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Phenolic acids and tanshinones are important bioactive components with multiple pharmacological properties accumulated in traditional Chinese medicinal plant Salvia miltiorrhiza. Abscisic acid (ABA) is effective to enhance the content of the two compounds in S. miltiorrhiza, while the regulation mechanism remains unknown. Deep transcriptome profile of S. miltiorrhiza hairy roots treated with ABA was conducted. Totally, 42,710 unigenes with the average length of 1,157 bp were obtained from de novo assembly from about 2.81 billion produced clean reads, of which 27,641 unigenes (64.72%) were successfully annotated. Unigenes encoding key enzymes such as PAL, TAT, C4H, RAS, CYP98A14, GGPPS expressed significantly higher than that in control. Candidate laccases showing similar expression with RAS and CYP98A14 in phenolic acid biosynthesis and potential P450 unigenes involved in tanshinone biosynthesis genes were screened out. Furthermore, transcription factor (TF) profiles revealed that 1,250 TFs representing 35 families were identified, of which MYB, AP2/ERF, bHLH and bZIP were most abundant. The present study provided a comprehensive transcriptional expression profile affected by ABA, which will help underly the biosynthesis and regulation mechanism. Transcriptomic analysis of ABA-treated Salvia miltiorrhiza.

α-Pinene, an important biologically active natural monoterpene, has been widely used in fragrances, medicines, and fine chemicals, especially, in high-density renewable fuels such as jet fuel. The development of an α-pinene production platform in a highly modifiable microbe from renewable substitute feedstocks could lead to a green, economical avenue, and sustainable biotechnological process for the biosynthesis of α-pinene. Here, we report engineering of an orthogonal biosynthetic pathway for efficient production of α-pinene in oleaginous yeast Yarrowia lipolytica that resulted in an α-pinene titer of 19.6 mg/L when using glucose as the sole carbon source, a significant 218-fold improvement than the initial titer. In addition, the potential of using waste cooking oil and lignocellulosic hydrolysate as carbon sources for α-pinene production from the engineered Y. lipolytica strains was analyzed. The results indicated that α-pinene titers of 33.8 and 36.1 mg/L were successfully obtained in waste cooking oil and lignocellulosic hydrolysate medium, thereby representing the highest titer reported to date in yeast. To our knowledge, this is also the first report related to microbial production of α-pinene from waste cooking oil and lignocellulosic hydrolysate.

Inflammatory responses stimulated by Propionibacterium acnes have been shown to be major etiological factors in the pathogenesis of acne. Scutellaria baicalensis, a popular traditional Chinese medicine, has been widely shown to have anti-inflammatory effects. In this study, primary component analysis and primary effective component analysis were conducted. The results showed that wogonin (1.15 mg/g S. baicalensis extract) possessed better anti-acne effects than wogonoside (8.71 mg/g S. baicalensis extract) in inhibiting the up-regulation of IL-1β and IL-8 level caused by P. acnes via inactivation of the MAPK and NF-κB signaling pathways. To enhance the anti-acne effects of S. baicalensis extract, an environmentally friendly and healthy plant fermentation strategy was used to efficiently convert glycoside-type constituents into bioactive aglycone. S. baicalensis extract was fermented by symbiotic fungus Penicillium decumbens f3-1 to transform wogonoside into wogonin with a conversion rate of 91.0% after 4 days. Fermented S. baicalensis extract (FSE) showed higher potential anti-acne effects than non-fermented S. baicalensis extract (NSE) by inhibiting the up-regulation of IL-1β and IL-8. Thus, P. decumbens-fermented S. baicalensis Extract may be used for developing new anti-acne cosmetic ingredients.

The oleaginous yeast Yarrowia lipolytica is an attractive cell factory platform strain and can be used for sustainable production of high-value oleochemical products. Wax esters (WEs) have a good lubricating property and are usually used as a base for the production of advanced lubricants and emollient oils. In this study, we reported the metabolic engineering of Y. lipolytica to heterologously biosynthesize high-content very-long-chain fatty acids (VLCFAs) and fatty alcohols and efficiently esterify them to obtain very-long-chain WEs. Co-expression of fatty acid elongases from different sources in Y. lipolytica could yield VLCFAs with carbon chain lengths up to 24. Combining with optimization of the central metabolic modules could further enhance the biosynthesis of VLCFAs. Furthermore, through the screening of heterologous fatty acyl reductases (FARs), we enabled high-level production of fatty alcohols. Genomic integration and heterologous expression of wax synthase (WS) and FAR in a VLCFA-producing Y. lipolytica strain yielded 95-650 mg/L WEs with carbon chain lengths from 32 to 44. Scaled-up fermentation in 5 L laboratory bioreactors significantly increased the production of WEs to 2.0 g/L, the highest content so far in yeasts. This study contributes to the further efficient biosynthesis of VLCFAs and their derivatives.

Farnesene is a typical sesquiterpene with applications as fragrance, flavor and precursor for the synthesis of vitamin E/K1. In this study, a series of strategies were employed to facilitate α-farnesene accumulation in Yarrowia lipolytica. Among them, the promoter optimization of OptFSLERG20, Sc-tHMG1 and IDI resulted in more than 62 % increase in α-farnesene production. Together with the overexpression of Yl-HMGR and ERG19, α-farnesene content was significantly improved by more than 3.5 times. The best metabolic engineered strain obtained was therefore used for a uniform design in shake flasks to determine the optimal medium compositions. Furthermore, a maximum α-farnesene production of approximately 2.57 g/L (34 mg/g DCW) was obtained in fed-batch fermentation where glycerol was supplemented as the feeding carbon source when initial glucose was depleted. This study has laid a good foundation for the development of Y. lipolytica as a promising chassis microbial cell for heterologous biosynthesis of α-farnesene and other sesquiterpenes.

Stable-isotope metabolic flux analysis is an important approach to unravel the metabolic network and its regulation in organisms. It has become a key analytical technology for biotechnological applications. During recent years non-model microorganisms have received increasing attention because they possess unique metabolic capabilities and can serve as a host for production of biofuels and biochemicals. Stable-isotope metabolic flux analysis has been widely used in these microorganisms for exploring novel pathways, elucidating the operation of central metabolic networks, and revealing the metabolic changes that result from genetic manipulations. Here, we review recent applications of stable-isotope metabolic flux analysis in characterizing non-model microbial hosts, guiding the development of rational engineering strategies for enhancement of biochemical production and extension of substrate range, and understanding of industrial production processes.

MicroRNAs can act as tumour suppressors or oncogenes by regulating cellular differentiation, proliferation and apoptosis, and the dysregulation of miRNA is involved in the occurrence and development of NSCLC. Here, we provided evidence that miR-92b as an oncogene in NSCLC by targeting PTEN/AKT. We found that miR-92b was up-regulated in human NSCLC tissues and cell lines. MiR-92b knockdown suppressed the NSCLC cells proliferation and migration in both in vivo and in vitro models. Conversely, miR-92b overexpression induced an aggressive phenotype. Moreover, miR-92b-mediated regulation of NSCLC cell proliferation and migration depended on binding to PTEN mRNA, which then led to the degradation of PTEN and activation of the downstream AKT signalling pathway. Overall, this study revealed the oncogenic roles of miR-92b in NSCLC by targeting PTEN/AKT, and provided novel insights for future treatments of NSCLC patients. SIGNIFICANCE OF THE STUDY: MiR-92b was up-regulated in human NSCLC tissues and cell lines. Our study demonstrated that miR-92b as an oncogene in NSCLC by targeting PTEN/AKT in both in vivo and in vitro models and provided novel insights for future treatments of NSCLC patients.

Genome-scale metabolic models (GEMs) are powerful tools for predicting metabolic flux distributions, understanding complex cell physiology, and guiding the improvement of cell metabolism and production. Yarrowia lipolytica is known for its ability to accumulate lipids and has been widely employed to produce many important metabolites as an ideal host microorganism. There are six GEMs reconstructed for this strain by different research groups, which, however, may cause confusion for model users. It is therefore necessary to understand and analyze the existing models comprehensively. Different simulation results of the published GEMs of Y. lipolytica were analyzed based on experimental data, in order to understand the differences among models and identify whether there were common problems in model construction. First, specific growth rates (μ) under various culture conditions were simulated by different models, showing that the biomass generation equation in models had significant influence on the accuracy of simulation results. In addition, simulation and analysis of intracellular flux distributions revealed several inaccurate descriptions on the reversibility of reactions involving currency metabolites in the models. Finally, specific metabolite formation rates were predicted for different target products, and large discrepancies among the different models were observed. The corresponding solutions were then proposed according to the findings of the above model problems. We have corrected the existing GEMs of Y. lipolytica and the prediction performances of the models have been significantly improved. Several suggestions for better construction and refinement of genome-scale metabolic network models were also provided.

Synthetic microbial consortia are a rapidly growing area of synthetic biology. So far, most consortia are designed without considering their environments; however, in nature, microbial interactions are constantly modulated by cellular contexts, which, in principle, can dramatically alter community behaviors. Here we present the construction, validation, and characterization of an engineered bacterial predator-prey consortium that involves a chloramphenicol (CM)-mediated, context-dependent cellular interaction. We show that varying the CM level in the environment can induce success in the ecosystem with distinct patterns from predator dominance to prey-predator crossover to ecosystem collapse. A mathematical model successfully captures the essential dynamics of the experimentally observed patterns. We also illustrate that such a dependence enriches community dynamics under different initial conditions and further test the resistance of the consortium to invasion with engineered bacterial strains. This work exemplifies the role of the context dependence of microbial interactions in modulating ecosystem dynamics, underscoring the importance of including contexts into the design of engineered ecosystems for synthetic biology applications.

Oridonin could induce NB (neuroblastoma) cells growth inhibition by inducing apoptosis and cell cycle arrest, and the molecular mechanisms behind the effects deserve to be further explored. Here, oridonin was confirmed to cause the reactivation of p53 (cellular tumor antigen p53) to promote the expression of a series of apoptosis‐ and cell cycle arrest‐related proteins for the biological effects. During the process, oridonin relied on the caspase activation to cleave p53‐induced Mdm2 (E3 ubiquitin‐protein ligase Mdm2) to generate Mdm2‐p60. The generation of Mdm2‐p60 stabilized p53, and resulted in p53 accumulation for p53 continuous activation. In our research, it was also found that the reactivation of p53 induced by oridonin was closely related with the generation of ROS (reactive oxygen species). Taken together, these findings explain that oridonin exerts its anticancer activity partially by targeting the Mdm2‐p53 axis in NB cells, which lay an experimental base for future research of exploring the effects and molecular mechanisms of oridonin.

As an alternative terpenoid producer, non-conventional oleaginous yeast Yarrowia lipolytica was chosen for limonene production. Y. lipolytica can give high biomass yield and metabolize a broad range of substrates such as glycerol, alkanes, fatty acid, fats, and oils. As previously reported, optimization of limonene synthesis pathway and mevalonate (MVA) pathway leads to the accumulation of 112-fold higher limonene as compared to an initial strain. In this study, we introduced an additional copy of limonene synthesis gene (LS), which resulted in an increase of limonene production. This engineered strain was used to carry out further optimization study. Amongst all the carbon sources tested, the highest level of limonene production was obtained from glycerol, and citrate was selected as an auxiliary carbon source. In fed-batch fermentation with an optimized medium, the engineered strain was found to produce 165.3 mg/L limonene, which corresponds to the highest yield till date for the production of limonene in Y. lipolytica.

Diabetic cardiomyopathy (DCM) is a serious complication of diabetes mellitus (DM). One of the hallmarks of the DCM is enhanced oxidative stress in myocardium. The aim of this study was to research the underlying mechanisms involved in the effects of dapagliflozin (Dap) on myocardial oxidative stress both in streptozotocin-induced DCM rats and rat embryonic cardiac myoblasts H9C2 cells exposed to high glucose (33.0 mM). In in vivo studies, diabetic rats were given Dap (1 mg/ kg/ day) by gavage for eight weeks. Dap treatment obviously ameliorated cardiac dysfunction, and improved myocardial fibrosis, apoptosis and oxidase stress. In in vitro studies, Dap also attenuated the enhanced levels of reactive oxygen species and cell death in H9C2 cells incubated with high glucose. Mechanically, Dap administration remarkably reduced the expression of membrane-bound nicotinamide adenine dinucleotide phosphate (NADPH) oxidase subunits gp91phox and p22phox, suppressed the p67phox subunit translocation to membrane, and decreased the compensatory elevated copper, zinc superoxide dismutase (Cu/Zn-SOD) protein expression and total SOD activity both in vivo and in vitro. Collectively, our results indicated that Dap protects cardiac myocytes from damage caused by hyperglycemia through suppressing NADPH oxidase-mediated oxidative stress.

Given the grave concerns over increasing consumption of petroleum resources and dramatic environmental changes arising from carbon dioxide emissions worldwide, microbial biosynthesis of fatty acid ethyl ester (FAEE) biofuels as renewable and sustainable replacements for petroleum-based fuels has attracted much attention. As one of the most important microbial chassis, the nonconventional oleaginous yeast Yarrowia lipolytica has emerged as a paradigm organism for the production of several advanced biofuels and chemicals. Here, we report the engineering of Y. lipolytica for use as an efficient dual biocatalytic system for in situ and one-pot production of FAEEs from renewable feedstock. Compared to glucose with 5.7% (w/w) conversion rate to FAEEs, sunflower seed oil in the culture medium was efficiently used to generate FAEEs with 84% (w/w) conversion rate to FAEEs by the engineered Y. lipolytica strain GQY20 that demonstrates an optimized intercellular heterologous FAEE synthesis pathway. In particular, the titer of extracellular FAEEs from sunflower seed oil reached 9.9 g/L, 10.9-fold higher than that with glucose as a carbon source. An efficient dual biocatalytic system combining ex vivo and strengthened in vitro FAEE production routes was constructed by overexpression of a lipase (Lip2) variant in the background strain GQY20, which further increased FAEEs levels to 13.5 g/L. Notably, deleting the ethanol metabolism pathway had minimal impact on FAEE production. Finally, waste cooking oil, a low-cost oil-based substance, was used as a carbon source for FAEE production in the Y. lipolytica dual biocatalytic system, resulting in production of 12.5 g/L FAEEs. Thus, the developed system represents a promising green and sustainable process for efficient biodiesel production. KEY POINTS: • FAEEs were produced by engineered Yarrowia lipolytica. • A Lip2 variant was overexpressed in the yeast to create a dual biocatalytic system. • Waste cooking oil as a substrate resulted in a high titer of 12.5 g/L FAEEs.

Erythritol (1,2,3,4-butanetetrol) is a 4-carbon sugar alcohol that occurs in nature as a metabolite or storage compound. In this study, a multiple gene integration strategy was employed to enhance erythritol production in Y. lipolytica. The effects on the production of erythritol in Y. lipolytica of seven key genes involved in the erythritol synthesis pathway were evaluated individually, among which transketolase (TKL1) and transaldolase (TAL1) showed important roles in enhancing erythritol production. The combined overexpression of four genes (GUT1, TPI1, TKL1, TAL1) and disruption of the EYD1 gene (encoding erythritol dehydrogenase), resulted in produce approximately 40 g/L erythritol production from glycerol. Further enhanced erythritol synthesis was obtained by overexpressing the RKI1 gene (encoding ribose 5-phosphate isomerase) and the AMPD gene (encoding AMP deaminase), indicating for the first time that these two genes are also related to the enhancement of erythritol production in Y. lipolytica. A combined gene overexpression strategy was developed to efficiently improve the production of erythritol in Y. lipolytica, suggesting a great capacity and promising potential of this non-conventional yeast in converting glycerol into erythritol.

Limonene, a valuable cyclic monoterpene, has been broadly studied in recent decades due to its wide application in the food, cosmetics and pharmaceutical industries. Engineering of the yeast Yarrowia lipolytica for fermentation of renewable biomass lignocellulosic hydrolysate may reduce the cost and improve the economics of bioconversion for the production of limonene. The aim of this study was to engineer Y. lipolytica to produce limonene from xylose and low-cost lignocellulosic feedstock. The heterologous genes XR and XDH and native gene XK encoding xylose assimilation enzymes, along with the heterologous genes tNDPS1 and tLS encoding orthogonal limonene biosynthetic enzymes, were introduced into the Po1f strain to facilitate xylose fermentation to limonene. The initially developed strain produced 0.44 mg/L of limonene in 72 h with 20 g/L of xylose. Overexpression of genes from the mevalonate pathway, including HMG1 and ERG12, significantly increased limonene production from xylose to ∼9.00 mg/L in 72 h. Furthermore, limonene production peaked at 20.57 mg/L with 50% hydrolysate after 72 h when detoxified lignocellulosic hydrolysate was used. This study is the first to report limonene production by yeast from lignocellulosic feedstock, and these results indicate the initial steps toward economical and sustainable production of isoprenoids from renewable biomass by engineered Y. lipolytica.

Lycopene has been broadly studied in recent decades due to its health benefits including cancer prevention, anti-atherogenic and anti-obesity effects, and modulation of the immune system. To obtain efficient synthesis of lycopene, extensive researches have been conducted in various microbial cells, including Yarrowia lipolytica, to heterologously produce lycopene using various genetic and metabolic engineering methods. In this study, the effects of copy numbers of lycopene synthesis genes, a variety of key central metabolic genes (especially AMP deaminase-encoding gene AMPD), and 5-L fermenter cultivation on lycopene production in Y. lipolytica were investigated and the engineered strains with significantly enhanced lycopene content (46–60 mg/g DCW) were achieved. It is therefore possible to make use of the obtained strains to meet the industrial demand of lycopene production on the basis of further genetic and process optimization.

Purpose There are limited therapeutic options for patients with advanced penile squamous cell carcinoma (PSCC) after chemotherapy failure. Thus, we evaluated the feasibility of salvage treatment using the epidermal growth factor receptor (EGFR) mono-antibody nimotuzumab in chemotherapy-failed PSCC patients and explored potential response or resistance biomarkers. Materials and methods Six chemotherapy-failed PSCC patients with locally advanced disease or distant metastasis were enrolled consecutively to nimotuzumab treatment. Clinical responses and side effects were evaluated, and genetic characteristics of cancer specimens were analyzed through the next-generation sequencing of hotspot regions in cancer-related genes. Results Two of 6 patients showed partial responses, one was identified as having stable disease, while the other 3 had disease progression after nimotuzumab therapy. Side effects were all welltolerated. Genetic analysis revealed that TP53, CDKN2A, RB1, SMAD4, FLT3, and PIK3CA were the most frequently mutated genes in PSCC specimens, while altered KRAS, HRAS, EGFR, ERBB2, and FLT3 may be correlated with nimotuzumab resistance. Furthermore, 3 patients that were human papillomavirus-positive each showed clinical response or stable disease. Conclusions EGFR mono-antibody may be a potential modality for locally advanced PSCC patients after chemotherapy failure. Further large-scale clinical studies are needed to elucidate the role of human papillomavirus status and critical gene mutations in the clinical response to EGFR-targeted therapy.

Living organisms have evolved mechanisms for adjusting their metabolism to adapt to environmental nutrient availability. Terrestrial animals utilize the ornithine–urea cycle to dispose of excess nitrogen derived from dietary protein. Here, we identified an active ornithine–ammonia cycle (OAC) in cyanobacteria through an approach combining dynamic 15N and 13C tracers, metabolomics, and mathematical modeling. The pathway starts with carbamoyl phosphate synthesis by the bacterial- and plant-type glutamine-dependent enzyme and ends with conversion of arginine to ornithine and ammonia by a novel arginine dihydrolase. An arginine dihydrolase–deficient mutant showed disruption of OAC and severely impaired cell growth when nitrogen availability oscillated. We demonstrated that the OAC allows for rapid remobilization of nitrogen reserves under starvation and a high rate of nitrogen assimilation and storage after the nutrient becomes available. Thus, the OAC serves as a conduit in the nitrogen storage-and-remobilization machinery in cyanobacteria and enables cellular adaptation to nitrogen fluctuations.

Squalene, a valuable acyclic triterpene, can be used as a chemical commodity for pharmacology, flavor, and biofuel industries. Microbial production of squalene has been of great interest due to its limited availability, and increasing prices extracted from animal and plant tissues. Here we report genetic perturbations that synergistically improve squalene production in Saccharomyces cerevisiae. As reported previously, overexpression of a truncated HMG-CoA reductase 1 (tHMG1) led to the accumulation 20-fold higher squalene than a parental strain. In order to further increase squalene accumulation in the tHMG1 overexpressing yeast, we introduced genetic perturbations-known to increase lipid contents in yeast-to enhance squalene accumulation as lipid body is a potential storage of squalene. Specifically, DGA1 coding for diacylglycerol acyltranferase was overexpressed to enhance lipid biosynthesis, and POX1 and PXA2 coding for acyl-CoA oxidase and a subunit of peroxisomal ABC transporter were deleted to reduce lipid β-oxidation. Simultaneous overexpression of tHMG1 and DGA1 coding for rate-limiting enzymes in the mevalonate and lipid biosynthesis pathways led to over 250-fold higher squalene accumulation than a control strain. However, deletion of POX1 and PXA2 in the tHMG1 overexpressing yeast did not improve squalene accumulation additionally. Fed-batch fermentation of the tHMG1 and DGA1 co-overexpressing yeast strain resulted in the production of squalene at a titer of 445.6 mg/L in a nitrogen-limited minimal medium. This report demonstrates that increasing storage capacity for hydrophobic compounds can enhance squalene production, suggesting that increasing lipid content is an effective strategy to overproduce a hydrophobic molecule in yeast.

Terpenoids from medicinal plants are widespread secondary metabolites in nature and exist as multiple types with different structures that are crucial in plant growth and development. Moreover, terpenoids exert a broad range of biological activities, including antitumor, antioxidation, anti-viral, and so on. In this study, artemisinin, tanshinone, and ginsenoside were selected as three representative examples, and progress in terms of research on biosynthetic genes, transcriptional regulation, metabolic engineering, synthetic biology, biosynthesis and transport was summarized. Future prospects including functional genes excavation and regulation mechanism network of terpenoids were also discussed.

Alpha-zingiberene, a functionally important active component of ginger, is used extensively in various applications in the fields of medicine, food, and agriculture. In this study, alpha-zingiberene was de novo biosynthesized from glucose using metabolically engineered Escherichia coli as hosts. First, the alpha-zingiberene synthase, VvPNaZin, was heterologously expressed in an E. coli strain. The resultant recombinant strain, LZ020, produced 0.012 ± 0.002 mg/L of alpha-zingiberene. Next, ERG20 was overexpressed in LZ021 to increase the farnesyl pyrophosphate (FPP) content, which enhanced the yield of alpha-zingiberene to 0.041 ± 0.017 mg/L. Finally, the heterologous mevalonate (MVA) pathway was introduced to increase the supply of dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) precursors, which induced LZ022 to produce 0.764 ± 0.048 mg/L of alpha-zingiberene, representing a 63.7-fold increase compared to that produced by the LZ020 strain. Thus, the current study established a technique that facilitates microbial synthesis of alpha-zingiberene directly from glucose, thereby providing methodology which enables sustainable production of alpha-zingiberene.

Yarrowia lipolytica is an oleaginous yeast with promise in producing terpenoids such as lycopene. Though methods for analyzing primary metabolic intermediates have been established, further work is needed to better analyze nucleotides and coenzymes. Here, we presented an optimized method for the separation of nucleotides and coenzymes in Y. lipolytica using the capillary electrophoresis. The separation of twelve metabolites including four coenzymes, five nucleotides and three nucleosides was achieved within 32 min using a voltage of 15 kV and 70 mM sodium carbonate/hydrogencarbonate buffer with 1.0% β -CD at pH 10. The results show that the concentrations of adenosine triphosphate and nicotinamide adenine dinucleotide phosphate changed significantly between lycopene producing strain and the control, indicating that these two metabolites may be closely related with lycopene production. The optimized method provides a useful approach for future metabolic analysis of fermentation process as well as industrial strain improvement.

BackgroundAlthough clear cell renal cell carcinoma (ccRCC) is well known as a highly immunogenic tumor, only a small subset of patients could benefit from current immunotherapy, which might be due to the heterogeneity of immune microenvironment in ccRCC. So, it is meaningful to explore novel immunotherapy or combination therapy for improving therapeutic efficacy. HHLA2, a newly discovered B7 family member, is prevalently expressed in numerous tumors, including ccRCC. This study aimed to investigate the prognostic impact of HHLA2/PD-L1 co-expression and its relationship with tumor-infiltrating lymphocytes (TILs).MethodsThe expression levels of HHLA2, PD-L1, CD8, and CD4 in cancer tissues from cases (206 in the training cohort and 197 in the validation cohort) with surgically resectable primary ccRCC were evaluated by immunohistochemistry.ResultsThe positive rates of HHLA2 were much higher than those of PD-L1 in ccRCC tissues. HHLA2-positive expression was significantly associated with necrosis, microvascular invasion, advanced Fuhrman nuclear, and TNM stage and indicated a shorter progression-free survival (PFS) and overall survival (OS) in both cohorts. Moreover, patients with HHLA2/PD-L1 co-expression suffered the highest risk of disease progression and death by a significant margin. Besides, HHLA2/PD-L1 co-expression was significantly associated with a high density of CD8+and CD4+TILs. Notably, a new immune classification, based on HHLA2/PD-L1 co-expression and TILs, successfully stratified PFS and OS, especially in patients with TILs positivity.ConclusionsThe expression of HHLA2 is more frequent than PD-L1 in ccRCC. HHLA2/PD-L1 co-expression had an adverse impact on the prognoses of patients with ccRCC; this finding provides a rationale for combination immunotherapy with anti-HHLA2 and PD-L1 blockage for patients with ccRCC in the future.

Carotenoids, as potent antioxidant compounds, have gained extensive attention, especially in human health. In this study, the combination of CRISPR/Cas9 integration strategy and fermenter cultivation was utilized to obtain efficient β-carotene-producing Yarrowia lipolytica cell factories for potential industrial application. The introduction of the genes of Mucor circinelloides, encoding phytoene dehydrogenase (carB) and bifunctional phytoene synthase/lycopene cyclase (carRP), contributed to the heterologous production of β-carotene in Y. lipolytica XK2. Furthermore, β-carotene production was efficiently enhanced by increasing the copy numbers of the carB and carRP genes and overexpressing of GGS1, ERG13, and HMG, the genes related to the mevalonate (MVA) pathway. Thus, the optimized strain overexpressed a total of eight genes, including three copies of carRP, two copies of carB, and single copies of GGS1, HMG, and ERG13. As a consequence, strain Y. lipolytica XK19 accumulated approximately 408 mg/L β-carotene in shake flask cultures, a twenty-four-fold increase compared to the parental strain Y. lipolytica XK2. 4.5 g/L β-carotene was obtained in a 5-L fermenter through a combination of genetic engineering and culture optimization, suggesting a great capacity and flexibility of Y. lipolytica in the production of carotenoids.

Genome-scale metabolic models (GEMs) can be utilized to better understand the genotype-phenotype relationship in microbial metabolism. Manipulation strategies based on analysis of metabolic flux distributions using constraint-based methods have been validated to be effective for designing strains. Herein, we first investigated the coupled relationship of growth and production, and subsequently proposed an algorithm, called analysis of production and growth coupling (APGC), to identify amplification targets for improving production of the desired metabolite. The logical transformation of the genome-scale metabolic models (LTM) could enable a gene-level prediction, that is, direct gene targets would be determined through APGC. This algorithm was successfully employed to simulate heterogeneous biosynthesis of the antioxidant lycopene in Escherichia coli, and target genes for the improvement of lycopene production were identified. These identified gene targets were unambiguous and were closely related to the supply of essential precursors and cofactors for lycopene production, and most of these have been validated as effective in enhancing the yield of lycopene.

Tanshinones and phenolic acids are two major groups of natural bioactive compounds in Salvia miltiorrhiza which exert excellent pharmacological activities. Due to low content in S.miltiorrhiza, it is urgent to enhance the production of the two compounds to meet the increasing need. The Arabidopsis basic helix-loop-helix (bHLH) transcription factor MYC2 was introduced into S. miltiorrhiza hairy roots. In the best transgenic line AtMYC2-3, tanshinone yield was 14.06 mg/g dw which was increased by 5.45-fold more than that in the control line, while phenolic acid production was enhanced to 95.9 mg/g dw, a 3.3-fold increase compared with the control. Transcript levels of some genes involved in biosynthesis of tanshinones and phenolic acids were noticeably upregulated. Dual-luciferase assay revealed that AtMYC2 activated the expression of biosynthetic genes including SmDXS2 and SmTAT. These results revealed that AtMYC2 plays a positive role in accumulation of both tanshinones and phenolic acids which provides a promising strategy for engineering tanshinone and phenolic acid production in S. miltiorrhiza.

Heterologous proteins induction by methylotrophic recombinant Pichia pastoris is generally implemented at high cells density condition. Methanol concentration (MeOH) and dissolved oxygen concentration (DO) are two crucial operating parameters controlling proteins production. It is difficult to control MeOH/DO at their desired levels simultaneously due to the extremely high oxygen consumption features. Methanol utilization plus (Mut+) and slow (MutS) strains are the two typical phenotypes of recombinant P. pastoris with quite different dynamic characteristics. Therefore, different MeOH/DO combinational control strategies or sub-optimal induction strategies could be adopted. Environments of “high MeOH/low DO” and “high DO/low MeOH” are the realistic induction strategies. In this study, we summarized our own experimental results (using Mut+/MutS strains to produce human serum albumin-human granulocyte colony stimulating factor—HSA-GCSFm/porcine interferon-α—pIFN-α), and compared to data from the literature using the above mentioned two induction strategies. The results suggested that, heterologous proteins production by Mut+ strains favors “high DO/low MeOH (DO ~ 10%, MeOH ~ 0 g/L)” induction condition, while proteins production by MutS strains prefers “high MeOH/low DO (MeOH 5–10 g/L, DO ~ 0%)” induction environment. Thus, based on the P. pastoris types, the corresponding sub-optimal induction strategies should be applied accordingly. The related metabolic analysis indicating methanol utilizing efficiency and the transcriptional analysis reflecting gene up- or down-regulations involved in several key routes in methanol and sorbitol metabolism were implemented. The analysis results strongly supported the conclusions of using the proposed sub-optimal induction strategies for different heterologous proteins production by Mut+ and MutS strains.

Cell line models are essential tools to study the molecular mechanisms underlying tumor initiation and progression. There are limited treatment options for penile squamous cell carcinoma (PSCC), accounting for 1–2% of male tumors in developing countries, and limited progress in preclinical research in PSCC due to lacking available models with identified genomic characteristics. Here, biological and molecular characteristics and whole-genomic alterations were analyzed in a panel of PSCC cell lines newly established in our laboratory. These cell lines were all human papillomavirus (HPV)-negative, epithelial-like, immortalized, and tumorigenic in nude mice, whereas they displayed different proliferation, migration and invasion capacities in vitro, and tumorigenic ability in nude mice. They were all cisplatin sensitive, anti-EGFR therapy resistant, and androgen irresponsive. Whole-genomic sequecing analysis revealed that transition mutations (C:G>T:A and T:A>C:G) were the most common substitution types in these cell lines, whereas ERCC5, TP53, PTH1, CLTCL1, NOTCH2, MAP2K3, CDK11A/B, USP6, ADCH5, BCLAF1, CDKN2A, FANCD2, HRAS, and NOTCH1 were the most frequently altered genes. Amplifications of MYC, PLAG1, NCOA2, RUNX1T1, COX6C, and EGFR and losses of FBXW7, TET2, XPC, and FANCE were frequently observed in cell lines. The exomic variations between cell lines and their corresponding cancer tissues were highly consistent. Genetic variations were mainly involved in the MAPK, Jak-STAT, TGF-beta, Notch, and apoptosis signaling pathways. Conclusively, these panel of PSCC cell lines established in our laboratory harbor some common or specific biological characteristics and genomic variations, and they may serve as optimal models to investigate the molecular mechanisms underlying the progression, metastasis, relapses, and treatment resistance of PSCC and to develop effective treatment strategy.

Recent advances in the production of biofuels by microbes have attracted attention due to increasingly limited fossil fuels. Biodiesels, especially fatty acid ethyl esters (FAEEs), are considered a potentially fully sustainable fuel in the near future due to similarities with petrodiesels and compatibility with existing infrastructure. However, biosynthesis of FAEEs is limited by the supply of precursor lipids and acetyl-CoA. In the present study, we explored the production potential of an engineered biosynthetic pathway coupled to the addition of ethanol in the oleaginous yeast Yarrowia lipolytica. This type of yeast is able to supply a greater amount of precursor lipids than species typically used. To construct the FAEEs synthesis pathway, WS genes that encode wax ester synthases (WSs) from different species were codon-optimized and heterologously expressed in Y. lipolytica. The most productive engineered strain was found to express a WS gene from Marinobacter hydrocarbonoclasticus strain DSM 8798. To stepwisely increase FAEEs production, we optimized the promoter of WS overexpression, eliminated β-oxidation by deleting the PEX10 gene in our engineered strains, and redirected metabolic flux toward acetyl-CoA. The new engineered strain, coupled with an optimized ethanol concentration, led to an approximate 5.5-fold increase in extracellular FAEEs levels compared to the wild-type strain and a maximum FAEEs titer of 1.18 g/L in shake flask cultures. In summary, the present study demonstrated that an engineered Y. lipolytica strain possessed a high capacity for FAEEs production and may serve as a platform for more efficient biodiesel production in the future.

In this study, the process of Eimeria tenella-induced apoptosis and the effect of calcium homeostasis were investigated in chick embryo cecal epithelial cells. In particular, we examined cytochrome c release into the cytoplasm, mitochondrial permeability transition pore (MPTP) opening, and changes in [Ca(2+)]c and apoptosis in host cells. Apoptosis, MPTP opening, cytochrome c release, and [Ca(2+)]c in host cells increased following infection. This trend was reversed by blocking the increase in [Ca(2+)]c using BAPTA/AM and EGTA (intra- and extracellular chelators of Ca(2+), respectively) and by applying heparin sodium and ryanodine (blockers of the inositol triphosphate and ryanodine receptors of the endoplasmic reticulum, respectively). These results indicate that [Ca(2+)]c plays a significant role in host cell mitochondrial apoptosis, which is induced via modulation of extracellular Ca(2+) levels and endoplasmic reticulum Ca(2+) channels. Thus, agents that restore Ca(2+) homeostasis may be useful for managing E. tenella infection in chickens.

The steroid metabolites 9-hydroxy-androstenedione (9-OH-AD), androstadienedione (ADD) and androstenedione (AD) are important steroidal pharmaceuticals. In order to raise the production of steroid metabolites, an efficient resting cell phytosterol bioconversion process was developed to produce 9-OH-AD in the presence of hydroxypropyl-b-cyclodextrin (HP-b-CD). Cell growth medium containing phytosterol as an inducer positively improved cell activity. Under aerobic conditions, bioconversion proceeded at 70 g L –1 phytosterol in the presence of HP-b-CD (the optimized molar ratio of HP-b-CD/phytosterol was 1:1) with 30 g L –1 resting Mycobacterium neoaurum NwIB-yV cells (cell dry mass) in a 5-L bioreactor, where 9-OH-AD production and space-time yield reached 36.4 g L –1 and 9.1 g L –1 d –1 , respectively. The recycling of cells and HP-b-CD enables cost-saving and industrial applications. This bioprocess was also applied for the production of ADD and AD. The production of these steroid metabolites was much higher than that reported in previous studies.

Coccidiosis causes considerable economic losses in the poultry industry. At present, the pathology of coccidiosis is preventable with anticoccidials and vaccination, although at considerable cost to the international poultry industry. The purpose of the present study was to elucidate the relationship between Eimeria tenella development and host cell apoptosis in chickens, which provides a theoretical basis for further study of the injury mechanism of E. tenella and the prevention and treatment of coccidiosis. Cecal epithelial cells from chick embryo were used as host cells in vitro. In addition, flow cytometry, terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate (dUTP) nick-end labeling, and histopathological assays were used to detect the dynamic changes in E. tenella infection rates, DNA injury rates, and apoptosis rates in groups treated with and without the caspase-9 inhibitor Z-LEHD-FMK. Following E. tenella infection, we demonstrated that untreated cells had less apoptosis at 4 h and, inversely, more apoptosis at 24 to 120 h compared with control cells. Furthermore, after the application of Z-LEHD-FMK, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assays, and translation of phosphatidyl serines to the host cell plasma membrane surface, the treated group chick embryo cecal epithelial cells exhibited decreased apoptosis and DNA injuries (P

Yarrowia lipolytica, a model microorganism of oleaginous yeasts with developed sophisticated genetic tools, is able to metabolize a wide range of substrates and accumulate large amounts of lipids. However, there is a lack of literature reporting the metabolic characteristics of Y. lipolytica metabolizing these substrates in a systematic view. In this study, Y. lipolytica was cultivated on a variety of carbon sources, among which cell growth and production characteristics on two representative substrates (glucose and oleic acid) were investigated in detail at metabolomic level. Metabolic pathway abundance was computed to interpret the metabolome data in a straightforward way. The results showed that most pathway abundances decreased in the shift from growth to production phase. Specifically, when cultivated on glucose, abundances of twelve pathways decreased markedly between the growth and lipid production phases, while thirteen pathways reduced and only three pathways increased significantly in abundances on oleic acid. In comparison, for the same cultivation phase only a few pathways exhibited significant changes between glucose-grown and oleic acid-grown cells. This study revealed that the pathway abundance could be used to effectively show the activity changes of pathways, providing a new perspective to employ metabolomics data for understanding cell metabolism and enhancing the production of target metabolites.

As a bioactive triterpenoid, squalene is widely used in the food industry, cosmetics, and pharmacology. Squalene’s major commercial sources are the liver oil of deep-sea sharks and plant oils. In this study, we focused on the enhancement of squalene biosynthesis in Yarrowia lipolytica, with particular attention to the engineering of acetyl-CoA metabolism based on genome-scale metabolic reaction network analysis. Although the overexpression of the rate-limiting endogenous ylHMG1 (3-hydroxy-3-methylglutaryl-CoA reductase gene) could improve squalene synthesis by 3.2-fold over that by the control strain, the availability of the key intracellular precursor, acetyl-CoA, was found to play a more significant role in elevating squalene production. Analysis of metabolic networks with the newly constructed genome-scale metabolic model of Y. lipolytica iYL_2.0 showed that the acetyl-CoA pool size could be increased by redirecting carbon flux of pyruvate dehydrogenation towards the ligation of acetate and CoA or the cleavage of citrate to form oxaloacetate and acetyl-CoA. The overexpression of either acetyl-CoA synthetase gene from Salmonella enterica (acs*) or the endogenous ATP citrate lyase gene (ylACL1) resulted in a more than 50% increase in the cytosolic acetyl-CoA level. Moreover, iterative chromosomal integration of the ylHMG1, asc*, and ylACL1 genes resulted in a significant improvement in squalene production (16.4-fold increase in squalene content over that in the control strain). We also found that supplementation with 10 mM citrate in a flask culture further enhanced squalene production to 10 mg/g DCW. The information obtained in this study demonstrates that rationally engineering acetyl-CoA metabolism to ensure the supply of this key metabolic precursor is an efficient strategy for the enhancement of squalene biosynthesis.

Aim: To establish a pancreatic cancer stem cell model using human pancreatic cancer cells in nude mice to provide a platform for pancreatic cancer stem cell research. Materials and Methods: To establish pancreatic cancer xenografts using human pancreatic cancer cell line SW1990, nude mice were randomly divided into control and gemcitabine groups. When the tumor grew to a volume of 125mm 3 , they treated with gemcitabine at a dose of 50mg/kg by intraperitoneal injection of 0.2ml in the gemcitabine group, while the mice in control group were treated with the same volume of normal saline. Gemcitabine was given 2 times a week for 3 times. When the model was established, the proliferation of pancreatic cancer stem cells was observed by clone formation assay, and the protein and/or mRNA expression of pancreatic stem cell surface markers including CD24, CD44, CD133, ALDH, transcription factors containing Oct-4, Sox-2, Nanog and Gli, the key nuclear transcription factor in Sonic Hedgehog signaling pathway was detected by Western blot and/or RT-PCR to verify the reliability of this model. Results: This model is feasible and safe. During the establishment, no mice died and the weight of nude mice maintained above 16.5g. The clone forming ability in gemcitabine group was stronger than that of the control group (p

Ansamitocin P-3 (AP-3) is an active and potent anti-tumor maytansinoid, which is usually produced by Actinosynnema spp. In this study, the effects of different carbon sources on biomass and AP-3 production by Actinosynnema mirum were investigated. The results showed great biomass production behavior of A. mirum in glucose medium comparatively to other carbon sources. Interestingly, when fructose was used as the sole carbon source, the highest yield of AP-3 was obtained, which was about fourfold than that of strain cultured in glucose after 168 h. Further analysis conducted in regard to better understanding of such observations in glucose and fructose defined media showed that fructose improves AP-3 production through the stimulation of the key genes of the secondary metabolism pathways. It was concluded that fructose could be a potential carbon source for cost-effective production of AP-3 from an industrial point of view.

Background: Yarrowia lipolytica is widely studied as a non-conventional model yeast owing to the high level of lipid accumulation. Therein, triacylglycerol (TAG) is a major component of liposome. In order to investigate the TAG biosynthesis mechanism at a systematic level, a novel genome-scale metabolic model of Y. lipolytica was reconstructed based on a previous model iYL619_PCP published by our lab and another model iYali4 published by Kerkhoven et al. Results: The novel model iYL_2.0 contains 645 genes, 1083 metabolites, and 1471 reactions, which was validated more effective on simulations of specific growth rate. The precision of 29 carbon sources utilities reached up to 96.6% when simulated by iYL_2.0. In minimal growth medium, 111 genes were identified as essential for cell growth, whereas 66 essential genes were identified in yeast extract medium, which were verified by database of essential genes, suggesting a better prediction ability of iYL_2.0 in comparison with other existing models. In addition, potential metabolic engineering targets of improving TAG production were predicted by three in silico methods developed in-house, and the effects of amino acids supplementation were investigated based on model iYL_2.0. Conclusions: The reconstructed model iYL_2.0 is a powerful platform for efficiently optimizing the metabolism of TAG and systematically understanding the physiological mechanism of Y. lipolytica. [Figure not available: see fulltext.]. QC 20181020

Reconstruction and application of genome-scale metabolic models (GEMs) have facilitated metabolic engineering by providing a platform on which systematic computational analysis of metabolic networks can be performed. In this study, a GEM of Escherichia coli NZN111 was employed by the analysis of production and growth coupling (APGC) algorithm to identify genetic strategies for the overproduction of succinate. Through in silico simulation and reaction expression analysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), triosephosphate isomerase (TPI), and phosphoenolpyruvate carboxylase (PPC), encoded by gapA, pgk, tpiA, and ppc, respectively, were selected for experimental overexpression. The results showed that overexpressing any of these could improve both growth and succinate production. Specifically, overexpression of GAPDH or PGK showed a significant effect with up to 24% increase in succinate production. These results indicate that the APGC algorithm can be effectively used to guide genetic manipulation for strain design by identifying genome-wide gene amplification targets.

Interleukin (IL)-33 is a member of the interleukin-1 cytokine family that is produced by many different types of tissues including the central nervous system (CNS). IL-33 mediates its effects via its heterodimeric receptor complex, comprised of ST2 and the IL-1 receptor accessory protein (IL-1RAcp). As a pleiotropic nuclear cytokine, IL-33 is a crucial factor in the development of cardiovascular diseases, allergic diseases, infectious diseases, and autoimmune diseases. Recently, accumulated evidence shows that the IL-33/ST2 axis plays a crucial and diverse role in the pathogenesis of CNS diseases, including neurodegenerative diseases, cerebrovascular diseases, infectious diseases, traumatic CNS injury, chronic pain, etc. In this review, we discuss the recent findings in the cellular signaling of IL-33 and advancement of the role of IL-33 in several CNS diseases, as well as its therapeutic potential for the treatment of those diseases.

In this study, stepwise increases in linalool production were obtained by combining metabolic engineering and process optimization of an unconventional oleaginous yeast Yarrowia lipolytica. The linalool synthetic pathway was successfully constructed by heterologously expressing a codon-optimized linalool synthase gene from Actinidia arguta in Y. lipolytica. To enhance linalool productivity, key genes involved in the mevalonate pathway were overexpressed in different combinations. Moreover, the overexpression of mutant ERG20F88W-N119W gene resulted in further linalool production. A maximum linalool titre of 6.96±0.29mg/L was achieved in shake flasks, which was the highest level ever reported in yeasts.

Gluconobacter oxydans, belonging to acetic acid bacteria, is widely used in industrial biotechnology. In our previous study, one of the main glucose metabolic pathways in G. oxydans 621H was blocked by the disruption of the mgdh gene, which is responsible for glucose oxidation to gluconate on cell membrane. The resulting 621H Δmgdh mutant strain showed an enhanced growth and biomass yield on glucose. In order to further understand the intracellular utilization of glucose by 621H Δmgdh, the functions of four fundamental genes, namely glucokinase-encoding glk1 gene, soluble glucose dehydrogenase-encoding sgdh gene, galactose-proton symporter-encoding galp1 and galp2 genes, were investigated. The obtained metabolic characteristics of 621H Δmgdh Δglk1 and 621H Δmgdh Δsgdh double-gene knockout mutants showed that, in vivo, glucose is preferentially phosphorylated to glucose-6-phosphate by glucokinase rather than being oxidized to gluconate by soluble glucose dehydrogenase. In addition, although the galactose-proton symporter-encoding genes were proved to be glucose transporter genes in other organisms, both galp genes (galp 1 and galp2) in G. oxydans were not found to be involved in glucose uptake system, implying that other unknown transporters might be responsible for transporting glucose into the cells.

Yarrowia lipolytica is the well-known oleaginous yeast able to accumulate amounts of lipids and a variety of high value products. The knowledge of its intracellular metabolites concentrations, which are directly linked to the sample preparation of corresponding intracellular metabolites, is of fundamental importance for the characterization of its metabolism. Therefore, in this study, we evaluated current sampling and extraction methods used in gas chromatography–mass spectrometry (GC–MS) analysis of the intracellular metabolites of microorganism. Mainly, the comparison between the methyl chloroformate (MCF) derivatization and the N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) derivatization applied to the analysis of a broad variety of Y. lipolytica's metabolites was performed. More importantly, the dimethyl sulfoxide (DMSO) solution quenching method was attempted with the purpose of reducing the intracellular metabolites leakage during quenching and adapting the leakage-free quenching method to both kinds of derivatization. The results obtained showed that the DMSO quenching method permits measurement of the concentration of intracellular metabolites and can be applicable for the analysis of multiple metabolites of important pathways in Y. lipolytica by available routine GC–MS platform.

Accumulation of advanced glycation end products (AGEs) contributes to ageing and age-related diseases, especially type 2 diabetes. The NLRP3 inflammasome, as a vital component of the innate immune system, is implicated in the pathogenesis of type 2 diabetes. However, the role of the NLRP3 inflammasome in AGE-induced pancreatic islet damage remains largely unclear. Results showed that administration of AGEs (120 mg/kg for 6 weeks) in C57BL/6J mice induced an abnormal response to glucose (as measured by glucose tolerance and insulin release), pancreaticβ-cell ultrastructural lesion, and cell death. These effects were associated with an excessive superoxide anion level, significant increased protein expression levels for NADPH oxidase 2 (NOX2), thioredoxin-interacting protein (TXNIP), NLRP3, and cleaved IL-1β, enhanced caspase-1 activity, and a significant increase in the levels of TXNIP–NLRP3 protein interaction. Ablation of the NLRP3 inflammasome or treatment with antioxidantN-acetyl-cysteine (NAC) clearly ameliorated these effects. In conclusion, our results reveal a possible mechanism for AGE-induced pancreatic islet damage upon NLRP3 inflammasome activation.

Candida glabrata has been recognized as an efficient industrial microorganism for the production of pyruvate, the most widely used α-oxocarboxylic acid in the areas of agrochemicals, drugs, and chemicals. To gain a comprehensive understanding of its physiology and cellular metabolism, the genome-scale metabolic model for C. glabrata (named iNX804), comprising 804 genes, 1287 reactions, and 1025 metabolites, was reconstructed by genome sequence annotation and biochemical data mining. The flux balance analysis data of model iNX804 exhibited good agreement with the experimental data, including the phenotypic data and the carbon flux distribution. The model iNX804 predicted that C. glabrata can synthesize a high concentration of pyruvate because it has a strong glucose transport capacity and three pyruvate biosynthesis pathways and is deficient in key steps in vitamin synthesis. Furthermore, the metabolic capacity of pyruvate and other fine chemicals derived from pyruvate was evaluated by in silico deletion and overexpression of several key genes. The metabolic model iNX804 provides a potential platform for global elucidation of the metabolism of C. glabrata.

Succinic acid is a valuable product due to its wide-ranging utilities. To improve succinate production and reduce by-products formation, Escherichia coli NZN111 was constructed by insertional inactivation of lactate dehydrogenase (LDH) and pyruvate formate lyase (PFL) encoded by the genes ldhA and pflB, respectively. However, this double-deletion mutant is incapable of anaerobically growing on glucose in rich or minimal medium even with acetate supplementation. A widespread hold view is that the inactivation of NADH-dependent LDH limits the regeneration of NAD+ and consequently disables proper growth under anaerobic conditions. In this study, genome-scale metabolic core model of E. coli was reconstructed and employed to perform all simulations in silico according to the reconstruction of engineered strain E. coli NZN111. Non-optimized artificial centering hit-and-run (ACHR) method and metabolite flux-sum analysis were utilized to evaluate metabolic characteristics of strains. Thus, metabolic characteristics of the strains wild-type E. coli, ldhA mutant, pflB mutant, and NZN111 under anaerobic conditions were successfully unraveled. We found a viewpoint contrary to the widespread realization that an NADH/NAD+ in NZN111 mainly resulted from the inactivation of PFL rather than the inactivation of LDH. In addition, the two alternative anaerobic fermentation pathways, lactate and ethanol production pathways, were blocked owing to the disruption of ldhA and pflB, resulting in insufficient NAD+ regeneration to oxidize or metabolize glucose for cell growth. Furthermore, we speculated reaction NADH16, the conversion of ubiquinone-8 (q8) to ubiquinol-8 (q8h2), as a potential amplification target for anaerobically improving cell growth and succinate production in NZN111.

Bioconversion of CO/syngas to produce ethanol is a novel route in bioethanol production, which can be accomplished by some acetogens. Specific culture vessels and techniques are needed to cultivate these microorganisms since they are anaerobic and substrates are gaseous. In this work, gas-sampling bag was applied as a gas-cultivation system to study CO/syngas bioconversion by Clostridium autoethanogenum and was demonstrated to be efficient because of its flexibility and excellent ability to maintain the headspace atmosphere. C. autoethanogenum can use CO as the sole carbon and energy source to produce ethanol, acetate as well as CO2. In the experimental range, higher ethanol production was favored by higher yeast extract concentrations, and the maximum ethanol concentration of 3.45g/L was obtained at 1.0g/L of yeast extract. Study with various bottled gases showed that C. autoethanogenum preferred to use CO other than CO2 and produced the highest level of ethanol with 100% CO as the substrate. C. autoethanogenum can also utilize biomass-generated syngas (36.2% CO, 23.0% H2, 15.4% CO2, 11.3% N2), but the process proceeded slowly and insufficiently due to the presence of O2 and C2H2. In our study, C. autoethanogenum showed a better performance in the bioconversion of CO to ethanol than Clostridium ljungdahlii, a strain which has been most studied, and for both strains, ethanol production was promoted by supplementing 0.5g/L of acetate.

The metabolomic studies were conducted for both the engineered lycopene-producing Yarrowia lipolytica strain and the control strain. The changes in metabolome profiling and main pathway abundance of Y. lipolytica with the introduction of heterologous crt genes were investigated by multiple analytical and statistical methods More importantly, the metabolome data were transformed into pathway abundances visualized by a pathway relationship network using Cytoscape software. This network provided a simple way to present the statistical results of pathway abundance and interpret the effects of the crt genes in a metabolic view, and the results highlighted the up-regulation of eight pathways and the down-regulation of three pathways in the lycopene fast production phase. The comprehensive analysis suggested that the synthesis of lycopene has remarkable effects on fructose and mannose metabolism, citrate cycle, glyoxylate and dicarboxylate metabolism, glycerophospholipid metabolism as well as the biosynthesis and metabolism of some amino acids including valine, leucine and isoleucine in Y. lipolytica.

Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.