Laboratory of Ecological and Evolutionary Biochemistry

Дерябина_small1 Yulia I. Deryabina
Ph.D.
Head of Laboratory
INBI, build. 1, room 353-355
Телефон +7 (495) 952-25-47
E-Mail deryabina@inbi.ras.ru; yul_der@mail.ru

Keywords

Stress, extremophiles, photoreception, photobiochemistry, abiogenesis, oxylipins, cell differentiation, evolution


Research areas

The study of relationship between ROS accumulation, antioxidant system function, and pathological cell process in the yeasts of various taxonomic groups.

  • Photoreception, redox-signaling and oxidation stress protection in fungal cell;
  • Abiogenesis and design of supramolecular modificator of light energy;
  • Research of photochemistry of coenzyme molecules in abiogenesis models;
  • Photo-biochemistry of coenzymes in the context of evolution;
  • The design of photo-biocatalyzers and energy-transforming systems based on photosynthetic pigment-protein complexes, enzymes and nanostructured inorganic semiconducters;
  • Investigation into bactericide and fungal activities of multi-functional bioactive surfaces with fixed nanocompounds;
  • Research of the nitrogen metabolism role in the mechanism of ascomycetes photo-reception;
  • Participation of various oxygenated derivatives unsaturated fatty acids in the process of fungi differentiation. Investigation into the mechanism of signal transmission of oxylipins in the fungi and their localization in Neurospora crassa;
  • Study of mechanism of microscopic fungi resistance (for the fungi isolated from the exclusion zone around Chernobyl nuclear power station) to increased radioactivity based on comparative genomic analysis of the metabolic systems of the Chernobyl fungi and the fungi from background ecotope.


The main methods

The complex of the methods, aimed at defining photochemical features of coenzymes is constantly used the complex is based on the methods and approach designed in the laboratory. Using morpho-phisiological and genetic features of the extremophiles the complicated method for study of mechanisms of adaptation of the unique microorganisms to unfavorable factors of the environment.

Methods of basic research:

  • Maintenance of the unique collections of selected and registered strains of yeast-extremophiles as well as fungi lines both mutant and extremophile strains, isolated from natural sources;
  • Assay of growth features of the yeast strains and cytomorphology of cell microstructure;
  • The definition of respiratory activity, induction of alternative oxidative pathways and the total energy cell status using methods of specific staining with fluorescent potentiometric probes;
  • Polarographic methods of multichannel test of cell suspension (including assay of K+ and Ca2+concentration);
  • Evaluation of pathological cell changes using methods of fluorescent and electronic microscopy;
  • Assay of proteomic composition in the cell (2D-electrophoresis) followed by mass-spectrometrical analysis;
  • Assay of antioxidant activities in yeast cell using polarographical and spectrometrical methods. Detection of generation rates of ROS in the yeast cell with fluorescent method;
  • Quant-chemical modelling of the structure and molecular dynamics of organic molecules (coenzymes) in the main, ionized and excited state;
  • Methods for organic compounds separation using various modifications in  HPLC with registration detectors adapted to analysis of different coenzymes and the products of their photochemical reactions;
  • Methods for preparates and samples radiation, using UV and visible sources of radiation including monochromatic light;
  • Methods for chemical modeling of abiogenesis of organic molecules and supramolecular structures;
  • Assessment of the structure and mechanism for action of photocatalysts and energy-converting systems with the methods impulse laser photolysis, fluorescent and absorption spectroscopy, TEM and atomic-powered microscopy, electrochemical and chromatographic methods;
  • Quantitative assay of light-relative sexual and agamogenesis in the wild type, strains with some damages of nitrogen metabolism and mutants in photoreceptor complex of Neurospora crassa in response to various compounds influence;
  • The set of methods for definition of nitrogen metabolism features of Neurospora crassa such as enzyme activities (nitrate reductase , nitrite reductase, no synthase), analysis of influence of specific enzyme inhibitors, dynamics of nitrite release from mycelium during photo-induced carotenogenesis and photo-stimulated conidiogenesis;
  • Assay of bacteriocidal and fungicide activities of the surfaces with nano-coating in solid nutritive media.


Short history of the laboratory

The laboratory was formed in 2013 being based on the laboratory of evolutionary biochemistry and the group “Biological oxidation under extreme conditions”.

 

Selected publications:

  1. Cooper AJ, Shurubor YI, Dorai T, Pinto JT, Isakova EP, Deryabina YI, Denton TT, Krasnikov BF. ω-Amidase: an underappreciated, but important enzyme in L-glutamine and L-asparagine metabolism; relevance to sulfur and nitrogen metabolism, tumor biology and hyperammonemic diseases. Amino Acids, 2016, 48(1):1-20.
  2. Shurubor YI, Cooper AJ, Isakova EP, Deryabina YI, Beal MF, Krasnikov BF. HPLC determination of α-ketoglutaramate [5-amino-2,5-dioxopentanoate] in biological samples. Anal Biochem. 2016, 494:52-4.
  3. Shurubor YI, Cooper AJ, Isakova EP, Deryabina YI, Beal MF, Krasnikov BF. Simultaneous determination of tricarboxylic acid cycle metabolites by high-performance liquid chromatography with ultraviolet detection. Anal Biochem. 2016, 503:8-10.
  4. Epova EY,u, Balovneva MV., Isakova EP., Kudykina YK., Zylkova MV., Deryabina YI., Shevelev AB. Expression System for Yarrowia lipolytica Based on a Promoter of the Mitochondrial Potential-dependent Porin VDAC Gene Biotechnology and Bioprocess Engineering, 2016, 21: 408-413
  5. Shurubor YI, D’Aurelio M, Clark-Matott J, Isakova EP, Deryabina YI, Beal MF, Cooper AJL, Krasnikov BF. Determination of Coenzyme A and Acetyl-Coenzyme A in Biological Samples Using HPLC with UV Detection Molecules. 2017, 23;22(9). pii: E1388.
  6. Buglak AA, Telegina TA. A theoretical study of 5,6,7,8-tetrahydro-6-hydroxymethylpterin: insight into intrinsic photoreceptor properties of 6-substituted tetrahydropterins.      Photochem Photobiol Sci. 2019;18(2):516-523.
  7. Buglak A.A., Telegina T.A., Vorotelyak E.A., Kononov A.I. Theoretical study of photoreactions between oxidized pterins and molecular oxygen. J Photochem Photobiol A. 2019;372:254-259.
  8. K.A. Chekanov, E.R. Schastnaya, K. V.Neverov, S. Leu, S. Boussiba, A. Zarka, A.E.Solovchenko. Non-photochemical quenching in the cells of the carotenogenic chlorophyte Haematococcus lacustris under favorable condition and under stress. BBA: General Subjects, 2019, https://doi.org/10.1016/j.bbagen.2019.05.002