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Functional proteins with the ability to isomerise free linoleic acid (LA) to conjugated linoleic acid (CLA) are termed linoleic acid isomerases (LAI). BBI is a novel LAI from Bifidobacterium breve with unique advantages in the production of a single CLA isomer; however, its complex membrane-bound form hampers over-expression of the protein in its natural host. To overcome this challenge, heterologous expression of BBI in Pichia pastoris was studied. Further, to investigate the influence of His-tags on the heterologous expression of BBI, three P. pastoris recombinant strains carrying either a C-terminal His-tag, an N-terminal His-tag, or none were constructed. The expression of recombinant proteins was analysed by dot and western blotting, and the enzyme activity was determined by GC-MS. The results show that the three P. pastoris recombinant strains successfully expressed the recombinant protein and had LAI activity. Compared with those BBIs without a His-tag or carrying a His-tag on the C-terminus, the BBI carrying an N-terminal His-tag had reduced expression and enzyme activity and that was also explained by the protein modelling analysis. Moreover, this study highlights the advantages of using P. pastoris for BBI expression to achieve efficient production of c 9, t 11-CLA monomers; the highest conversion rate of the substrate LA was over 80%, resulting in the production of 0.81 mg of c 9, t 11-CLA per mg of crude enzyme., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

Enzyme catalyzed desaturation of intracellular fatty acids plays an important role in various physiological and pathological processes related to lipids. Limited to the multiple transmembrane domains, it is difficult to obtain their three-dimensional structure of fatty acid desaturases. So how they interact with their substrates is unclear. Here, we predicted the complex of Micromonas pusilla delta 6 desaturase (MpFADS6) with the substrate linoleinyl-CoA (ALA-CoA) by trRosetta software and docking poses by Dock 6 software. The potential enzyme-substrate binding sites were anchored by analysis of the complex. Then, site-directed mutagenesis and activity verification clarified that W290, W224, and F352 were critical residues of the substrate tunnel and directly bonded to ALA-CoA. H94 and H69 were indispensable for transporting electrons with heme. H452, N445, and H358 significantly influenced the recognition and attraction of MpFADS6 to the substrate. These findings provide new insights and methods to determine the structure, mechanisms and directed transformation of membrane-bound desaturases., (© 2022. The Author(s).)

Amino acids are the building blocks of protein, promoting the balance between growth and lipid synthesis. However, the accumulation of microbial lipids involves multiple pathways, which requires the analysis of the global cellular metabolic network in which amino acid metabolism is involved. This review illustrates the dependence patterns of intracellular amino acids and lipids of oleaginous eukaryotic microorganisms in different environments and points out the contribution of amino acid metabolic precursors to the de novo synthesis of fatty acids. We emphasized the key role of amino acid metabolism in lipid remodeling and autophagy behavior and highlighted the regulatory effects of amino acids and their secondary metabolites as signal factors for microbial lipid synthesis. The application prospects of omics technology and genetic engineering technology in the field of microbial lipids are described. KEY POINTS: • Overview of microbial lipid synthesis mediated by amino acid metabolism • Insight into metabolic mechanisms founding multiple regulatory networks is provided • Description of microbial lipid homeostasis mediated by amino acid excitation signal., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The electron-transfer capabilities of cytochrome b 5 reductase (Cyt b 5 R) and NADPH supply have been shown to be critical factors in microbial fatty acid synthesis. Unfortunately, Cyt b 5 R substrate specificity is limited to the coenzyme NADH. In this study, we discovered that a novel Cyt b 5 R from Mortierella alpina ( Ma Cytb5RII) displays affinity for NADPH and NADH. The enzymatic characteristics of high-purity Ma Cytb5RII were determined with the K m, NADPH and K m, NADH being 0.42 and 0.07 mM, respectively. Ma Cytb5RII shows high specific activity at 4 °C and pH 9.0. We anchored the residues that interacted with the coenzymes using the homology models of Ma Cytb5Rs docking NAD(P)H and FAD. The enzyme activity analysis of the purified mutants Ma Cytb5RII [S230N] , Ma Cytb5RII [Y242F] , and Ma Cytb5RII [S272A] revealed that Ser230 is essential for Ma Cytb5RII to have dual NAD(P)H dependence, whereas Tyr242 influences Ma Cytb5RII's NADPH affinity and Ala272 greatly decreases Ma Cytb5RII's NADH affinity.

The present study was designed to explore the possibility of improving lipid production in oleaginous filamentous fungus Mortierella alpina based on an autophagy regulation strategy. According to multiomics information, vacuolate-centered macroautophagy was identified as the main type of autophagy in M. alpina under nitrogen-limited conditions. Mutation of autophagy-related gene MAatg8 led to impaired fatty acid synthesis, while overexpression of both MAatg8 and phosphatidylserine decarboxylases ( MApsd2 ) showed promoting effects on fatty acid synthesis. MAatg8 overexpression strain with external supply of ethanolamine significantly increased arachidonic acid (ARA)-rich triacylglycerol (TAG) and biomass synthesis in M. alpina , and the final fatty acid content increased by approximately 110% compared with that in the wild-type strain. Metabolomics and lipidomics analyses revealed that cell autophagy enhanced the recycling of preformed carbon, nitrogen, and lipid in mycelium, and the released carbon skeleton and energy were contributed to the accumulation of TAG in M. alpina . This study suggests that regulation of autophagy-related MAatg8-phosphatidylethanolamine (MAatg8-PE) conjugation system could be a promising strategy for attaining higher lipid production and biomass growth. The mechanism of autophagy in regulating nitrogen limitation-induced lipid accumulation elucidated in this study provides a reference for development of autophagy-based strategies for improving nutrient use efficiency and high value-added lipid production by oleaginous microorganism. IMPORTANCE Studies have indicated that functional oil accumulation occurs in oleaginous microorganisms under nitrogen limitation. However, until now, large-scale application of nitrogen-deficiency strategies was limited by low biomass. Therefore, the identification of the critical nodes of nitrogen deficiency-induced lipid accumulation is urgently needed to further guide functional oil production. The significance of our research is in uncovering the function of cell autophagy in the ARA-rich TAG accumulation of oleaginous fungus M. alpina and demonstrating the feasibility of improving lipid production based on an autophagy regulation strategy at the molecular and omics levels. Our study proves that regulation of cell autophagy through the MAatg8-PE conjugation system-related gene overexpression or exogenous supply of ethanolamine would be an efficient strategy to increase and maintain biomass productivity when high TAG content is obtained under nitrogen deficiency, which could be useful for the development of new strategies that will achieve more biomass and maximal lipid productivity.

Fatty acid desaturase (FADS) generates double bond at a certain position of the corresponding polyunsaturated fatty acids (PUFAs) with high selectivity, the enzyme activity and PUFAs products of which are essential to biological systems and are associated with a variety of physiological diseases. Little is known about the structure of FADSs and their amino acid residues related to catalytic activities. Identifying key residues of Micromonas pusilla delta 6 desaturase (MpFADS6) provides a point of departure for a better understanding of desaturation. In this study, conserved amino acids were anchored through gene consensus analysis, thereby generating corresponding variants by site-directed mutagenesis. To achieve stable and high-efficiency expression of MpFADS6 and its variants in Saccharomyces cerevisiae, the key points of induced expression were optimized. The contribution of conserved residues to the function of enzyme was determined by analyzing enzyme activity of the variants. Molecular modeling indicated that these residues are essential to catalytic activities, or substrate binding. Mutants MpFADS6 [Q409R] and MpFADS6 [M242P] abolished desaturation, while MpFADS6 [F419V] and MpFADS6 [A374Q] significantly reduced catalytic activities. Given that certain residues have been identified to have a significant impact on MpFADS6 activities, it is put forward that histidine-conserved region III of FADS6 is related to electronic transfer during desaturation, while histidine-conserved regions I and II are related to desaturation. These findings provide new insights and methods to determine the structure, mechanism and directed transformation of membrane-bound desaturases., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

This study aimed to explore the effects and differences of conjugated linoleic acid (CLA)-producing Bifidobacterium longum on the alleviation of dextran sulfate sodium (DSS)-induced colitis and to explore its patterns. Different B. longum strains were administered at 10 9 cfu/day 7 days before DSS treatment. B. longum CCFM681 significantly increased goblet cells, mucin2 (MUC2), claudin-3, α-catenin1, and ZO-1, but neither B. longum CCFM760 nor B. longum CCFM642 had those protective effects. Interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) were downregulated, while IL-10 was upregulated by B. longum CCFM681 but neither by B. longum CCFM760 nor by B. longum CCFM642. Moreover, B. longum CCFM681 treatment inhibited the toll-like receptor-4 (TLR4)/nuclear factor kappa-B (NF-κB) pathway. Furthermore, B. longum CCFM681 treatment rebalanced gut microbiota via regulating the diversity and key microorganisms. Colonic CLA concentrations in mice fed with B. longum CCFM681 were significantly higher than that of DSS-exposed mice, while those in B. longum CCFM760 and B. longum CCFM642 groups showed insignificant difference compared with the DSS group. Moreover, CLA showed a significantly positive correlation with the effectiveness of relieving colitis. B. longum CCFM681 alleviated colitis by protecting the intestinal mechanical barrier, modulating the gut microbiota, and inhibiting the TLR4/NF-κB pathway and associated pro-inflammatory cytokines. These results will help the clinical trials of probiotics and the development of functional products for colitis.

A sucrose nonfermenting protein kinase 1 (SNF1) complex is an important metabolic regulator in fungi that is critical to cell metabolism and stress response. In this study, the role of an SNF1 β-subunit in the oleaginous fungus Mortierella alpina ( MaSip2 ) was investigated. The MaSip2 contained a glycogen-binding domain and a conserved SNF1-complex interaction region; its transcriptional level during lipogenesis shared high consistency with a previously reported SNF1 γ-subunit ( MaSnf4 ). Overexpression of MaSip2 in M. alpina significantly promoted glucose uptake and resulted in 34.1% increased total biomass, leading to 44.8% increased arachidonic acid yield after 7 day fermentation. MaSip2 also regulated the balance between polyunsaturated fatty acids and carbohydrates in M. alpina. Intracellular metabolite analysis revealed increased carbohydrate-related metabolite accumulation in MaSip2 overexpression strains. On the contrary, knockdown of MaSip2 increased the total fatty acid unsaturation degree, especially under low-temperature conditions. This research improved our knowledge of SNF1 complex in M. alpina and provided a target gene for enhancing glucose utilization and modulating fatty acid composition for better application of oleaginous fungi.

Mortierella alpina has a strong capacity for lipid accumulation. Isocitrate dehydrogenase (IDH) plays an important role in affecting the flow of intracellular carbon sources and reducing power NADPH for lipid biosynthesis. In this study, the effect of various IDHs (NAD + - and NADP + -specific) in M. alpina on the lipid accumulation was investigated through homologous overexpression. The results showed that the transcription level and enzyme activity of the IDHs from M. alpina (MaIDHs) in homologous overexpressing strains were higher than those of the control strain, but that their biomass was not significantly different. Among the various NAD + -specific MaIDH1/2/3 overexpression, NAD + -MaIDH3 reduced total lipid content by 12.5%, whereas overexpression NAD + -MaIDH1 and NAD + -MaIDH2 had no effect on fatty acid content. Intracellular metabolites analysis indicated that the overexpression NAD + -MaIDH3 strain had reduced the fatty acid accumulation, due to its greater carbon flux with the tricarboxylic acid cycle and less carbon flux with fatty acid biosynthesis. For the NADP + -MaIDH4/5/6 recombinant strains overexpressing only NADP + -MaIDH4 enhanced the total fatty acid content by 8.2%. NADPH analysis suggested that this increase in lipid accumulation may have been due to the great reducing power NADPH is produced in this recombinant strain. This study provides theoretical basis and guidance for the analysis of the mechanism of IDH function and the potential to improve lipid production in M. alpina ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Tang, Sun, Wang, Zhang, Chen, Zhao, Chen and Chen.)

Serine protease inhibitors of Kazal-type (SPINKs) were widely identified in vertebrates and invertebrates, and played regulatory roles in digestion, coagulation, and fibrinolysis. In this study, we reported the important role of SPINK7 in regulating immune defense of silkworm, Bombyx mori . SPINK7 contains three Kazal domains and has 6 conserved cysteine residues in each domain. Quantitative real-time PCR analyses revealed that SPINK7 was exclusively expressed in hemocytes and was upregulated after infection with two fungi, Saccharomyces cerevisiae and Candida albicans . Enzyme activity inhibition test showed that SPINK7 significantly inhibited the activity of proteinase K from C. albicans . Additionally, SPINK7 inhibited the growth of three fungal spores, including S. cerevisiae , C. albicans , and Beauveria bassiana . The pathogen-associated molecular patterns (PAMP) binding assays suggested that SPINK7 could bind to β-D-glucan and agglutinate B. bassiana and C. albicans . In vitro assays were performed using SPINK7-coated agarose beads, and indicated that SPINK7 promoted encapsulation and melanization of agarose beads by B. mori hemocytes. Furthermore, co-localization studies using immunofluorescence revealed that SPINK7 induced hemocytes to aggregate and entrap the fungi spores of B. bassiana and C. albicans . Our study revealed that SPINK7 could recognize fungal PAMP and induce the aggregation, melanization, and encapsulation of hemocytes, and provided valuable clues for understanding the innate immunity and cellular immunity in insects., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Dong, An, Lu, Tang, Chen, Huang, Hou, Shen, Zhang, Zhang, Xia and Zhao.)

Mortierella alpina is an oleaginous filamentous fungus with considerable lipid productivity, and it has been widely used for industrial production of arachidonic acid. The fermentation process of M. alpina is complicated and can be affected by various factors; therefore, a comprehensive knowledge of its metabolic characteristics and key factors governing lipid biosynthesis is required to further improve its industrial performance. In this review, we discuss the metabolic features and extracellular factors that affect lipid biosynthesis in M. alpina. The current progress in fermentation optimisation and metabolic engineering to improve lipid yield are also summarised. Moreover, we review the applications of M. alpina in the food industry and propose fermentation strategies for better utilisation of this genus in the future. In our opinion, the economic performance of M. alpina should be enhanced from multiple levels, including strains with ideal traits, efficient fermentation strategies, controllable fermentation costs, and competitive products of both high value and productivity. By reviewing the peculiarities of M. alpina and current progress to improve its suitability for biotechnological production, we wish to provide more efficient strategies for future development of M. alpina as a high-value lipid cell factory. KEY POINTS: • Understanding M. alpina metabolism is helpful for rational design of its fermentation processes. • Nitrogen source is a key point that affects PUFA's component and fermentation cost in M. alpina. • Dynamic fermentation strategy combined with breeding is needed to increase lipid yield in M. alpina., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Phenylalanine hydroxylase (PAH) catalyses the irreversible hydroxylation of phenylalanine to tyrosine, which is the rate-limiting reaction in phenylalanine metabolism in animals. A variety of polyunsaturated fatty acids can be synthesized by the lipid-producing fungus Mortierella alpina , which has a wide range of industrial applications in the production of arachidonic acid. In this study, RNA interference (RNAi) with the gene PAH was used to explore the role of phenylalanine hydroxylation in lipid biosynthesis in M. alpina . Our results indicated that PAH knockdown decreased the PAH transcript level by approximately 55% and attenuated cellular fatty acid biosynthesis. Furthermore, the level of NADPH, which is a critical reducing agent and the limiting factor in lipogenesis, was decreased in response to PAH RNAi, in addition to the downregulated transcription of other genes involved in NADPH production. Our study indicates that PAH is part of an overall enzymatic and regulatory mechanism supplying NADPH required for lipogenesis in M. alpina .

A linoleate isomerase complex including myosin-cross-reactive antigen, short-chain dehydrogenase/oxidoreductase, and acetoacetate decarboxylase has been confirmed as the pivotal factor for conjugated linoleic acid (CLA) production in Lactobacillus plantarum . However, its role in the metabolism and health-associated benefits of Lactobacillus remain unclear. In the current study, the mild type, knockout, and complemented mutants of the linoleate isomerase complex of L. plantarum ZS2058 were used to investigate those putative effects. The metabonomic results showed that a linoleate isomerase complex could significantly influence the glycol-metabolism, lipid metabolism, and antioxidant compounds. Especially, with the stress of linoleic acid, linoleate isomerase complex knockout mutants induced the increase of several antioxidant compounds, such as glutamic acid, glycine, l-cysteine, glycerol, and l-sorbosone. Moreover, the linoleate isomerase complex played a pivotal role in ameliorating DSS-induced colitis. The knockout mutants showed effects similar to those in the DSS group, whereas complementation of the corresponding gene in the knockout mutants could restore the anti-inflammatory activity, wherein the integrity of a mucus layer was repaired, the level of pro-inflammatory cytokines decreased, and the amount of anti-inflammatory cytokines increased significantly. All the results indicated that the linoleate isomerase complex plays a key role in CLA production and metabolism as well as the health-associated benefits of L. plantarum ZS2058. These results are conducive to promote clinical trials and product development of probiotics for colitis.

Introduction The Chief Resident (CR) selection process is described by many residency programs as a collective effort from the residency program leadership, key faculty members, and resident peers. Unfortunately, the literature does not show any established guidelines, methods, or psychometric sound instruments to aid this process. The purpose of this study was to evaluate the properties of the newly developed CRs selection survey across two years using the Multi-Facet Rasch Model (MFRM). Methods This study used the MFRM to analyze two-year data from the newly developed CRs selection survey. After the first implementation of the tool in 2015, this instrument had its second-round evaluation process for the CRs selection in 2016. We applied a three-facet Rasch model (candidates, questions, and raters). We used Facets v. 3.66 and SAS 9.4 (SAS Institute Inc., Cary, NC) for data analysis. Results In 2015, 40 out of100 residents completed the survey to select three of the four candidates for the 2017-2018 CRs positions. The mean rating for each candidate showed that Candidate 1 received the highest rating of 5.56 while Candidates 2 and 4 received the exact same ratings. The majority of survey items performed very well based on the results from the MFRM while leaving room for improvement for a few items. In 2016, 55 out of 100 residents completed the revised survey to select three of the six candidates for the 2018-2019 CR positions. The mean rating showed that Candidate 3 received the highest mean rating of 5.81 while Candidate 2 received the lowest mean rating of 5.12. The item reliability was improved from 0.70 to 0.88 based on the results from the revised survey. The results were used to help inform decisions regarding the selection of chief residents. Conclusions The CR selection process requires a fair and collective effort from program leadership, relevant faculty members, and input from the resident group. Our study demonstrated that the survey tool we developed is appropriate to select CR candidates and MFRM is a promising technique in survey development and the evaluation of survey items., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2021, Lewis et al.)

Objectives: The transport of citrate from the mitochondria to the cytoplasm is essential during lipid accumulation. This study aimed to explore the role of mitochondrial citrate-oxoglutarate carrier in lipid accumulation in the oleaginous fungus Mortierella alpina., Results: Homologous MaYHM (the gene encoding the mitochondrial citrate-oxoglutarate carrier) was overexpressed in M. alpina. The fatty acid content of MaYHM-overexpressing recombinant strains was increased by up to 30% compared with the control. Moreover, the intracellular α-ketoglutarate level in recombinant strains was increased by 2.2 fold, together with a 23-35% decrease in NAD + -isocitrate dehydrogenase activity compared with the control. The overexpression of MaYHM altered the metabolic flux in the glutamate dehydrogenase shunt and 4-aminobutyric acid shunt during metabolic reprogramming, supplying more carbon to synthesize fatty acids., Conclusions: Overexpression of MaYHM resulted in more efflux of citrate from mitochondria to the cytoplasm and enhanced lipid accumulation. These findings provide new perspectives for the improvement of industrial lipid production in M. alpina.

Objectives: To establish reliable methods for the extraction and quantification of the total carbohydrate and intracellular saccharides from Mortierella alpina and study the changes between carbohydrate and lipid in fermentation process., Results: The extraction of mycelia with HCl following a photometric phenol-sulphuric acid reaction was identified as an optimal method for total carbohydrate analysis in Mortierella alpina, which the extraction efficiency performed 1.1-3.6 fold than other five methods. The total carbohydrate content increased from initial 19.26 to 25.86% during early fermentation process and declined gradually thereafter, while the fatty acid was increasing from 8.47 to 31.03%. For separation and qualitative estimation of intracellular saccharides, the acetonitrile/water freeze-thaw method for extraction and Sugar-Pak I column for separation proved to be possible. With the glucose rapidly decreasing at the beginning of growth, the trehalose accumulated rapidly from 1.63 to 5.04% and then decreased slightly but maintain above 4% of dry biomass., Conclusions: This work established comprehensive carbohydrate extraction and analysis methods of Mortierella alpina and identified the main saccharide in fermentation process which indicated that the accumulation of fatty acids was related to the change of intracellular carbohydrate content.

Microbial oils are potential resources of fuels and food oils in the future. In recent years, with the rapid development of systems biology technology, understanding the physiological metabolism and lipid accumulation characteristics of oleaginous microorganisms from a global perspective has become a research focus. As an important tool for systems biology research, omics technology has been widely used to reveal the mechanism of high-efficiency production of oils by oleaginous microorganisms. This provides a basis for rational genetic modification and fermentation process control of oleaginous microorganisms. In this article, we summarize the application of omics technology in oleaginous microorganisms, introduced the commonly used sample pre-processing and data analysis methods for omics analysis of oleaginous microorganisms, reviewe the researches for revealing the mechanism of efficient lipid production by oleaginous microorganisms based on omics technologies including genomics, transcriptomics, proteomics (modification) and metabolomics (lipidomics), as well as mathematical models based on omics data. The future development and application of omics technology for microbial oil production are also proposed.

Lipid hyperaccumulation in oleaginous microorganisms is generally induced by nitrogen limitation, while oxygen supply can influence biomass growth and cell metabolism. Although strategies based on nitrogen limitation or oxygen control have been extensively explored and applied in various oleaginous microorganisms, the role of oxygen supply in nitrogen limitation induced lipid hyperaccumulation still remains unclear. Here, we systematically surveyed the effects of oxygen supply on the oleaginous fungus M. alpina cultured in nitrogen limited conditions through integration of physiochemical parameters and metabolomics analysis. Our results indicated that a high oxygen supply promoted carbon/nitrogen consumption and was used for rapid biomass synthesis, while either high or low oxygen supply conditions were adverse to lipid and ARA accumulation. Different oxygen supply level significantly affected the balance between fermentation for lipid synthesis and respiration for energy generation. Under nitrogen limitation, a suitable oxygen supply promoted the recycling of preformed nitrogen and increased the redirection of carbon towards fatty acid synthesis through the hub centred around glutamic acid coupled to the intermediate metabolism of carbon in the TCA cycle, while a high oxygen supply favored the respiration process and enhanced the degradation of LC-PUFAs, rather than fermentation for fatty acid synthesis. This system-level insight reveals the underlying metabolic mechanism of oxygen control in nitrogen limitation induced lipid accumulation, and provides theoretical support for the integration of oxygen control with nutrient supply for efficient microbial oil production., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Δ6 fatty acid desaturases (FADS6) have different substrate specificities that impact the ratio of omega-6/omega-3 polyunsaturated fatty acids, which are involved in regulating multiple signalling pathways associated with various diseases. For decades, FADS6 with different substrate specificities have been characterized and the functions of these crucial enzymes have been investigated, while it remains enigmatic that the substrate specificities of FADS6 from various species have a huge difference. This review summarizes the substrate specificities of FADS6 in different species and reveals the underlying relationship. Further evaluation of biochemical properties has revealed that the FADS6 prefer linoleic acid that is more hydrophilic and stable. Domain-swapping and site-directed mutagenesis have been employed to delineate the regions and sites that affect the substrate specificities of FADS6. These analyses improve our understanding of the functions of FADS6 and offer information for the discovery of novel biological resources. KEY POINTS: • Outline of the excavation and identification of Δ6 fatty acid desaturases. • Overview of methods used to determine the pivotal resides of desaturases. • Application of substrate properties to generate specific fatty acids.

Objective: To assess the clinical value of individualized pharmaceutical services for patients receiving vancomycin for severe infections and establish clinical monitoring procedures during vancomycin treatment., Methods: Data were collected from patients with severe infections who received vancomycin treatment with individualized pharmacy services (test group, 144 cases) or without such services (control group, 884 cases) between January, 2017 and December, 2018. Using propensity score matching, the patients in the two groups with comparable baseline data were selected for inclusion in the study (62 in each group), and the efficacy, safety and economic indicators were compared between the two groups., Results: The curative effects of the treatment did not differ significantly between the two groups, with the overall response rates of 95.16% in the test group and 91.94% in the control group ( P > 0.05). The percentage of neutrophils before vancomycin treatment and calcitonin level after the treatment differed significantly between the two groups ( P < 0.05). No significant difference was found in the incidence of adverse events associated with the treatment between the test and control groups (8.06% vs 9.68%, P > 0.05); a significant difference in creatinine level was noted between the two groups after vancomycin treatment ( P < 0.05). The number of days of medication, the cost of vancomycin and its proportion in the total expenses differed significantly between the two groups ( P < 0.05). Cost-effectiveness analysis showed a better cost-effectiveness in the test group than in the control group (50052.78 vs 57601.23). The intensity of vancomycin use was also lower in the test group than in the control group (0.11 vs 0.36)., Conclusions: The participation of clinical pharmacists during the treatment can improve the clinical benefits of vancomycin in patients with severe infections.

Dissolved oxygen and pH are critical factors influencing cell growth and metabolism. In our previous work, we constructed the recombinant strain Mortierella alpina CCFM698, which has the ability to produce EPA at room temperature. However, our experiments showed that the dissolved oxygen produced by the aeration and agitation of the fermenter was insufficient for cell growth and EPA synthesis by this recombinant strain. Moreover, the optimum pH for cell growth was incompatible with that of EPA accumulation. This study introduced a combined strategy of two-stage pH control with oxygen-enriched air in fed-batch fermentation to facilitate both cell growth and EPA production in M. alpina CCFM698. After 10 days of fermentation in a 7.5 L tank, the biomass production reached 41.2 g/L, with a lipid content of 31.5%, and EPA accounting for 26.7% of total lipids. The final EPA production reached 3.47 g/L, which is the highest yet achieved by M. alpina. This study reveals the critical role of dissolved oxygen and pH control for EPA production of M. alpina, and provides an easy and efficient strategy for industrial production of EPA.

Background: Global resource reallocation is an established critical strategy through which organisms deal with environmental stress. The regulation of intracellular lipid storage or utilization is one of the most important strategies for maintaining energy homeostasis and optimizing growth. Oleaginous microorganisms respond to nitrogen deprivation by inducing lipid hyper accumulation; however, the associations between resource allocation and lipid accumulation are poorly understood., Results: Here, the time-resolved metabolomics, lipidomics, and proteomics data were generated in response to nutrient availability to examine how metabolic alternations induced by nitrogen deprivation drive the triacylglycerols (TAG) accumulation in M. alpina . The subsequent accumulation of TAG under nitrogen deprivation was a consequence of the reallocation of carbon, nitrogen sources, and lipids, rather than an up-regulation of TAG biosynthesis genes. On one hand, nitrogen deprivation induced the down-regulation of isocitrate dehydrogenase level in TCA cycle and redirected glycolytic flux of carbon from amino acid biosynthesis into fatty acids' synthesis; on the other hand, nitrogen deprivation induced the up-regulation of cell autophagy and ubiquitin-mediated protein proteolysis which resulted in a recycling of preformed protein nitrogen and carbon. Combining with the up-regulation of glutamate decarboxylase and succinic semialdehyde dehydrogenase in GABA shunt, and the phosphoenolpyruvate carboxykinase in the central hub involving pyruvate/phosphoenolpyruvate/oxaloacetate, the products from nitrogen-containing compounds degradation were recycled to be intermediates of TCA cycle and be shunted toward de novo biosynthesis of fatty acids. We found that nitrogen deprivation increased the protein level of phospholipase C/D that contributes to degradation of phosphatidylcholine and phosphatidylethanolamine, and supplied acyl chains for TAG biosynthesis pathway. In addition, ATP from substrate phosphorylation was presumed to be a critical factor regulation of the global resource allocation and fatty acids' synthesis rate., Conclusions: The present findings offer a panoramic view of resource allocation by M. alpina in response to nutrient stress and revealed a set of intriguing associations between resource reallocation and TAG accumulation. This system-level insight provides a rich resource with which to explore in-depth functional characterization and gain information about the strategic combination of strain development and process integration to achieve optimal lipid productivity under nutrient stress., Competing Interests: Competing interestsThe authors declare that they have no competing interests, (© The Author(s) 2020.)

Mucor circinelloides is a valuable oleaginous filamentous fungus rich in γ-linolenic acid (GLA, 18:3; n-6), which is beneficial for human health. Our previous comparative proteomic analysis between high lipid-producing M. circinelloides WJ11 and low lipid-producing M. circinelloides CBS 277.49 indicated that glucose 6-phosphate dehydrogenase (G6PDH) and β-isopropylmalate dehydrogenase (IPMDH) were closely involved in lipid accumulation. Transcription analysis suggested that in the strain WJ11, g 6 pdh 1 and g 6 pdh 2, which encode G6PDH, and leuB , which encodes IPMDH, could be the key genes regulating lipid accumulation. To further analyze the effects of these three genes (i.e., g 6 pdh 1, g 6 pdh 2, and leuB ) on lipid accumulation, we respectively overexpressed these genes from M. circinelloides WJ11 in defective CBS 277.49 strains in this study. The results showed that overexpression of g 6 pdh 1 and g 6 pdh 2 genes from strain WJ11 increased the fatty acid content of cell dry weight by 23-38 and 41-47%, respectively, compared with the control strain. Furthermore, overexpression of the leuB gene from strain WJ11 increased the fatty acid content of cell dry weight by up to 67-73%. These results suggest that g 6 pdh 1, g 6 pdh 2, and especially leuB genes play important roles in regulating fatty acid synthesis in M. circinelloides .

The ω-3 fatty acid desaturase (ω3Des) is a key enzyme in the biosynthesis of polyunsaturated fatty acids (PUFAs). However, the enzyme exhibits a significant preference towards different fatty acid substrates. To examine the molecular mechanism of its substrate specificity, a series of site-directed mutants were constructed based on the membrane topology model and functionally characterised by heterologous expression in Saccharomyces cerevisiae. Our results revealed that the W106F and V137T mutations markedly decreased the enzyme activity which indicated that these two residues were associated with substrate recognition. In contrast, the A44S, M156I and W291M mutations showed significant increments (30 to 40%) of the conversion rate for AA substrate desaturation, which suggests that these residues play a pivotal role in desaturation of longer chain-length substrates. Through homology modelling of 3-dimensional structures and molecular docking of FADS15, we propose that the critical residues that bind to the CoA groups may affect substrate localisation and govern substrate preference and chain-length specificity. Our work increases the understanding of the structure-function relationships of the microbial membrane-bound desaturases. The growing knowledge of the molecular mechanism will also aid in the efficient production of value-added fatty acids.

Thioesterases (TEs) play an essential role in the metabolism of fatty acids (FAs). To explore the role of TEs in mediating intracellular lipid metabolism in the oleaginous fungus Mortierella alpina, the acyl-CoA thioesterase ACOT8I was overexpressed. The contents of total fatty acids (TFAs) were the same in the recombinant strains as in the wild-type M. alpina, whilst the production of free fatty acids (FFAs) was enhanced from about 0.9% (wild-type) to 2.8% (recombinant), a roughly threefold increase. Linoleic acid content in FFA form constituted about 9% of the TFAs in the FFA fraction in the recombinant strains but only about 1.3% in the wild-type M. alpina. The gamma-linolenic acid and arachidonic acid contents in FFA form accounted for about 4 and 25%, respectively, of the TFAs in the FFA fraction in the recombinant strains, whilst neither of them in FFA form were detected in the wild-type M. alpina. Overexpression of the TE ACOT8I in the oleaginous fungus M. alpina reinforced the flux from acyl-CoAs to FFAs, improved the production of FFAs and tailored the FA profiles of the lipid species.

Functional genomics of filamentous fungi has gradually uncovered gene information for constructing 'cell factories' and controlling pathogens. Available gene manipulation methods of filamentous fungi include random integration methods, gene targeting technology, gene editing with artificial nucleases and RNA technology. This review describes random gene integration constructed by restriction enzyme-mediated integration (REMI); Agrobacterium-mediated transformation (AMT); transposon-arrayed gene knockout (TAGKO); gene targeting technology, mainly about homologous recombination; and modern gene editing strategies containing transcription activator-like effector nucleases (TALENs) and a clustered regularly interspaced short palindromic repeat/associated protein system (CRISPR/Cas) developed in filamentous fungi and RNA technology including RNA interference (RNAi) and ribozymes. This review describes historical and modern gene manipulation methods in filamentous fungi and presents the molecular tools available to researchers investigating filamentous fungi. The biggest difference of this review from the previous ones is the addition of successful application and details of the promising gene editing tool CRISPR/Cas9 system in filamentous fungi.

Objectives: To generate lycopene-overproducing strains of the fungus Mucor circinelloides with interest for industrial production and to gain insight into the catalytic mechanism of lycopene cyclase and regulatory process during lycopene overaccumulation., Results: Three lycopene-overproducing mutants were generated by classic mutagenesis techniques from a β-carotene-overproducing strain. They carried distinct mutations in the carRP gene encoding lycopene cyclase that produced loss of enzymatic activity to different extents. In one mutant (MU616), the lycopene cyclase was completely destroyed, and a 43.8% (1.1 mg/g dry mass) increase in lycopene production was observed in comparison to that by the previously existing lycopene overproducer. In addition, feedback regulation of the end product was suggested in lycopene-overproducing strains., Conclusions: A lycopene-overaccumulating strain of the fungus M. circinelloides was generated that could be an alternative for the industrial production of lycopene. Vital catalytic residues for lycopene cyclase activity and the potential mechanism of lycopene formation and accumulation were identified.

Objective: To improve the production of trans-10,cis-12-conjugated linoleic acid (t10,c12-CLA) from linoleic acid in recombinant Yarrowia lipolytica., Results: Cells of the yeast were permeabilized by freeze/thawing. The optimal conditions for t10,c12-CLA production by the permeabilized cells were at 28 °C, pH 7, 200 rpm with 1.5 g sodium acetate l -1 , 100 g wet cells l -1 , and 25 g LA l -1 . Under these conditions, the permeabilized cells produced 15.6 g t10,c12-CLA l -1 after 40 h, with a conversion yield of 62 %. The permeabilized cells could be used repeatedly for three cycles, with the t10,c12-CLA extracellular production remaining above 10 g l -1 ., Conclusion: Synthesis of t10,c12-CLA was achieved using a novel method, and the production reported in this work is the highest value reported to date.

GDP-l-fucose functions as a biological donor for fucosyltransferases, which are required for the catalysis of l-fucose to various acceptor molecules including oligosaccharides, glycoproteins and glycolipids. Mortierella alpina is one of the highest lipid-producing fungi and can biosynthesis GDP-l-fucose in the de novo pathway. Analysis of the M. alpina genome suggests that there is a gene encoding l-fucokinase (FUK) for the conversion of fucose to l-fucose-1-phosphate in the GDP-l-fucose salvage pathway, which has never been found in fungi before. This gene was characterized to explore its role in GDP-l-fucose synthesis. The yield of GDP-l-fucose is relatively higher in lipid accumulation phase (0.096 mg per g cell) than that in cell multiplication phase (0.074 mg per g cell) of M. alpina Additionally, the transcript level of FUK is up regulated by nitrogen exhaustion when M. alpina starts to accumulate lipid, highlights the functional significance of FUK in the GDP-l-fucose biosynthesis in M. alpina Gene encoding FUK was expressed heterologously in Escherichia coli and the resulting protein was purified to homogeneity. The product of FUK reaction was analyzed by liquid chromatography and mass spectrometry. Kinetic parameters and other properties of FUK were investigated. Comparative analyses between the FUK protein and other homologous proteins were performed. To our knowledge, this study is the first to report a comprehensive characterization of FUK in a fungus. Mortierella alpina could be used as an alternative source for the production of GDP-l-fucose., (© The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objective: We aimed at characterizing a malic enzyme isoform V from Mucor circinelloides., Methods: me1 gene encoding malic enzyme isoform V was amplified and cloned into expression vector pET28a. High-purity recombinant protein BLME1 was obtained by affinity chromatography using. Ni-NTA column and characterized subsequently., Results: The optimum conditions were pH at 8.0 and temperature at 33 degrees C. Under optimum conditions, BLME1 activity achieved 92.8 U/mg. The K(m) for L-malate and NADP+ were 0.74960 ± 0.06120 mmol/L and 0.22070 ± 0.01810 mmol/L, the V(max) for L-malate and NADP+ were 72.820 ± 1.077 U/mg and 86.110 ± 1.665 U/mg, respectively. In addition, ions played important roles in BLME1 activity; several ions such as Mn2+, Mg2+, Co2+, Ni2+ could activate BLME1, whereas Ca2+, Cu2+ could be used as inhibitors. Additionally, the metabolic intermediates such as oxaloacetic acid and α-ketoglutaric acid inhibited the activity of BLME1, whereas succinic acid activated it., Conclusion: A malic enzyme isoform V from Mucor circinelloides was characterized, providing the references for further studies on this enzyme.

The ω6 and ω3 pathways are two major pathways in the biosynthesis of PUFAs. In both of these, delta 6 desaturase (FADS6) is a key bifunctional enzyme desaturating linoleic acid or α-linolenic acid. Microbial species have different propensity for accumulating ω6- or ω3-series PUFAs, which may be determined by the substrate preference of FADS6 enzyme. In the present study, we analyzed the molecular mechanism of FADS6 substrate specificity. FADS6 cDNAs were cloned from Mortierella alpina (ATCC 32222) and Micromonas pusilla (CCMP1545) that synthesized high levels of arachidonic acid and EPA, respectively. M. alpina FADS6 (MaFADS6-I) showed substrate preference for LA; whereas, M. pusilla FADS6 (MpFADS6) preferred ALA. To understand the structural basis of substrate specificity, MaFADS6-I and MpFADS6 sequences were divided into five sections and a domain swapping approach was used to examine the role of each section in substrate preference. Our results showed that sequences between the histidine boxes I and II played a pivotal role in substrate preference. Based on our domain swapping results, nine amino acid (aa) residues were targeted for further analysis by site-directed mutagenesis. G194L, E222S, M227K, and V399I/I400E substitutions interfered with substrate recognition, which suggests that the corresponding aa residues play an important role in this process., (Copyright © 2015 by the American Society for Biochemistry and Molecular Biology, Inc.)

Context: The value of reflective practices has gained momentum in osteopathic medical education. However, the use of reflective pedagogies has not been explored in the larger context of medical course delivery and design, to the authors' knowledge., Objective: To determine the types of reflection demonstrated by osteopathic medical students on an online discussion board and to explore differences in discussion engagement caused by the use of a reflective learning self-assessment tool., Methods: Using a mixed-method approach, reflection processes in an osteopathic surgery clinical clerkship online module were investigated in third-year osteopathic medical students. Discussion board messages were captured and coded. Both manual coding techniques and automated interrogation using NVivo9 (a computer program) for qualitative data were applied. Correlations of scores across 4 case-based discussion tasks and scores for self-reflection were computed as quantitative data., Results: Twenty-eight students were included. Four main types of reflection (ie, content, contextual, dialogic, and personal) along with corresponding differentiated subthemes for each type of case-based discussion board group message were identified. Group collaboration revealed insights about the reflection process itself and also about the evidence of collective efforts, group engagements, and intragroup support among students. Student preparation revealed that students' metacognition was triggered when they judged their own contributions to group work. Challenges in completing readings and meeting deadlines were related to the students' long work hours., Conclusion: Reflective practices are essential to the practice of osteopathic medicine and medical education. Curricula can promote the development of reflective skills by integrating these deliberate practices in educational activities.

Objective: Curdlan is produced by Agrobacterium sp. ATCC 31749 under nitrogen limiting condition. The biosynthesis of crudlan is a typical aerobic bioprocess, and the production of curdlan would be severely restricted under micro-aerobic and anoxic conditions. Proteomic analysis of Agrobacterium sp. was conducted to investigate the effect of dissolved oxygen on the crucial enzymes involved in curdlan biosynthesis., Methods: Two-dimensional gel electrophoresis was performed to separate and visualize the differential expression of the intracellular proteins extracted from Agrobacterium sp. ATCC 31749 cultured under various dissolved oxygen levels (75%, 50%, 25% and 5%). In addition, a comparative proteomic analysis of the intracellular proteins expression level under various dissolved oxygen levels was done. Significant differently expressed proteins were identified by MALDI-TOF/TOF., Results: Finally, we identified 15 differently expressed proteins involved in polysaccharide synthesis, fatty acid synthesis, amino acid synthesis pathway. Among these proteins, phosphoglucomutase and orotidine 5-phosphate decarboxylase were the key metabolic enzymes directing curdlan biosynthesis., Conclusion: Oxygen could affect the expression of the proteins taking charge of curdlan synthesis significantly.

Objective: We used 50-amino acid-long peptides from the N-terminus of 4 different non-classically secreted proteins to study the secretion efficiency of Bacillus subtilis LipaseA via non-classical secretion pathway., Methods: We amplified the coding sequences (CDs) of LipaseA and N-terminus of non-classically secreted proteins, constructed 8 fusion protein expression vectors containing both LipaseA CD and different secretion signal peptide and transformed them into B. subtilis WB800. Secretion efficiency of these fusion proteins was analyzed by enzyme activity, SDS-PAGE and Western-Blot., Results: Recombinant LipaseA containing coding sequences of PdhA or N-terminus of SodA and Eno as secretion signals was efficiently secreted., Conclusion: Parts of non-classically secreted proteins or N-terminus (50 amino acids) could guide LipaseA protein secretion.

Moonlighting proteins, characterized by their multiple autonomous functions, have been detected in bacteria. Surprisingly, many of these proteins are conserved and involved in metabolic pathway or the cell stress response. They localise to the bacterial surface to take on additional activities, which have been hypothesised to contribute to bacterial virulence or bacterial benefit. In this review, we compare the functions of moonlighting proteins in bacteria, describe the structural basis of moonlighting functions, and summarise the regulation of secretion and localisation of moonlighting proteins.

NB-Cl gene is a potential class IIa bacteriocin gene. To obtain its soluble expression, NB-C1 was fused with the green fluorescent protein (GFP) gene and a recombinant expression vector plVEX 2.4d-GFP-NB-C1 was constructed, which was transformed into Escherichia coli BL21(DE3) pLysS. The expressed fusion protein GFP-NB-CI was purified by Ni-NTA affinity chromatography and the bioactivity was examined using Listeria monocytogenes as the indicator bacteria. The results showed that the expressed fusion protein GFP-NB-C1 was soluble and the final concentration of the purified fusion protein was 36.1 mg/L E. coli culture and had the purity above 95%. The antimicrobial assay of GFP-NB-C1 was analyzed and showed its high activity against Listeria monocytogenes.

Most selections of antihapten recombinant antibodies from antibody libraries were against hapten-carrier conjugates, which are different from free haptens in antigen specificity and often mislead the screening due to immunodominant epitopes in carriers. In the present study, aflatoxin B(1) (AFB(1)) was directly coated to enzyme-linked immunosorbent assay (ELISA) plates and anti-AFB(1) single chain fragment variables (scFvs) were selected with the AFB(1)-coated plates. Compared to the selection against AFB(1)-bovine serum albumin conjugate (31 positives out of 46 random clones), the isolated scFvs against AFB(1) (44 positives out of 46 random clones) showed higher specificities for AFB(1). The clone H4 with K(D) of 9.8 x 10(-11) M to AFB(1)-BSA and K(D) of 1.2 x 10(-12) to AFB1 was sequenced. In addition, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was applied to describe the biopanning for the first time. Our research presents a quick and robust selection technique for antihapten recombinant antibody from large naive libraries.

Objective: Studying the kinetics of conjugated linoleic acid (CLA) bioconversion by Lactobacillus plantarum ZS2058., Methods: We studied the effects of the substrate concentration, cell mass, reaction pH and temperature on the reaction rate of producing CLA by L. plantarum ZS2058, and established the equations of reaction rate at the initial response stage under different substrate concentrations by double-reciprocal plot and Hanes-Woolf plot method., Results: A marked substrate inhibition effect existed, and the early reaction rate of producing c9, t11-CLA reached the maximum of 15.99 microg/(mL x h) when linoleic acid concentration was 0.4 mg/mL. The early reaction rate increased with the cell mass increase, and when the cell mass was at 5 x 10(10) cfu/mL, the response reaction rate close to the maximum. The optimum pH and temperature of bioconversion of CLA were 6.5 and 40 degrees C. Michaelis constant was obtained by double-reciprocal plot and Hanes-Woolf plot method, the reaction rate equation followed the classic Michaelis-Mentent equation at the low substrate concentration, while there existed in a marked substrate inhibition effect at the high substrate concentration., Conclusion: Rough exploring the various factors of CLA bioconversion by L. plantarum ZS2058, we established the reaction rate equations of the initial response stage under different substrate concentrations, and got the optimal reaction conditions. These results will, contribute to the CLA production and its physiological functions research.

Human beta-defensin-2 (hBD2) is A small cationic peptide with A broad range of antimicrobial activity. An E. coli cell-free system was employed to express the hBD2 fusion protein by using the hBD2 gene with 14 rare codons. The results showed that the expression level of trxA-hBD2 fusion protein was 0.35 mg/ml, which is the same as that obtained with A synthetic codon-optimized gene. By using another fusion partner (GFP), similar high-level expression was also achieved in this cell-free system. This meant that human beta-defensin-2 gene could be directly used to express hBD2 fusion protein efficiently in an E. coli cell-free system without the optimization of codons. The expression level of hBD2 fused with thioredoxin could be further improved up to 2.0 mg/ml by adopting A continuous exchange cell-free system. A simple one-stage affinity purification procedure was also developed to recover this fusion protein efficiently.