Metabolic and regulatory network analysis of DHA-producing recombinant Yarrowia lipolytica

Heterologous expression of myxobacterial PKS-like PUFA cluster in recently created recombinant Yarrowia lipolytica Af4 strain allowed formation of DHA, polyunsaturated fatty acid with significant impact on human health. The focus of this work was to unravel the complex underlying metabolism of the oleaginous yeast using systems biology tools. Growth-decoupled production of DHA occurred during the stationary phase. The transition triggered drastic changes in global transcription and reduced availability of the two DHA precursors, acetyl and malonyl-CoA up to 98%. Upregulation of genes belonging to PUFA cluster coincided with the activated degradation of lipid bodies and fatty acids and the associated glyoxylate shunt, reactions involved in cellular stress-response, and interestingly, catabolic routes of branched-chain amino acids and L-lysine. This inspired the creation of time-resolved feeding strategies that supplemented the cultures with citrate, L-lysine, L-leucine and L-isoleucine, respectively to provide additional acetyl-CoA. Beneficially, the novel strategy increased DHA production up to 38%. Careful 13C tracer studies then unraveled that the supplemented carbon was significantly incorporated into intracellular CoA-esters, amino acids, and DHA itself. Fed by small amounts of L-lysine, the recombinant producer Y. lipolytica Af4 accumulated DHA up to the gram scale in the fed-batch process, and surpassed previous efforts three-fold.Die heterologe Expression eines myxobakteriellen PUFA-Clusters in dem kürzlich geschaffenen rekombinanten Yarrowia lipolytica Af4 ermöglichte die Synthese von DHA, einer mehrfach ungesättigten Fettsäure mit erheblichen Auswirkungen auf die Gesundheit. Der Schwerpunkt dieser Arbeit lag auf der Aufklärung des komplexen zugrunde liegenden Stoffwechsels der öligen Hefe mit systembiologischen Methoden. Die Produktion von DHA erfolgte wachstumsentkoppelt in der stationären Phase. Der Übergang löste drastische Veränderungen in der globalen Transkription aus und verringerte die Verfügbarkeit der beiden DHA-Vorstufen Acetyl- und Malonyl-CoA um bis zu 98%. Die Hochregulierung des PUFA-Clusters, fiel mit dem aktivierten Abbau von Lipiden und dem damit verbundenen Glyoxylat-Shunt, mit verstärkter Stressreaktion, und interessanterweise auch mit katabolen Wegen von verzweigtkettigen Aminosäuren und L-Lysin zusammen. Dies inspirierte zur Entwicklung von zeitaufgelösten Fütterungsstrategien, bei denen Citrat, L Lysin, L Leucin bzw. L Isoleucin zugeführt wurden, um zusätzliches Acetyl-CoA bereitzustellen. Mit dieser neuen Strategie konnte die DHA-Produktion um bis zu 38% gesteigert werden. 13C-Tracer-Studien ergaben, dass der zugeführte Kohlenstoff in großem Umfang in CoA-Ester, Aminosäuren und DHA eingebaut wurde. Im Fed-Batch-Verfahren produzierte Y. lipolytica Af4, der mit geringen Mengen L Lysin gefüttert wurde, DHA bis in den Grammbereich und übertraf frühere Ansätze um das Dreifache

The "problem" of character in contemporary circus in Quebec

In this thesis, I explore the nature of character in Québec (Canada) contemporary circus focusing on two case studies: Patinoire (Patrick Léonard, 7 doigts de la main) and The Whore of Babylon (Andréane Leclerc, Nadère arts vivants). Given that circus studies is a relatively new and interdisciplinary research field, I rely on the theory from other art forms. Circus theory provides circus performance analysis models that I use to study circus shows and companies from Québec (Hurley, 2016, Batson, 2016). Theatre provides a rich theoretical framework for understanding and representing character ranging from Aristotle to Lehmann. Louis Patrick Leroux’s “Conceptual Model for Circus Dramaturgy” is useful for studying how the performer’s persona and body influence circus character (Leroux, 2016). My research also draws on interviews with Patrick Léonard and Québec contortionist Andréane Leclerc on the intentionality and execution of their shows, and the relationship between their performance experience and spectators’ reception. After analyzing the performances, their dramaturgy, aesthetics, and artistic intentionality, and informed by the interviews, I argue that the contemporary circus character becomes manifest through its striving to unite the represented character, the performer’s body and the performer’s persona. Though only two shows were analyzed, these two were distinctive case studies of current trends in contemporary circus in Québec beyond the well-known Cirque du Soleil’s own aesthetics and narrative

Microbial production of polyunsaturated fatty acids : high-value ingredients for aquafeed, superfoods, and pharmaceuticals

Polyunsaturated fatty acids (PUFAs), primarily docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have received worldwide attention in recent years due to an increasing awareness of their uniqueness in improving diet and human health and their apparently inevitable shortage in global availability. Microbial cell factories are a major solution to supplying these precious molecules in sufficient amounts and providing PUFA-rich aquafeed, superfoods, and medical formulations. This review assesses the PUFA world markets and highlights recent advances in upgrading and streamlining microalgae, yeasts, fungi, and bacteria for high-level PUFA production and broadening of the PUFA spectrum

Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability

Background Long-chain polyunsaturated fatty acids (LC-PUFAs), such as docosahexaenoic acid (DHA), are essential for human health and have been widely used in the food and pharmaceutical industries. However, the limited availa‑ bility of natural sources, such as oily fsh, has led to the pursuit of microbial production as a promising alternative. Yarrowia lipolytica can produce various PUFAs via genetic modifcation. A recent study upgraded Y. lipolytica for DHA pro‑ duction by expressing a four-gene cluster encoding a myxobacterial PKS-like PUFA synthase, reducing the demand for redox power. However, the genetic architecture of gene expression in Y. lipolytica is complex and involves various control elements, ofering space for additional improvement of DHA production. This study was designed to optimize the expression of the PUFA cluster using a modular cloning approach. Results Expression of the monocistronic cluster with each gene under the control of the constitutive TEF promoter led to low-level DHA production. By using the minLEU2 promoter instead and incorporating additional upstream activating UAS1B4 sequences, 5’ promoter introns, and intergenic spacers, DHA production was increased by 16-fold. The producers remained stable over 185 h of cultivation. Benefcially, the diferent genetic control elements acted synergistically: UAS1B elements generally increased expression, while the intron caused gene-specifc efects. Mutants with UAS1B16 sequences within 2–8 kb distance, however, were found to be genetically unstable, which limited pro‑ duction performance over time, suggesting the avoidance of long repetitive sequence blocks in synthetic multigene clusters and careful monitoring of genetic stability in producing strains. Conclusions Overall, the results demonstrate the efectiveness of synthetic heterologous gene clusters to drive DHA production in Y. lipolytica. The combinatorial exploration of diferent genetic control elements allowed the optimiza‑ tion of DHA production. These fndings have important implications for developing Y. lipolytica strains for the indus‑ trial-scale production of valuable polyunsaturated fatty acids

Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale

DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids L-lysine, L-leucine, and L-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, L-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors

A common approach for absolute quantification of short chain CoA thioesters in prokaryotic and eukaryotic microbes

Background Thioesters of coenzyme A participate in 5% of all enzymatic reactions. In microbial cell factories, they function as building blocks for products of recognized commercial value, including natural products such as polyketides, polyunsaturated fatty acids, biofuels, and biopolymers. A core spectrum of approximately 5–10 short chain thioesters is present in many microbes, as inferred from their genomic repertoire. The relevance of these metabolites explains the high interest to trace and quantify them in microbial cells. Results Here, we describe a common workflow for extraction and absolute quantification of short chain CoA thioesters in different gram-positive and gram-negative bacteria and eukaryotic yeast, i.e. Corynebacterium glutamicum, Streptomyces albus, Pseudomonas putida, and Yarrowia lipolytica. The approach assessed intracellular CoA thioesters down to the picomolar level and exhibited high precision and reproducibility for all microbes, as shown by principal component analysis. Furthermore, it provided interesting insights into microbial CoA metabolism. A succinyl-CoA synthase defective mutant of C. glutamicum exhibited an unaffected level of succinyl-CoA that indicated a complete compensation by the L-lysine pathway to bypass the disrupted TCA cycle. Methylmalonyl-CoA, an important building block of high-value polyketides, was identified as dominant CoA thioester in the actinomycete S. albus. The microbe revealed a more than 10,000-fold difference in the abundance of intracellular CoA thioesters. A recombinant strain of S. albus, which produced different derivatives of the antituberculosis polyketide pamamycin, revealed a significant depletion of CoA thioesters of the ethylmalonyl CoA pathway, influencing product level and spectrum. Conclusions The high relevance of short chain CoA thioesters to synthetize industrial products and the interesting insights gained from the examples shown in this work, suggest analyzing these metabolites in microbial cell factories more routinely than done so far. Due to its broad application range, the developed approach appears useful to be applied this purpose. Hereby, the possibility to use one single protocol promises to facilitate automatized efforts, which rely on standardized workflows

Tumor necrosis factor-alpha as differential diagnostic marker for patients with fever of unknown origin

© 2019, University of Kragujevac, Faculty of Science. All rights reserved. Febrile conditions of unidentified origin are still unknown in modern medicine despite the development of diagnostic procedures. There are various agents of long-term temperature encompassing numerous infectious or non-infectious diseases. The aim of this study was to determine if there was a statistically significant difference in the values of proinfl ammatory cytokines (IL-1, TNFa, IL-6) in patients who meet the criteria for febrile conditions of unidentified origin, between the group of infectious, malignant, rheumatic, “other” diseases and undiagnosed patients. The study was conducted in the Immunology laboratory of the Center for Molecular Medicine and Stem Cells Research of the Faculty of Medical Sciences in Kragujevac. Blood samples were taken from patients tested at the Clinic for Infectious Diseases, of the Clinical Center of Kragujevac, in the period from 2014 to 2016. The study included 70 patients. The measured values of the level of TNFa showed significantly higher values in a group of malignant diseases than in the group of infectious diseases, while the values of IL-1 and IL-6 did not show statistical significance. TNFa can improve diagnosing in case of patients with an unknown febrile condition, which can shorten the length of the hospital stay and reduce the volume of performance of diagnostic procedures

Upregulation of cardioprotective SUR2A by sub-hypoxic drop in oxygen

AbstractThe effects of hypoxia on gene expression have been vigorously studied, but possible effects of small changes in oxygen tension have never been addressed. SUR2A is an atypical ABC protein serving as a regulatory subunit of sarcolemmal ATP-sensitive K+ (KATP) channels. Up-regulation of SUR2A is associated with cardioprotection and improved physical endurance. Here, we have found that a 24h-long exposure to slightly decreased ambient fractional concentration of oxygen (20% oxygen), which is an equivalent to oxygen tension at 350m above sea level, significantly increased levels of SUR2A in the heart despite that this drop of oxygen did not affect levels of O2, CO2 and hematocrit in the blood or myocardial levels of ATP, lactate and NAD/NADH/NAD+. Hearts from mice exposed to 20% oxygen were significantly more resistant to ischaemia-reperfusion when compared to control ones. Decrease in fractional oxygen concentration of just 0.9% was associated with phosphorylation of ERK1/2, but not Akt, which was essential for up-regulation of SUR2A. These findings indicate that a small drop in oxygen tension up-regulates SUR2A in the heart by activating ERK signaling pathway. This is the first report to suggest that a minimal change in oxygen tension could have a profound signaling effect

WP4 ‐ Modernization of teaching contents 4.1. Need analysis for knowledge refreshment

This brochure is a result of the TEMPUS project “Building Capacity of Serbian Agricultural Education to Link with Society” (CaSA) 544072-TEMPUS-1-2013-1-RS-TEMPUS-SMHES (2013-4604/001-001). Daniela Šćepanović and Steve Quarrie were responsible for questionnaire construction, assisted by Slavica Čolić. Analysis of questionnaires was coordinated by Daniela Šćepanović, as well as final preparation and presentation of the results. For final document preparation, all CaSA Steering Committee members gave valuable contribution. For brochure final preparation Daniela Šćepanović, Vesna Poleksić and Goran Topisirović were in charge.TEMPUS Project: Building Capacity of Serbian Agricultural Education to Link with Society (CaSA) 544072-TEMPUS-1-2013-1-RS-TEMPUS-SMHES (2013 – 4604 / 001 - 001) Coordinator: University of Belgrade, Faculty of Agricultur