Article
Biochemistry & Molecular Biology
Andras Micsonai, Eva Moussong, Frank Wien, Eszter Boros, Henrietta Vadaszi, Nikoletta Murvai, Young-Ho Lee, Tamas Molnar, Matthieu Refregiers, Yuji Goto, Agnes Tantos, Jozsef Kardos
Summary: The BeStSel method is a powerful tool for analyzing protein secondary structure composition, providing accurate information and predicting protein folding down to the topology/homology level. It also helps distinguish intrinsically disordered proteins and assists in experimental verification and in silico modeling using CD spectroscopy.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Jan Blasius, Katrin Drysch, Frank Hendrik Pilz, Tom Froembgen, Patrycja Kielb, Barbara Kirchner
Summary: In this study, a novel cluster approach is presented for the fast and robust calculation of mole fraction dependent infrared and vibrational circular dichroism spectra using the example of acetonitrile/(R)-butan-2-ol mixtures. By assigning weights to a limited number of quantum chemically calculated clusters, vibrational spectra at any desired composition can be obtained through a weighted average. The study demonstrates accurate modeling of mole fraction dependent peak shifts and high accuracy in reproducing experimentally recorded infrared spectra over the entire mixing range. This approach provides a valuable and computationally efficient tool for accessing mole fraction dependent spectra of mixtures.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Microbiology
Lu Liu, Zhipeng Wang, Zhihong Zheng, Ze Li, Xiaofeng Ji, Haihua Cong, Haiying Wang
Summary: In this study, a novel alginate lyase, Alyw203, was cloned from Vibrio sp. W2 and expressed in food-grade Yarrowia lipolytica. Alyw203 showed unique heat recovery performance, high alkaline activity, independence from NaCl and resistance to metal ions, with hydrolyzates mainly concentrated in oligosaccharides of DP1-DP2, making it a potential candidate for industrial production of monosaccharides and disaccharides.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Physical
Tobias Guckeisen, Saman Hosseinpour, Wolfgang Peukert
Summary: The change in protein secondary structure affects functionality and performance, with proteins responding differently to chemical denaturation in different environments. The liquid/air interface can either enhance or decrease protein conformation stability, while the presence of urea induces denaturation in bulk solution but may be prevented at the liquid/air interface.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Physical
Qin Yang, Josef Kapitan, Petr Bour, Julien Bloino
Summary: Combining Raman scattering and Raman optical activity (ROA) with computer simulations allows for the characterization of chiral molecules' fine structure and physicochemical properties. This study presents an accurate and simple approach based on three-quanta anharmonic perturbative mode, showing the significance of anharmonic Raman and ROA spectroscopies in understanding chiral molecules' vibrations and calibrating computational models.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Optics
Kun Zhang, Yan Liu, Shixia Li, Feng Xia, Weijin Kong
Summary: This work introduces an actively tunable bi-functional metamirror based on a bi-layer graphene structure, which can achieve spin-selective absorption and polarization conversion under different polarization conditions, with stable performance.
Article
Multidisciplinary Sciences
Dipankar Baisya, Adithya Ramesh, Cory Schwartz, Stefano Lonardi, Ian Wheeldon
Summary: In this paper, the authors propose a neural network-based architecture called DeepGuide, which learns from genome-wide CRISPR activity profiles to accurately design high activity sgRNAs. The experimental validation confirms the effectiveness of DeepGuide in predicting high activity sgRNAs in the oleaginous yeast Yarrowia lipolytica.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Han Liang, Liangliang Li, Houguo Fei, Yongkang Zhang, Pan Qi, Liwen Su, Yu Zhang, Cunlan Guo
Summary: Researchers have designed three improved light-oxygen-voltage (iLOV) domains, and successfully regulated the charge transport properties of iLOV self-assembled monolayers (SAMs) through pH-induced conformation changes. The current density can be controlled within an order of magnitude. This study proposes a new approach to investigate charge transport in complex molecular systems and enhances our understanding of the relationship between protein structure and charge transport.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Erdem Carsanba, Bilal Agirman, Seraphim Papanikolaou, Patrick Fickers, Huseyin Erten
Summary: The increase in bread wastage leads to ecological problems like methane and CO2 production. To reduce this, a sustainable system of waste bread management should be established. Waste bread has a high potential to be used as feedstock for the production of value-added bio products.
FERMENTATION-BASEL
(2023)
Article
Chemistry, Analytical
Jehan Waeytens, Joelle De Meutter, Erik Goormaghtigh, Alexandre Dazzi, Vincent Raussens
Summary: Nanoscale infrared spectroscopy (AFMIR) has become an important tool for analyzing biological samples, particularly protein assemblies, at the nanoscale level. A method for studying the secondary structure of proteins is introduced based on a protein library of 38 well-characterized proteins. Ascending stepwise linear regression (ASLR) and partial least square (PLS) regression were used to correlate characteristic bands in the spectra with major secondary structures (alpha helices and beta sheets). ASLR appears to provide better results than PLS. The secondary structure predictions have a root mean square standard error of 6.39% for alpha helices and 6.23% for beta sheets in cross validation.
ANALYTICAL CHEMISTRY
(2023)
Article
Acoustics
Jin Wang, Jun Wang, Sai Kranthi Vanga, Vijaya Raghavan
Summary: High-intensity ultrasound treatment can significantly reduce the allergen content of Act d 2 in kiwifruit samples, improve protein in-vitro digestibility, and alter their secondary structure, but may adversely affect the solubility of proteins in the samples.
ULTRASONICS SONOCHEMISTRY
(2021)
Article
Polymer Science
Yang Zhao, Jingfa Yang, Minghua Liu, Jiang Zhao
Summary: Switchable inversion of chirality between opposite handedness by varying pH is found in a histidine pendant polymer, PBHis. This phenomenon is demonstrated by circular dichroism and fluorescence correlation spectroscopy, which measure the changes of hydrodynamic radius at the single molecular level. Below pH 8.0, the polyelectrolyte adopts M-helicity, while above pH 8.0, it changes into P-helicity. Above pH 10.6, the helicity further inverses into M-chirality. The protonation and deprotonation of the imidazole group, as well as the hydroxide-ion-mediated hydrogen bonding, determine the mutual orientation and handedness of the helical structure.
Article
Physics, Multidisciplinary
JuHyeon Lee, Johannes Bischoff, A. O. Hernandez-Castillo, Boris Sartakov, Gerard Meijer, Sandra Eibenberger-Arias
Summary: In this study, we quantitatively investigated enantiomer-specific state transfer using a pulsed supersonic molecular beam. By using optical pumping and microwave pulses, we were able to improve enantiomer enrichment and create a molecular beam with an enantiomer-pure rotational level, which holds great potential for future spectroscopic and scattering studies.
PHYSICAL REVIEW LETTERS
(2022)
Article
Energy & Fuels
Mattia Colacicco, Cosetta Ciliberti, Gennaro Agrimi, Antonino Biundo, Isabella Pisano
Summary: The yeast Yarrowia lipolytica has been used to convert waste cooking oil into high-value bio-based products. This study focused on the simultaneous production of intracellular lipids and extracellular lipases by optimizing the culture conditions. The results showed a direct correlation between the availability of free fatty acids in the media and the levels of lipase activity and single-cell oil accumulation.
Article
Chemistry, Physical
Aidan P. Holman, Kimberly Quinn, Rakesh Kumar, Sebastian Kmiecik, Abid Ali, Dmitry Kurouski
Summary: Long-chain unsaturated and polyunsaturated fatty acids are important components of cell membranes and are involved in cell signaling and metabolism. They are widely used as food supplements but their role in the self-assembly of misfolded proteins is still unclear.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Microbiology
Macarena Larroude, Djamila Onesime, Olivier Rue, Jean-Marc Nicaud, Tristan Rossignol
Summary: In this study, the yeast Yarrowia lipolytica was engineered to overproduce pyomelanin by optimizing a chassis strain to increase homogentisic acid synthesis. The overexpression of the 4HPPD gene led to significantly higher pyomelanin yields, with the pathway being strongly induced by phenylalanine supplementation.
Article
Biochemistry & Molecular Biology
Piotr Hapeta, Patrycja Szczepanska, Tadeusz Witkowski, Jean-Marc Nicaud, Anne-Marie Crutz-Le Coq, Zbigniew Lazar
Summary: The translation explores the use of molasses as a substrate for bioprocesses, focusing on the role of hexose transporters and hexokinase in glucose preference in Yarrowia lipolytica. Overexpression of hexokinase with hexose transporters accelerated citric acid biosynthesis and enhanced pentose phosphate pathway, leading to increased production of polyols. Additionally, overexpression of fructophilic hexokinase resulted in a shorter processing time and higher polyol yield compared to the glycerol medium.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Food Science & Technology
Sara Mitri, Mohamed Koubaa, Richard G. Maroun, Tristan Rossignol, Jean-Marc Nicaud, Nicolas Louka
Summary: Due to the pleasant rosy scent, there is a huge market demand for the aromatic alcohol 2-phenylethanol (2-PE). The most promising method for its production is through microbial fermentation, particularly using yeasts, which have the ability to produce 2-PE using l-Phe as precursor. Some agro-industrial waste and by-products with high nutritional value can be utilized as suitable media for microbial growth, including the production of 2-PE through yeast fermentation.
Article
Biochemistry & Molecular Biology
Sonia Abreu, Young-Kyoung Park, Camilla Pires de Souza, Lea Vidal, Pierre Chaminade, Jean-Marc Nicaud
Summary: Yarrowia lipolytica is a promising yeast for producing unusual lipids. Recent studies have shown that optimizing substrate combination and metabolic pathways can improve lipid production. In this study, the lipid composition of obese LP and obese L strains was compared, revealing differences in the fatty acid composition and molecular species distributions of various lipids.
Article
Biotechnology & Applied Microbiology
Lea Vidal, Esteban Lebrun, Young-Kyoung Park, Guillaume Mottet, Jean-Marc Nicaud
Summary: In this study, novel bidirectional and hybrid bidirectional promoters were developed, whose expression can be fine-tuned to meet the demand for versatile promoters in the yeast Y. lipolytica. This study provides effective tools for smoothly adjusting the erythritol-inducible co-expression of two target genes in biotechnology applications. BDPs developed in this study have potential applications in the fields of heterologous protein production, metabolic engineering, and synthetic biology.
MICROBIAL CELL FACTORIES
(2023)
Article
Microbiology
Jaroslav Hambalko, Peter Gajdos, Jean-Marc Nicaud, Rodrigo Ledesma-Amaro, Michal Tupec, Iva Pichova, Milan Certik
Summary: Research has found that sex pheromone mixtures of certain insect species can produce unique C16 long conjugated fatty acids with two or three conjugated double bonds. The supplementation of fatty acid methyl esters into the medium resulted in the identification of 20 new fatty acids with two or three double bonds. The study proves that Y. lipolytica is capable of synthesizing C16-conjugated fatty acids, and further optimization could lead to increased production of novel fatty acid derivatives with biotechnologically interesting properties.
Article
Biotechnology & Applied Microbiology
Maria Gorczyca, Jean-Marc Nicaud, Ewelina Celinska
Summary: Resistance to environmental stress and synthesis of recombinant proteins (r-Prots) are complex biological traits that rely on multiple genes. Modifying the operation of transcription factors (TFs) associated with these traits can be a strategy to engineer them. This study examined the implications of five selected TFs in stress resistance and r-Prot synthesis in Yarrowia lipolytica. Over-expression or deletion of the TFs in a host strain resulted in significant changes in growth and r-Prot yields under specific conditions. Mathematical modeling assisted in understanding the contribution of individual TFs and identifying new functions of the studied TFs.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Veronika Urbanikova, Young-Kyoung Park, Daniela Krajciova, Mehdi Tachekort, Milan Certik, Ioana Grigoras, Roman Holic, Jean-Marc Nicaud, Peter Gajdos
Summary: In this study, the oleaginous yeast Yarrowia lipolytica was used as a host for the production of Punicic acid (PuA). By supplementing the medium with pomegranate seed oil, lipids containing PuA esters were accumulated up to 31.2% in Y. lipolytica. Strategies involving the expression of the bifunctional fatty acid conjugase/desaturase gene from Punica granatum (PgFADX) allowed for de novo production of PuA in Y. lipolytica. The optimized promoter for PgFADX expression resulted in a PuA production of 36.6 mg/L. These findings highlight the potential of Y. lipolytica as a promising host for PuA production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Georgio Nemer, Nicolas Louka, Paul Rabiller Blandin, Richard G. Maroun, Eugene Vorobiev, Tristan Rossignol, Jean-Marc Nicaud, Erwann Guenin, Mohamed Koubaa
Summary: This study focuses on the biosynthesis of a mixture of violacein and deoxyviolacein using a genetically modified Y. lipolytica strain as a production chassis. The intracellular pigments were extracted and purified using column chromatography. The optimal separation between the pigments was achieved using an ethyl acetate/cyclohexane mixture with different ratios, followed by analysis using thin-layer chromatography and nuclear magnetic resonance.
Article
Biotechnology & Applied Microbiology
Lea Vidal, Zehui Dong, Kim Olofsson, Eva Nordberg Karlsson, Jean-Marc Nicaud
Summary: Yarrowia lipolytica is a suitable yeast for producing foreign proteins. A set of 18 chromogenic cloning vectors were developed, each containing an excisable auxotrophic selective marker and a different promoter. An improved recipient strain was developed by eliminating filamentation and introducing an auxotrophy for lysine. The optimal targeting sequence for Rhizopus oryzae ROL lipase secretion was determined and higher lipase activity was achieved with certain promoters.
FEMS YEAST RESEARCH
(2023)
Article
Biochemical Research Methods
Esteban Lebrun, Vasily Shenshin, Cecile Plaire, Vincent Vigneres, Theo Pizette, Bruno Dumas, Jean-Marc Nicaud, Guillaume Mottet
Summary: The search for new antibodies is time-consuming and expensive due to repeated library screenings. A new antibody screening platform based on the encapsulation of antibody-secreting yeast cells into picoreactor droplets is proposed in this study. This platform enables high-throughput screening of millions of antibodies per day and is useful in various contexts.
Article
Biotechnology & Applied Microbiology
Wendy Al Sahyouni, Sally El Kantar, Anissa Khelfa, Young-Kyoung Park, Jean-Marc Nicaud, Nicolas Louka, Mohamed Koubaa
Summary: This study investigated the production of odd-chain fatty acid-enriched lipids through fermentation using a genetically engineered strain. The optimal conditions for maximizing cell density and fatty acid content were determined, and the results show potential for industrial production.
FERMENTATION-BASEL
(2022)
Review
Biotechnology & Applied Microbiology
Young-Kyoung Park, Cristina Gonzalez-Fernandez, Raul Robles-Iglesias, Lea Vidal, Pierre Fontanille, Christian Kennes, Elia Tomas Pejo, Jean-Marc Nicaud, Patrick Fickers
Summary: This review discusses the processes of creating valuable molecules from organic wastes-derived VFAs, the pathways used by oleaginous yeast Yarrowia lipolytica to metabolize such molecules, and the relationship between organic waste composition, anaerobic digestion, and VFA profiles. It also summarizes the current knowledge about VFA toxicity, the metabolic pathways of VFAs, and the metabolic engineering strategies in Y. lipolytica for producing value-added biobased compounds from VFAs.
FEMS YEAST RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Young-Kyoung Park, Florence Bordes, Fabien Letisse, Jean-Marc Nicaud
Summary: Microbial production of odd-chain fatty acids (OCFAs) has gained significant interest for its diverse applications, and this study successfully increased OCFA accumulation through strain engineering and optimizing the precursors balance. The highest recombinant OCFAs titer reported in yeast was achieved, showing the potential of microbial production in various applications.
METABOLIC ENGINEERING COMMUNICATIONS
(2021)
Review
Biotechnology & Applied Microbiology
Georgio Nemer, Nicolas Louka, Eugene Vorobiev, Dominique Salameh, Jean-Marc Nicaud, Richard G. Maroun, Mohamed Koubaa
Summary: The production of pigments using single cell microorganisms is emerging as a sustainable alternative to conventional synthesis methods heavily reliant on petrochemicals. Research is focused on producing pigments coveted for their unique qualities beyond just dyeing abilities. Efforts are also directed towards developing effective cell disruption methods to ensure successful recovery of biosynthetic pigments.
FERMENTATION-BASEL
(2021)