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1.
Cell Death Discov ; 10(1): 238, 2024 May 18.
Article in English | MEDLINE | ID: mdl-38762529

ABSTRACT

Esophageal cancer is a common type of cancer that poses a significant threat to human health. While the pro-inflammatory cytokine IL-1ß has been known to contribute to the development of various types of tumors, its role in regulating esophageal cancer progression has not been extensively studied. Our studies found that the expression of IL-1ß and FOXO3A was increased in esophageal squamous cell carcinoma (ESCC). IL-1ß not only increased the proliferation, migration, and invasion of two ESCC cell lines but also promoted tumor growth and metastasis in nude mice. We also observed that IL-1ß and FOXO3A regulated the process of epithelial-mesenchymal transition (EMT) and autophagy. The PI3K/AKT pathway was found to be involved in the changes of FOXO3A with the expression level of IL-1ß. The AKT agonist (SC79) reversed the reduction of FOXO3A expression caused by the knockdown of IL-1ß, indicating that IL-1ß plays a role through the PI3K/AKT/FOXO3A pathway. Furthermore, the knockdown of FOXO3A inhibited ESCC development and attenuated the pro-cancer effect of overexpressed IL-1ß. Targeting IL-1ß and FOXO3A may be potentially valuable for the diagnosis and treatment of ESCC.

2.
PLoS Pathog ; 19(12): e1011856, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38048356

ABSTRACT

The rapid emergence of SARS-CoV-2 variants of concern (VOCs) calls for efforts to study broadly neutralizing antibodies elicited by infection or vaccination so as to inform the development of vaccines and antibody therapeutics with broad protection. Here, we identified two convalescents of breakthrough infection with relatively high neutralizing titers against all tested viruses. Among 50 spike-specific monoclonal antibodies (mAbs) cloned from their B cells, the top 6 neutralizing mAbs (KXD01-06) belong to previously defined IGHV3-53/3-66 public antibodies. Although most antibodies in this class are dramatically escaped by VOCs, KXD01-06 all exhibit broad neutralizing capacity, particularly KXD01-03, which neutralize SARS-CoV-2 from prototype to the emerging EG.5.1 and FL.1.5.1. Deep mutational scanning reveals that KXD01-06 can be escaped by current and prospective variants with mutations on D420, Y421, L455, F456, N460, A475 and N487. Genetic and functional analysis further indicates that the extent of somatic hypermutation is critical for the breadth of KXD01-06 and other IGHV3-53/3-66 public antibodies. Overall, the prevalence of broadly neutralizing IGHV3-53/3-66 public antibodies in these two convalescents provides rationale for novel vaccines based on this class of antibodies. Meanwhile, KXD01-06 can be developed as candidates of therapeutics against SARS-CoV-2 through further affinity maturation.


Subject(s)
COVID-19 , Vaccines , Humans , SARS-CoV-2/genetics , Breakthrough Infections , Prospective Studies , Antibodies, Monoclonal , Antibodies, Monoclonal, Humanized , Antibodies, Viral , Antibodies, Neutralizing , Spike Glycoprotein, Coronavirus/genetics
3.
J Agric Food Chem ; 71(22): 8497-8507, 2023 Jun 07.
Article in English | MEDLINE | ID: mdl-37221163

ABSTRACT

Promiscuous enzymes show great potential to establish new-to-nature pathways and expand chemical diversity. Enzyme engineering strategies are often employed to tailor such enzymes to improve their activity or specificity. It is paramount to identify the target residues to be mutated. Here, by exploring the inactivation mechanism with the aid of mass spectrometry, we have identified and mutated critical residues at the dimer interface region of the promiscuous methyltransferase (pMT) that converts psi-ionone to irone. The optimized pMT12 mutant showed ∼1.6-4.8-fold higher kcat than the previously reported best mutant, pMT10, and increased the cis-α-irone percentage from ∼70 to ∼83%. By one-step biotransformation, ∼121.8 mg L-1 cis-α-irone was produced from psi-ionone by the pMT12 mutant. The study offers new opportunities to engineer enzymes with enhanced activity and specificity.


Subject(s)
Methyltransferases , Norisoprenoids , Norisoprenoids/chemistry , Methyltransferases/genetics , Methyltransferases/metabolism , Mutagenesis, Site-Directed , Mutagenesis , Substrate Specificity
4.
J Agric Food Chem ; 71(22): 8479-8487, 2023 Jun 07.
Article in English | MEDLINE | ID: mdl-37148252

ABSTRACT

Isoprenoids, or terpenoids, have wide applications in food, feed, pharmaceutical, and cosmetic industries. Nerolidol, an acyclic C15 isoprenoid, is widely used in cosmetics, food, and personal care products. Current supply of nerolidol is mainly from plant extraction that is inefficient, costly, and of inconsistent quality. Here, we screened various nerolidol synthases from bacteria, fungi, and plants and found that the strawberry nerolidol synthase was most active in Escherichia coli. Through systematic optimization of the biosynthetic pathways, carbon sources, inducer, and genome editing, we constructed a series of deletion strains (single mutants ΔldhA, ΔpoxB, ΔpflB, and ΔtnaA; double mutants ΔadhE-ΔldhA; and triple mutants and beyond ΔadhE-ΔldhA-ΔpflB and ΔadhE-ΔldhA-ΔackA-pta) that produced high yields of 100% trans-nerolidol. In flasks, the highest nerolidol titers were 1.8 and 3.3 g/L in glucose-only and glucose-lactose-glycerol media, respectively. The highest yield reached 26.2% (g/g), >90% of the theoretic yield. In two-phase extractive fed-batch fermentation, our strain produced ∼16 g/L nerolidol within 4 days with about 9% carbon yield (g/g). In a single-phase fed-batch fermentation, the strain produced >6.8 g/L nerolidol in 3 days. To the best of our knowledge, our titers and productivity are the highest in the literature, paving the way for future commercialization and inspiring biosynthesis of other isoprenoids.


Subject(s)
Glycerol , Sugars , Sugars/metabolism , Glycerol/metabolism , Fermentation , Glucose/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Terpenes/metabolism , Metabolic Engineering
5.
J Agric Food Chem ; 71(11): 4683-4695, 2023 Mar 22.
Article in English | MEDLINE | ID: mdl-36888893

ABSTRACT

Cytochromes P450, forming a superfamily of monooxygenases containing heme as a cofactor, show great versatility in substrate specificity. Metabolic engineering can take advantage of this feature to unlock novel metabolic pathways. However, the cytochromes P450 often show difficulty being expressed in a heterologous chassis. As a case study in the prokaryotic host Escherichia coli, the heterologous synthesis of ß-cryptoxanthin was addressed. This carotenoid intermediate is difficult to produce, as its synthesis requires a monoterminal hydroxylation of ß-carotene whereas most of the classic carotene hydroxylases are dihydroxylases. This study was focused on the optimization of the in vivo activity of CYP97H1, an original P450 ß-carotene monohydroxylase. Engineering the N-terminal part of CYP97H1, identifying the matching redox partners, defining the optimal cellular background and adjusting the culture and induction conditions improved the production by 400 times compared to that of the initial strain, representing 2.7 mg/L ß-cryptoxanthin and 20% of the total carotenoids produced.


Subject(s)
Beta-Cryptoxanthin , beta Carotene , beta Carotene/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Carotenoids/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism
6.
Biomolecules ; 13(2)2023 02 15.
Article in English | MEDLINE | ID: mdl-36830734

ABSTRACT

Molecular biodiversity results from branched metabolic pathways driven by enzymatic regioselectivities. An additional complexity occurs in metabolites with an internal structural symmetry, offering identical extremities to the enzymes. For example, in the terpene family, ß-carotene presents two identical terminal closed-ring structures. Theses cycles can be hydroxylated by cytochrome P450s from the CYP97 family. Two sequential hydroxylations lead first to the formation of monohydroxylated ß-cryptoxanthin and subsequently to that of dihydroxylated zeaxanthin. Among the CYP97 dihydroxylases, CYP97H1 from Euglena gracilis has been described as the only monohydroxylase. This study aims to determine which enzymatic domains are involved in this regioselectivity, conferring unique monohydroxylase activity on a substrate offering two identical sites for hydroxylation. We explored the effect of truncations, substitutions and domain swapping with other CYP97 members and found that CYP97H1 harbours a unique N-terminal globular domain. This CYP97H1 N-terminal domain harbours a hydrophobic patch at the entrance of the substrate channel, which is involved in the monohydroxylase activity of CYP97H1. This domain, at the surface of the enzyme, highlights the role of distal and non-catalytic domains in regulating enzyme specificity.


Subject(s)
Euglena gracilis , beta Carotene , Euglena gracilis/metabolism , Cytochrome P-450 Enzyme System/metabolism , Substrate Specificity
7.
Nat Commun ; 13(1): 7421, 2022 12 02.
Article in English | MEDLINE | ID: mdl-36456636

ABSTRACT

Metabolic engineering has become an attractive method for the efficient production of natural products. However, one important pre-requisite is to establish the biosynthetic pathways. Many commercially interesting molecules cannot be biosynthesized as their native biochemical pathways are not fully elucidated. Cis-α-irone, a top-end perfumery molecule, is an example. Retrobiosynthetic pathway design by employing promiscuous enzymes provides an alternative solution to this challenge. In this work, we design a synthetic pathway to produce cis-α-irone with a promiscuous methyltransferase (pMT). Using structure-guided enzyme engineering strategies, we improve pMT activity and specificity towards cis-α-irone by >10,000-fold and >1000-fold, respectively. By incorporating the optimized methyltransferase into our engineered microbial cells, ~86 mg l-1 cis-α-irone is produced from glucose in a 5 l bioreactor. Our work illustrates that integrated retrobiosynthetic pathway design and enzyme engineering can offer opportunities to expand the scope of natural molecules that can be biosynthesized.


Subject(s)
Carbon , Protein Biosynthesis , Norisoprenoids , Methyltransferases
8.
Microb Cell Fact ; 21(1): 246, 2022 Nov 23.
Article in English | MEDLINE | ID: mdl-36424649

ABSTRACT

BACKGROUND: α-Ionone is highly valued in cosmetics and perfumery with a global usage of 100-1000 tons per year. Metabolic engineering by microbial fermentation offers a promising way to produce natural (R)-α-ionone in a cost-effective manner. Apart from optimizing the metabolic pathways, the approach is also highly dependent on generating a robust strain which retains productivity during the scale-up process. To our knowledge, no study has investigated strain robustness while increasing α-ionone yield. RESULTS: Built on our previous work, here, we further increased α-ionone yield to 11.4 mg/L/OD in 1 mL tubes by overexpressing the bottleneck dioxygenase CCD1 and re-engineering the pathway, which is > 65% enhancement as compared to our previously best strain. However, the yield decreased greatly to 2.4 mg/L/OD when tested in 10 mL flasks. Further investigation uncovered an unexpected inhibition that excessive overexpression of CCD1 was accompanied with increased hydrogen peroxide (H2O2) production. Excessive H2O2 broke down lycopene, the precursor to α-ionone, leading to the decrease in α-ionone production in flasks. This proved that expressing too much CCD1 can lead to reduced production of α-ionone, despite CCD1 being the rate-limiting enzyme. Overexpressing the alkyl hydroperoxide reductase (ahpC/F) partially solved this issue and improved α-ionone yield to 5.0 mg/L/OD in flasks by reducing oxidative stress from H2O2. The strain exhibited improved robustness and produced ~ 700 mg/L in 5L bioreactors, the highest titer reported in the literature. CONCLUSION: Our study provides an insight on the importance of mediating the oxidative stress to improve strain robustness and microbial production of α-ionone during scaling up. This new strategy may be inspiring to the biosynthesis of other high-value apocarotenoids such as retinol and crocin, in which oxygenases are also involved.


Subject(s)
Hydrogen Peroxide , Norisoprenoids , Norisoprenoids/metabolism , Metabolic Engineering , Oxidative Stress
9.
Contrast Media Mol Imaging ; 2022: 8522842, 2022.
Article in English | MEDLINE | ID: mdl-35935301

ABSTRACT

In order to investigate the expression levels of procalcitonin (PCT), B-type brain natriuretic peptide (BNP), and lactic acid (Lac) in serum of patients with sepsis, a retrospective analysis is conducted. 80 sepsis patients admitted to the ICU of our hospital from January 2019 to June 2020 are selected, and the application value of these factors combined with Apache II score in early diagnosis and prediction of death risk is analyzed. All patients are classified into survival group (n = 57) and death group (n = 23), and examined by blood routine. Lac, PCT, and BNP, and the serum PCT, BNP, and Lac levels were compared between the nonsepsis group and the control group. Furthermore, Acute Physiology and Chronic Health Status scoring System II (Apache II) is applied to evaluate the score difference between the sepsis group and the control group. The ROC curve demonstrates that PCT, BNP, and Lac combined with Apache II score can obtain high value for early diagnosis of sepsis. Compared with nonsepsis patients, the scores of serum Lac, PCT, and BNP and Apache II are significantly higher in sepsis patients. It is clearly evident that the combined detection of those indicators is valuable for early diagnosis and prediction of death, and will be suitable for widespread clinical application.


Subject(s)
Procalcitonin , Sepsis , Early Diagnosis , Humans , Lactic Acid , Natriuretic Peptide, Brain , Procalcitonin/metabolism , Prognosis , Retrospective Studies , Sepsis/diagnosis , Sepsis/metabolism
10.
Comput Math Methods Med ; 2022: 7870434, 2022.
Article in English | MEDLINE | ID: mdl-35991153

ABSTRACT

Purpose: To analyze the clinical significance of the sequential organ failure assessment (SOFA) score in the diagnosis, treatment, and prognostic assessment of sepsis. Methods: 140 patients with sepsis from January 2020 to January 2021 were selected as the observation group, and 40 healthy people were selected as the control group. The observation group was divided into mild group, severe group, and septic shock group by single blind grouping according to the condition of the disease, and they were also divided into survival group and death group according to the prognosis. Collect the fasting venous blood of the subjects in each group in the morning, compare the levels of total bilirubin (TBIL), blood creatinine (CR), and platelet count (PLT) in each group, and record and compare the patients' respiratory system oxygen partial pressure/inhaled oxygen concentration (po2/fio2), acute physiology and chronic health scoring system II (APACHE II), sequential organ failure assessment (sofa) score, q-SOFA score, and △SOFA score; Pearson analysis was used to analyze the correlation between SOFA score and other indicators; multivariate logistic regression was used to analyze the prognostic risk factors of patients with sepsis; receiver-operating characteristic curve (ROC) was used to analyze the value of SOFA score alone and in combination in the diagnosis, condition, and prognosis of sepsis. Results: There were significant differences in Apache II score, SOFA score, q-SOFA score map, po2/fio2, PLT, GCS, TBIL, and serum creatinine (SCR) between the control group and the observation group (P < 0.05). There were significant differences in Apache II score, SOFA score, q-SOFA score, mean arterial pressure (map) po2/fio2, PLT, Glasgow Coma Score (GCS), TBIL, SCR, and △SOFA score among patients in mild, severe, and septic shock groups (P < 0.05). There were significant differences in age, Apache II score, SOFA score, q-SOFA score, map, po2/fio2, PLT, GCS, TBIL, SCR, and △SOFA score between survival group and death group (P < 0.05). SOFA score and q-SOFA score were significantly positively correlated with TBIL and SCR and significantly negatively correlated with po2/fio2 and PLT; △SOFA score was significantly negatively correlated with TBIL and SCR and significantly positively correlated with map, po2/fio2, PLT, and GCS. Apache II score, SOFA score, and q-SOFA score were independent risk factors for sepsis patients, and △SOFA score, po2/fio2, and GCS score were protective factors (P < 0.05). ROC curve analysis showed that the AUC of sepsis combined with SOFA score and q-SOFA score was 0.880; the AUC of sepsis assessed by SOFA score, q-SOFA score, and △SOFA score was 0.929; the AUC of sepsis prognosis assessed by SOFA score, q-SOFA score, and △SOFA score was 0.900. Conclusion: SOFA score, q-SOFA score, and △SOFA score were abnormally expressed in patients with sepsis and were risk factors for the severity of the patient's condition and prognosis. The SOFA score, q-SOFA score, and △SOFA score were risk factors for the severity and prognosis of patients with sepsis and had some value in diagnosing sepsis and assessing the condition and prognosis, of which the combined value of the three was higher.


Subject(s)
Sepsis , Shock, Septic , Humans , Intensive Care Units , Organ Dysfunction Scores , Oxygen , Prognosis , ROC Curve , Retrospective Studies , Sepsis/diagnosis , Sepsis/therapy , Shock, Septic/diagnosis , Shock, Septic/therapy , Single-Blind Method
11.
Microb Cell Fact ; 21(1): 19, 2022 Feb 05.
Article in English | MEDLINE | ID: mdl-35123478

ABSTRACT

BACKGROUND: The recent CRISPR-Cas coupled with λ recombinase mediated genome recombineering has become a common laboratory practice to modify bacterial genomes. It requires supplying a template DNA with homology arms for precise genome editing. However, generation of homology arms is a time-consuming, costly and inefficient process that is often overlooked. RESULTS: In this study, we first optimized a CRISPR-Cas genome engineering protocol in the Escherichia coli (E. coli) BL21 strain and successfully deleted 10 kb of DNA from the genome in one round of editing. To further simplify the protocol, asymmetric homology arms were produced by PCR in a single step with two primers and then purified using a desalting column. Unlike conventional homology arms that are prepared through overlapping PCR, cloning into a plasmid or annealing synthetic DNA fragments, our method significantly both shortened the time taken and reduced the cost of homology arm preparation. To test the robustness of the optimized workflow, we successfully deleted 26 / 27 genes across the BL21 genome. Noteworthy, gRNA design is important for the CRISPR-Cas system and a general heuristic gRNA design has been proposed in this study. To apply our established protocol, we targeted 16 genes and iteratively deleted 7 genes from BL21 genome. The resulting strain increased lycopene yield by ~ threefold. CONCLUSIONS: Our work has optimized the homology arms design for gene deletion in BL21. The protocol efficiently edited BL21 to improve lycopene production. The same workflow is applicable to any E. coli strain in which genome engineering would be useful to further increase metabolite production.


Subject(s)
CRISPR-Cas Systems , Escherichia coli/genetics , Escherichia coli/metabolism , Lycopene/metabolism , Metabolic Engineering , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Gene Deletion , Gene Editing , Genome, Bacterial , Plasmids/genetics , Plasmids/metabolism , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism , Recombinases/genetics , Recombinases/metabolism
12.
Sensors (Basel) ; 23(1)2022 Dec 30.
Article in English | MEDLINE | ID: mdl-36616995

ABSTRACT

Micro-image strain sensing (MISS) is an innovative technology to measure strain within a measurement range of ±8300 microstrains. It has been proved to be effective and satisfy all requirements in the field of structural health monitoring. However, there is still room for improvement and extend the range of measurement. In this paper, an improved method is proposed to increase the measurement range of strain and displacement. Moreover, various tests were conducted to verify the efficiency of the improved method. The results showed that the modified method is efficient and accurate and can be readily used to extend the measurement range of both strain and displacement. This research will likely help stimulate the development of multifunctional sensors to obtain abundant useful information about structures in the field of structural health monitoring. It will allow measuring strain and displacement, which require different levels of accuracy, using one unified sensor.

13.
Commun Biol ; 4(1): 223, 2021 02 17.
Article in English | MEDLINE | ID: mdl-33597725

ABSTRACT

Enzymes empower chemical industries and are the keystone for metabolic engineering. For example, linalool synthases are indispensable for the biosynthesis of linalool, an important fragrance used in 60-80% cosmetic and personal care products. However, plant linalool synthases have low activities while expressed in microbes. Aided by bioinformatics analysis, four linalool/nerolidol synthases (LNSs) from various Agaricomycetes were accurately predicted and validated experimentally. Furthermore, we discovered a linalool synthase (Ap.LS) with exceptionally high levels of selectivity and activity from Agrocybe pediades, ideal for linalool bioproduction. It effectively converted glucose into enantiopure (R)-linalool in Escherichia coli, 44-fold and 287-fold more efficient than its bacterial and plant counterparts, respectively. Phylogenetic analysis indicated the divergent evolution paths for plant, bacterial and fungal linalool synthases. More critically, structural comparison provided catalytic insights into Ap.LS superior specificity and activity, and mutational experiments validated the key residues responsible for the specificity.


Subject(s)
Acyclic Monoterpenes/metabolism , Agaricales/enzymology , Computational Biology , Fungal Proteins/metabolism , Hydro-Lyases/metabolism , Industrial Microbiology , Agaricales/genetics , Evolution, Molecular , Fungal Proteins/genetics , Hydro-Lyases/genetics , Kinetics , Phylogeny , Protein Conformation , Structure-Activity Relationship
14.
Bioresour Bioprocess ; 8(1): 72, 2021 Aug 11.
Article in English | MEDLINE | ID: mdl-38650197

ABSTRACT

In the biosynthesis of natural products, methylation is a common and essential transformation to alter molecules' bioavailability and bioactivity. The main methylation reaction is performed by S-adenosylmethionine (SAM)-dependent methyltransferases (MTs). With advancements in genomic and chemical profiling technologies, novel MTs have been discovered to accept complex substrates and synthesize industrially valuable natural products. However, to achieve a high yield of small molecules in microbial hosts, many methyltransferase activities have been reported to be insufficient. Moreover, inadequate co-factor supplies and feedback inhibition of the by-product, S-adenosylhomocysteine (SAH), further limit MTs' activities. Here, we review recent advances in SAM-dependent MTs to produce and diversify natural products. First, we surveyed recently identified novel methyltransferases in natural product biosynthesis. Second, we summarized enzyme engineering strategies to improve methyltransferase activity, with a particular focus on high-throughput assay design and application. Finally, we reviewed innovations in co-factor regeneration and diversification, both in vitro and in vivo. Noteworthily, many MTs are able to accept multiple structurally similar substrates. Such promiscuous methyltransferases are versatile and can be tailored to design de novo pathways to produce molecules whose biosynthetic pathway is unknown or non-existent in nature, thus broadening the scope of biosynthesized functional molecules.

15.
Bioresour Bioprocess ; 8(1): 67, 2021 Jul 29.
Article in English | MEDLINE | ID: mdl-38650269

ABSTRACT

Because of wide applications in food, feed, pharmaceutical and cosmetic industries, the carotenoid market is growing rapidly. Most carotenoids are hydrophobic, which limits their bioavailability. Glycosylation is a natural route that substantially increases the water solubility, as well as the bioavailability, photostability and biological activities of carotenoids. Here, we report metabolic engineering efforts (e.g., promoter and RBS engineering, optimization of carbon sources and supplementation of bottleneck genes) to produce glycosylated carotenoids in Escherichia coli. By fine-tuning the carotenoid-biosynthetic genes (crtX, crtZ and crtY), our strain produced up to 47.2 mg/L (~ 11,670 ppm) of zeaxanthin glucosides, ~ 78% of the total carotenoids produced. In another construct with mevalonate, astaxanthin pathway and crtX genes, the strain produced a mixture of carotenoid glucosides including astaxanthin and adonixanthin glucosides with a total yield of 8.1 mg/L (1774 ppm). Our work demonstrated a proof-of-concept study for the microbial biosynthesis of glycosylated carotenoids.

16.
Appl Microbiol Biotechnol ; 104(13): 5725-5737, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32399589

ABSTRACT

Astaxanthin is a natural pigment, known for its strong antioxidant activity and numerous health benefits to human and animals. Its antioxidant activity is known to be substantially greater than ß-carotene and about a thousand times more effective than vitamin E. The potential health benefits have generated a growing commercial interest, and the escalating demand has prompted the exploration of alternative supply chain. Astaxanthin naturally occurs in many sea creatures such as trout, shrimp, and microalgae, some fungi, bacteria, and flowering plants, acting to protect hosts against environmental stress and adverse conditions. Due to the rapid growth and simple growth medium requirement, microbes, such as the microalga, Haematococcus pluvialis, and the fungus Xanthophyllomyces dendrorhous, have been developed to produce astaxanthin. With advances in metabolic engineering, non-carotenogenic microbes, such as Escherichia coli and Saccharomyces cerevisiae, have been purposed to produce astaxanthin and significant progress has been achieved. Here, we review the recent achievements in microbial astaxanthin biosynthesis (with reference to metabolic engineering strategies) and extraction methods, current challenges (technical and regulatory), and commercialization outlook. Due to greenness, sustainability, and dramatic cost reduction, we envision microbial synthesis of astaxanthin offers an alternative means of production (e.g. chemical synthesis) in the near future.


Subject(s)
Bacteria/metabolism , Fungi/metabolism , Metabolic Engineering , Microalgae/metabolism , Bacteria/classification , Bacteria/genetics , Bioreactors , Biosynthetic Pathways/genetics , Fungi/classification , Fungi/genetics , Microalgae/classification , Microalgae/genetics , Xanthophylls/isolation & purification , Xanthophylls/metabolism , beta Carotene/metabolism
17.
ACS Chem Biol ; 15(5): 1268-1277, 2020 05 15.
Article in English | MEDLINE | ID: mdl-32233445

ABSTRACT

Terpenoids constitute a structurally diverse group of natural products with wide applications in the pharmaceutical, nutritional, flavor and fragrance industries. Fungi are known to produce a large variety of terpenoids, yet fungal terpene synthases remain largely unexploited. Here, we report the sesquiterpene network and gene clusters of the black poplar mushroom Agrocybe aegerita. Among 11 putative sesquiterpene synthases (STSs) identified in its genome, nine are functional, including two novel synthases producing viridiflorol and viridiflorene. On this basis, an additional 1133 STS homologues from higher fungi have been curated and used for a sequence similarity network to probe isofunctional STS groups. With the focus on two STS groups, one producing viridiflorene/viridiflorol and one Δ6-protoilludene, the isofunctionality was probed and verified. Three new Δ6-protoilludene synthases and two new viridflorene/viridiflorol synthases from five different fungi were correctly predicted. The study herein serves as a fundamental predictive framework for the discovery of fungal STSs and biosynthesis of novel terpenoids. Furthermore, it becomes clear that fungal STS function differs between the phyla Ascomycota and Basidiomycota with the latter phylum being more dominant in the overall number and variability. This study aims to encourage the scientific community to further work on fungal STS and the products, biological functions, and potential applications of this vast source of natural products.


Subject(s)
Agrocybe/enzymology , Alkyl and Aryl Transferases/metabolism , Biological Products/chemistry , Sesquiterpenes/chemistry , Agrocybe/genetics , Agrocybe/metabolism , Alkyl and Aryl Transferases/genetics , Amino Acid Sequence , Base Sequence , Basidiomycota/enzymology , Basidiomycota/genetics , Basidiomycota/metabolism , Biological Products/metabolism , Biosynthetic Pathways , Cloning, Molecular , Escherichia coli/genetics , Gene Expression Regulation, Fungal , Genome, Fungal , Molecular Structure , Multigene Family , Sequence Homology, Nucleic Acid , Sesquiterpenes/metabolism
18.
IEEE Trans Neural Netw Learn Syst ; 31(7): 2441-2454, 2020 Jul.
Article in English | MEDLINE | ID: mdl-31425056

ABSTRACT

Estimating covariance matrix from massive high-dimensional and distributed data is significant for various real-world applications. In this paper, we propose a data-aware weighted sampling-based covariance matrix estimator, namely DACE, which can provide an unbiased covariance matrix estimation and attain more accurate estimation under the same compression ratio. Moreover, we extend our proposed DACE to tackle multiclass classification problems with theoretical justification and conduct extensive experiments on both synthetic and real-world data sets to demonstrate the superior performance of our DACE.

19.
J Agric Food Chem ; 68(38): 10252-10264, 2020 Sep 23.
Article in English | MEDLINE | ID: mdl-31865696

ABSTRACT

Terpenoids derived from plant material are widely applied in the flavor and fragrance industry. Traditional extraction methods are unsustainable, but microbial synthesis offers a promising solution to attain efficient production of natural-identical terpenoids. Overproduction of terpenoids in microbes requires careful balancing of the synthesis pathway constituents within the constraints of host cell metabolism. Advances in metabolic engineering have greatly facilitated overcoming the challenges of achieving high titers, rates, and yields (TRYs). The review summarizes recent development in the molecular biology toolbox to achieve high TRYs for terpenoid biosynthesis, mainly in the two industrial platform microorganisms: Escherichia coli and Saccharomyces cerevisiae. The biosynthetic pathways, including alternative pathway designs, are briefly introduced, followed by recently developed methodologies used for pathway, genome, and strain optimization. Integrated applications of these tools are important to achieve high "TRYs" of terpenoid production and pave the way for translating laboratory research into successful commercial manufacturing.


Subject(s)
Escherichia coli/genetics , Escherichia coli/metabolism , Flavoring Agents/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Terpenes/metabolism , Biosynthetic Pathways , Flavoring Agents/chemistry , Metabolic Engineering , Terpenes/chemistry
20.
Metab Eng ; 55: 170-178, 2019 09.
Article in English | MEDLINE | ID: mdl-31326469

ABSTRACT

Isoprenoids, widely used as pharmaceuticals, flavors and nutraceuticals, represent one of the largest groups of natural products. Yet the low availability of top-quality (enantiopure) products and high cost limit the wide application of many valuable terpenoids. An example being viridiflorol, currently used in cosmetics and personal care products, may have other unexplored applications (e.g. as insect repellents; anti-inflammatory supplements). Here, we systematically optimized an auxotrophic Escherichia coli to produce viridiflorol with transcription, translation, enzyme and strain engineering. The best strain achieved 25.7 g/L and a yield of 0.22 g-viridiflorol/g-glucose in 2.5 days. Statistical analysis revealed the correlation between viridiflorol yields with the transcriptional levels and translation initiation rates, which enabled better understanding of the isoprenoid pathway and guiding future strain optimization. As a proof-of-concept example, we applied the knowledge to amorphadiene, anti-malaria drug artemisinin precursor, achieved 30 g/L. Hence, this study paved the way for commercialization of microbial terpenoid production.


Subject(s)
Escherichia coli , Metabolic Engineering , Polycyclic Sesquiterpenes/metabolism , Terpenes/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism
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