S-benzyl-cysteine (SBMA), p-nitrophenol (PNP), methylhippuric acids (MHA), p-Aminophenol (PAP), mandelic acid (MA), phenylglyoxylic acid (PGA) and 1-hydroxypyrene (1-OHP) in urine. After adding 20 μL of β-glucuronidase and 1 mL ammonium acetate buffer solution in 1 mL of urine, the sample was digested in a 37 ℃ incubator for 20 h. After digestion, the enzymatic hydrolysate was purified by PRIME HLB solid phase extraction column. The target compounds were eluted with 4 mL of acetonitrile and blown to dryness with nitrogen, reconstituted with 0.20 mL of methanol. Injected the sample solution into LC-MS/MS system for analysis after filtering with 0.22 μm filter membrane. LC separation was carried out on a reversed-phase C18 column (2.1 mm×150 mm, 3.5 μm); gradient eluting was performed at a flow rate of 0.2 mL/min. The water containing 0.1% formic acid was used as mobile phase A and methanol was used as mobile phase B. The mass spectrometry was performed with multiple reaction monitoring (MRM) mode, using alternating positive and negative ions, and internal standard curves were used for quantification. The eight metabolites showed good linearity within the range of 1-100 ng/mL, with a correlation coefficients greater than 0.995, and the relative precision deviation (RSDs) was 0.050%-9.95%. The method detection limits (MDLs) of the eight target metabolites were 0.041-0.12 ng/mL. The proposed method was used for urine sample analysis and the spiked recoveries were 80.1%-114.0%. The established method is quick, sensitive and accurate; it meets the requirementof the biological monitoring of aromatic compounds for the general population and occupational population.

Fumonisin B1-Induced Changes in Cotton Fiber Elongation Revealed by Sphingolipidomics and Proteomics.

Sphingolipids are essential biomolecules and membrane components, but their regulatory role in cotton fiber development is poorly understood. Here, we found that fumonisin B1 (FB1)—a sphingolipid synthesis inhibitor—could block fiber elongation severely. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we detected 95 sphingolipids that were altered by FB1 treatment; of these, 29 (mainly simple sphingolipids) were significantly increased, while 33 (mostly complex sphingolipids) were significantly decreased. A quantitative analysis of the global proteome, using an integrated quantitative approach with tandem mass tag (TMT) labeling and LC-MS/MS, indicated the upregulation of 633 and the downregulation of 672 proteins after FB1 treatment. Most differentially expressed proteins (DEPs) were involved in processes related to phenylpropanoid and flavonoid biosynthesis. In addition, up to 20 peroxidases (POD) were found to be upregulated, and POD activity was also increased by the inhibitor. To our knowledge, this is the first report on the effects of FB1 treatment on cotton fiber and ovule sphingolipidomics and proteomics. Our findings provide target metabolites and biological pathways for cotton fiber improvement.

ATP regulation strategy and its application in the synthesis of microbial metabolites

Cofactor engineering, as a new branch of metabolic engineering, mainly involves ATP/ADP, NADH/NAD⁺, NADPH/NADP⁺ and other cofactors. Cofactor engineering can maximize metabolic flow by directly regulating the concentration and form of the cofactor of key enzymes in cells, and quickly direct carbon flow to target metabolites. ATP, as an important cofactor, is involved in many enzyme-catalyzed reactions in microbial cells, and leads to the restriction of the distribution of metabolic pathways by connecting or linking them into a complex network. Therefore, ATP regulation strategy is expected to be a favorable tool for industrial strain modification, to improve the concentration and production capacity of target metabolites, strengthen microbial tolerance to the environment and promote substrate utilization rate. The present review focuses on the recently used effective ATP regulation strategies and the effects of ATP regulation on cell metabolism in order to provide references for the efficient construction of microbial cell factories.

Metabolic Responses of Carotenoid and Cordycepin Biosynthetic Pathways in Cordyceps militaris under Light-Programming Exposure through Genome-Wide Transcriptional Analysis.

Cordyceps militaris is currently exploited for commercial production of specialty products as its biomass constituents are enriched in bioactive compounds, such as cordycepin. The rational process development is important for economically feasible production of high quality bioproducts. Light is an abiotic factor affecting the cultivation process of this entomopathogenic fungus, particularly in its carotenoid formation. To uncover the cell response to light exposure, this study aimed to systematically investigate the metabolic responses of C. militaris strain TBRC6039 using integrative genome-wide transcriptome and genome-scale metabolic network (GSMN)-driven analysis. The genome-wide transcriptome analysis showed 8747 expressed genes in the glucose and sucrose cultures grown under light-programming and dark conditions. Of them, 689 differentially expressed genes were significant in response to the light-programming exposure. Through integration with the GSMN-driven analysis using the improved network (iRT1467), the reporter metabolites, e.g., adenosine-5′-monophosphate (AMP) and 2-oxoglutarate, were identified when cultivated under the carotenoid-producing condition controlled by light-programming exposure, linking to up-regulations of the metabolic genes involved in glyoxalase system, as well as cordycepin and carotenoid biosynthesis. These results indicated that C. militaris had a metabolic control in acclimatization to light exposure through transcriptional co-regulation, which supported the cell growth and cordycepin production in addition to the accumulation of carotenoid as a photo-protective bio-pigment. This study provides a perspective in manipulating the metabolic fluxes towards the target metabolites through either genetic or physiological approaches.

Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts

Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used tocreate heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.

Modulating microbiome metabolites in vivo

A new genetic tool enables mechanistic dissection of microbiome–host interactions