LABORATORY OF BIOLOGICAL OXIDATION
Head of Laboratory
The main scientific interests
The unique methods
The international collaboration
The laboratory of Biological Oxidation was organized in 1935, just at the same time as the Institute was. From 1935 to 1947 the laboratory was headed by Academician A.N. Bach, from 1947 to 1959 – by Professor D.L. Mikhlin, and from 1959 to 1986 – by Professor A.V. Kotel’nikova
Head of Laboratory:
Renata A. Zvyagilskaya
, Professor, Ph. D, D.Biol. Sci., the Bach Prize winner.
renata_z AT inbi.ras.ru
The main scientific interests:
1. Structure, functions, biogenesis and regulation of activity of mitochondria and peroxisomes of low eukaryotes (yeasts and fungi), as well as the role of these organelles in cellular metabolism. Our special emphasis is placed on study of energy metabolism (at cellular and mitochondrial levels) of yeast-extremophiles inhabiting extreme environments. For this purpose, we have isolated the unique yeast strains, which can grow in the wide range of pH values (pH 2.5-9.7), in the presence of high salinity (up to 12% NaCl) or at relatively high (50
C) temperature. Their study would permit to reveal the extremes (temperature, pH values, salt concentrations), at which the mitochondrial eukaryotic system of oxidative phosphorylation is still functioning, as well as roles of mitochondria in cell adaptation to extreme conditions.
2. Identification, purification, properties of nonconvential molybdenum-free nitrate reductases from microorganisms-extremophiles.
1. Using as a background the designed in the Laboratory methodology for to evaluation of energy parameters of intact cells and isolated tightly-coupled mitochondria, specific features of energy metabolism of different yeasts and yeast-like fungi, including thermo-, salt- and pH-tolerant strains were revealed. The scale of variability of energy status of yeast cells was established. It was found, in the first time, that yeast mitochondria can perform oxidative phosphorylation as efficiently as do mitochondria of higher eukaryotes. The concept of “economization” of energy metabolism upon growth limitation was formulated. Some specific features of energy transduction (conservation) in yeast mitochondria were revealed. It was shown, in the first time, that yeast mitochondria (e.g.
) can efficiently take up Ca
in an energy-dependent manner via the uniport mechanism. Physiological (natural) activators of this process were found. A Na+-independent system for Ca
release from Ca
-loaded yeast mitochondria was characterized and its regulation (activators and inhibitors) was examined in detail.
2. Phosphate (P
) transport systems of the newly isolated osmo-, salt- and alkalitolerant
yeast strain have been studied. It was shown, to our knowledge, in the first time, that yeasts harbor not only a highly effective H
-cotransport system, but also a high-affinity, high capacitive, finely regulated Na
-cotransport system. Kinetic properties of these two systems, their regulation and relative contribution to the total phosphate transport activity upon cell growth under different conditions were examined.
3. Topology of the active center in the dicarboxylate transporter of rat liver mitochondria has been studied. For this purpose, some derivatives of malonic acid (an inhibitor of the transporter) were synthesized and energy of interaction of different zones of the linear hydrophobic probe with the active center of the transporter was determined. It was suggested that the active zones revealed in the active center are the elements of its rotating mechanism. A reliable method for measuring in vivo activity of the dicarboxylate transporter of the
cytoplasmic membrane was developed. Substrate specificity, kinetic parameters of this transporter were determined and its specific competitive inhibitor was found. It was shown that transport of dicarboxylates mediated by the transporter is driven by ΔpH.
4. Several mutants of the methylotrophic
yeast, harboring different defects in translocation and assembly of multiprotein enzymatic complexes of peroxisomal matrix were identified.
5. Existence of a new class of molybdenum-free nitrate reductases is established. These enzymes are generally typical for microorganisms inhabiting extreme environments. In collaboration with the Laboratory of enzyme engineering, the electrophoretically homogenous octaheme-containing polyreductase from
was crystallized and its structure was solved to 1.3 Å resolution. The prime structure, physoco-chemical and kinetic properties of this enzyme were determined.
The unique methods:
The unique yeast strains covering the whole spectrum of energy metabolism and growing under extreme conditions (at very low and high pH values, under severe salinity) has been isolated or collected. The own data base on components and metabolic reactions of yeast mitochondria and their compartments has been established. A rapid effective method for preparation of homogenous nitrate reductases has been developed.
The international collaboration:
Recently, the Laboratory has been successfully collaborated with Department of Biochemistry and Biophysics (Prof. B.L. Persson, Sweden) and Vikki Biocenter, Helsinki, (Prof. N.-E. Saris, Finland).
The Projects and Programs in which the Laboratory is engaged at present
¹ 04-04-49132, 2004 - 2006.
Diagnosis of the functional state of single energy-transducing cellular organelles using the novel method of dynamic phase microscopy (the supervisor – Prof. V.A.Tychynsky, the investigator – R.A.Zvyagilskaya).
¹ 4-04-49112, 2004-2006.
Structures of molybdenum – and molybdocofactor-free nitrate reductases (the supervisor – Dr. A.N.Antipov).
¹ 04-04-49670, 2004-2006.
Study on structure and functional mechanisms of dicarboxylate transporters (the supervisor - Ph.D. D.A.Aliverdieva, the investigator - Ph.D. D.V. Mamaev)
¹ 05-04-49316, 2005 - 2007.
Adaptive generation of reactive oxygen species in different taxonomic organisms (the supervisor - Ph. D. Y.A.Labas, the investigator – R.A.Zvyagilskaya).
¹ 06-04-49687, 2006 - 2008.
Apoptosis in yeast cells, a role of nonspecific permeability transition of the inner mitochondrial membrane (pore) in apoptogenic signal transition (the the supervisor – R.A. Zvyagilskaya).
6. The program of RAS on Cellular and Molecular Biology
Bioenergetics of photosynthesis and respiration under stress environmental conditions (the supervisor - Prof. N.V. Karapetyan, the co-supervisor - R.A. Zvyagilskaya).
Selected Projects and Programs in which the Laboratory was recently engaged
¹ 00-04-48277, 2000-2002.
Mechanisms underlying ionic homeostasis in yeasts under salt and pH stresses. Na
-ATPase and Na
-antiporter) of the cytoplasmic membrane of the newly isolated salt- and alkali-tolerant
strain: identification, properties and purification; identification of genes encoding the Na
-transporters (the supervisor - R.A. Zvyagilskaya).
¹ 01-04-49837, 2001-2003.
Biogenesis of peroxisomes in yeasts: mechanisms of translocation and assemly of peroxisomal enzymes in methylotrophic yeasts (the supervisor – Ya. M. Rabinovich).
¹ 01-04-48553, 2001-2003.
Structure of molybdenum – and molybdocofactor-free nitrate reductases (the supervisor – A.N. Antipov).
¹ 03-04-48388, 2003-2005.
Phosphate transport systems of the Yarrowia lipolytica yeast: transport characteristics, identification, characterization and regulation of plasma membrane H
- and Na
-coupled transporters, identification of genes encoding these transporters (the supervisor - R.A. Zvyagilskaya).
¹ 4-04-49132, 2004-2006.
Structures of molybdenum – and molybdocofactor-free nitrate reductases (the supervisor – Dr. A.N. Antipov).
Molybdenum- and molybdocofactor-free nitrate reductases (the supervisor – Dr. A.N. Antipov).
7. The program of Federal Agency on Science and Innovations
The modeling of the eukaryotic cell (the supervisor – Academician E.D. Sverdlov, the local supervisor - R.A. Zvyagilskaya).
Selected recent Publications:
1. Bazhenova E.N., Deryabina Yu.I., Eriksson O., Zvyagilskaya R.A., and Saris N.-E. Characterization of a high-capacity calcium transport system in mitochondria of the yeast
J. Biol. Chem
. 1998, 273: 4372-4377.
2. P. Martinez, R. Zvyagilskaya, P. Allard and B. Persson. Physiological regulation of the derepressible phosphate transporter in
. 1998, 180: 2253-2256.
3. Deryabina, Yu, Bazhenova, E., Saris, N.-E., Zvyagilskaya, R. Ca
efflux from mitochondria of the yeast
J. Biol. Chem
., 2001, 276 (51):47901-47906.
4. Zvygilskaya, R.A., Parchomenko, O., Abramova, N., Allard P., Panaretakis T., Pattison-Granberg J., Persson B.L. Proton- and sodium-coupled phosphate transport systems and energy status of
cells grown at acidic and alkaline growth conditions.
J. Membr. Biol
., 2001, 183 (1), 39-50.
5. Behre, A., Zvyagilskaya, R., Lagerstedt, J., Pratt, J., Persson, B.L. Functional significance of cysteine residues and properties of the cysteine-less Pho84 phosphate transpoprter of
Biochem. Biophys. Res. Commun
., 2001, 1287 (4): 837-842.
6. Antipov A.N., Sorokin D.Y., L’vov N.P., Kuenen J.G. 2003. New enzyme belonging to the family of molybdenum-free nitrate reductases.
., 369 (Pt 1):185-189.
7. Zvyagilskaya R.A., Persson B.L. 2005. A novel alkalitolerant
strain for dissecting Na
-coupled phosphate transport systems.
Cell Biolol. Intern
. 29 (1): 87-94.
8. Tikhonova T.V., Slutsky A., Antipov A.N., Boyko K.M., Polyakov K.M., Sorokin D.Y., Zvyagilskaya R.A., Popov V.O. 2006. Molecular and catalytic properties of a novel cytochrome
nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium
Biochim Biophys Acta, Proteins and Proteomics
, 1764 (4): 715-723.
Last review: 17 June, 2006
© A.N.Bach Institute of Biochemistry of the R.A.S., 2001-2007