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Laboratory of Nucleic Acids

Head of laboratory, Doctor, Professor T. Beridze

Contacts

Phone: (995 32) 392540
E-mail: tberidze@hotmail.com

Main Directions

Structural feature of satellite DNA
Bends in satellite DNA
Comparative study of   plant nuclear and chloroplast transcriptional systems.

Research Activity

Study of satellite DNA
Laboratory of Nucleic Acids of the Institute of Biochemistry and Biotechnology has a great experience in investigation of plant genome organization, especially of satellite DNA and chloroplast DNA. It was first shown with the Phaseolus genus, that closely related higher plant species within one genus can differ in the quantity of satellite DNAs (Beridze,1972). Marked differences in the quantitative content of satellite DNA have been found in species of the Brassica family with different chromosome number (Beridze, 1976). Data on the satellite DNA content in citric plants are also of interest. The citric plants studied in our work involve four genera (14 species). The satellite DNA content varied within the limits of 10-30% (Bragvadze, 1983).
Later satellite DNA of citric plants was characterized by cloning and sequencing 10 to 14 repeats of each plant (Citrus limon, C.sinensis, C.ichangensis, Poncirus trifoliata). The monomers are mostly 181 bp in length with a GC-content between 58 to 68 %, respectively (significantly higher than average GC content of the Citrus group genoms). Similarity among the repeats indicate that they belong to a satellite family that have under gone species-specific modifications which are reflected in their phylogenetic relationships (Fann et al., 2001).
The studies during the past two decades have shown clearly that linear DNA molecules have significant conformational flexibility. The DNA helical configuration is not an absolutely regular one.  Local bends in the DNA molecules were detected in adenine tract locations (n=2-9). When A-tracts are repeated in phase with the helix screw, the total bend grows in size and can be observed by various methods (Marini et al., 1982).
Satellite DNAs are tandemly arranged highly reiterated sequences. If a bend appears in a monomer, due to the regular repeating organization, the long chains ought to reveal a tertiary structure. Computer modeling has suggested that such molecules are of a hypothetical solenoid form termed the coiled double helix (CDH-form) (Beridze, 1992; 1994). The solenoid parameters, i.e. diameter and number of base pairs per turn will vary depending on the length and quantity of A-tracts and their arrangement along the monomer chain.
In our earlier study, the sequence of the Citrus ichangensis satellite DNA repeating unit was determined. The repeat is 181 bp long and contains four pentanucleotides of adenine residues (Beridze et al., 1992). Oligomers of the C.ichangensis satellite DNA (dimer and trimer) were shown to migrate more slowly in polyacrylamide than agarose gels, indicating the presence of curvature in the monomer. A hexamer of the repeating unit of Citrus ichangensis satellite DNA was cloned. Polyacrylamide gel electrophoresis demonstrated that the shape of the cloned hexamer is not linear (Beridze et al., 1994). A comparative analysis of satellite DNA hexamer, revealed that it migrates in PAGE at 60oC as a 1,1 kb molecule, which corresponds to its actual size. However, the hexamer migrates as a 1,3 kb molecule in the same gel at lower temperature.
An electron microscopic analysis revealed small diameter circles in the hexamer under analysis. Unlike the hexamer, control molecules are s-shaped. It was proposed that the circular structures observed under the electron microscope confirm computer models and may be considered proof of the presence of the coiled double helix structure in the satellite DNA of C. ichangensis (Beridze et al., 1994).
Subsequently satellite DNAs of citric plants were characterized by sequencing and cloning of 10 to 14 repeats of each plant’s satellite DNA (Citrus limon, C.sinensis, C.ichangensis, Poncirus trifoliata). The monomers are mostly 181 bp in length with a GC-content between 58 to 68 %. Similarity among the repeats indicates that they belong to a satellite family that underwent species-specific modifications what are reflected in their phylogenetic relationships. Curvature provoked by A-stretches within the repeats was compared among species, thereby supporting the heterochromatic structure of satellite DNA (Fann et al., 2001).

Study  of Chloroplast DNA
By the method of DNA-DNA hybridization  homology degree of nucleotide sequences of  chloroplast DNA of higher plants has been studied. Maximum homology has been observed between the chloroplast DNA of spinach and  beet  belonging  to the same family (80-83 %). In systematically distant  species the degree of hybridization decreases  to 34 %. Study of  thermal stability of DNA-DNA hybrids has shown reduction of melting temperature of  heterologous hybrids to 10 degree as compared to homologous ones (Tabidze, 1980).
Chloroplast and nuclear DNAs from higher plants of  6 species belonging to different classes and orders were investigated by high resolution thermal melting. All of the chloroplast DNAs showed considerable intramolecular heterogeneity. In most plants 8 thermal components were detected. In contrast to the corresponding nuclear genomes, chloroplast DNAs of different plants demonstrated similar melting properties (Tabidze, Beridze, 1979).
The nucleotide sequence of a 1,1 kb fragment of the leek chloroplast DNA has been determined. The fragment contains the 3’ part of the tRNA Gly (UUC) gene and the tRNA Arg (UCU) gene on the same strand, and the 3’ end of the atpA gene encoding the CF1 ATPase ?-subunit which is located on the opposite strand. The gene rearrangement and nucleotide sequence of this fragment are similar to those of the corresponding region in the tobacco chloroplast DNA but differ significantly from what has been observed in other monocotyledonous plants such as wheat and rice, in which the region containing these genes has undergone intensive rearrangement (Tabidze et.al, 1994).
For the functional study  of chloroplast  ATP synthase  site-directed mutagenesis were used to generate C-terminal mutations in chloroplast ATPase e subunit. After expression  in   E.coli , these mutants are reconstituted with CF1(-e) both in solution and on membranes and can be used to study inhibition potency and proton permeability of  ATP synthase. Unlike the  N-terminal mutants  of   e  subunit,  the C-terminal mutant did not affect structural stability of  e  subunit, and  ATP synthase normal  function. These  e subunit mutants   fully inhibit the ATPase activity and completely restore proton impermeability both in solution and membranes. 
The primary structure one of the flower-specific cDNA clone from sunflower has been determined. The clone contains  C-terminal part of the cytochrome P450 gene. Comparison study show that the sunflower cytochrome P450 is considerably different from the already known plant and animal cytochromes  and represents a new P450 subfamily.

Comparative study of nuclear and chloroplast transcriptional systems in higher plants.
Research was elaborated under the guidance of corresponding member of the academy D. Djokhadze (1927-2004)
It’s a common knowledge that, transcriptional (RNA-polymerize) systems of nuclei and chloroplast are characterized with some sorts of  autonomy and hormones, especially gibberellins, had a great influence on the functioning of this systems. In particular in nucleus they can change the quantity and activity of basic forms DNA-dependent RNA-polymerize. This fact is of a very important feature, which directly show that hormones are selectively interacted with different regions of genome, because, each form of  RNA-polymerize is served for functioning of the defined  group of genes.
Fraction of gibberellin-specific protein which reveals function of a mediator between gibberellins and  genome in nucleus and chloroplasts were isolated from the nucleus of  French been and corn leaves. The mediator function between gibberellins and  genome in nucleus and chloroplasts also was observed on the level of RNA-polymeraze and DNA of these organelles. 
Three basic forms of RNA-polymeraze  were isolated and characterized  from   Spirulina
(comparative studies with pea nuclear RNA-polymeraze were performed). In local forms of this algae (from Kumisi lake) quantity of  ficocyanines,  Cytochrome  P-450 and  vitamins have been determined.          
Addition of  Spirulina in  mulberry leaves which are used for the silkworm feeding can drastically improved her industrial quality.  Stimulating effects of  Spirulina  on development of some microorganisms and  vine yeast also was found.
By isoelectric focusing techniques proteins isolated from the mulberry buds have been studied. In all  four species and 80 varieties of mulberry from Georgia have been investigated. Investigation has revealed  typical marker protein components for the each species. It was found that, isoelectric distribution patterns is variety-specific and may be used for the  identification and registration different varieties of plant.

Population-genetic Study of Human Population in the Caucasus
Population-genetic structure of  human population in the Caucasus have been studied. The  Caucasus is genetically heterogeneous, it is subdivided, and to be partially composed of independent evolutionary units. The most important in gene pool formation was an evolutionary process in which linguistic and genetic divergence has resulted from population subdivision and from  processes of elite dominance, that is, language replacement not associated with major migratory movements (Barbujani et al., 1994).  Hypotheses that classify North and South Caucasian languages into distinct families or that treat all north Caucasian languages as independent linguistic entities fail to account whereas genetic and geographic distances between groups appear significantly associated for genetic variation better than simpler models (Nasidze, 1995).

Members

  1. Beridze Tengiz - Academician, chief scientist, head of laboratory
  2. Tabidze Vazha - Doctor, senior scientist
  3. Gigolashvili George - PhD, scientist
  4. Pipia Ia - PhD,  scientist
  5. Gogniashvili Marie - PhD, technician
  6. Chokheli Liana - Technician

Beridze Tengiz

1939 – Born
1962 - Tbilisi State University
1967 - Candidate of Biological Sciences
1980 – Doctor of Biological Sciences
1993 - Academician
1969 - Head of Laboratory

Selected Publications

  1. Beridze T. Satellite DNA, Springer-Verlag, Berlin, Heidelberg, New York, Tokyo1986.
  2. Kondrashov A.S., Beridze T.G., Chiaureli N.B. Two regions of M13 phage genome hybridizing with human DNA are similar to several keratin genes. Biochimie, 1990, 72, 867-871.
  3. Beridze T., Tsirekidze N., Roytberg M.A. On the tertiary structure of satellite DNAs, Biochimie, 1992, 74, 187-194.
  4. Beridze T., Tsirekidze N., Turishcheva M.S. On the tertiary structure of Citrus ichangensis  satellite DNA. FEBS Letters, 1994 , 338, 179-182.
  5. Tabidze V.D., Kartvelischvili M.G., Jincharadze A.G., Beridze T.G. Nucleotide sequence and organization of tRNA gly, tRNA arg and CF1-ATPase a-subunit genes of chloroplast DNA of Allium porrum, Biochemistry(Moscow), 1994, 59,309-314.
  6. Tabidze V., Kartvelischvili M., Jincharadze A., Beridze T. Unlike in          other Monocotyledo­nous plants such as wheat and rice, the region containing the tRNA gly (UCC), tRNA arg (UCU) and CF1 ATPase ?-subunite genes has not undergone recombination in the leek chloroplast DNA, Plant Science, 1994,100, 165-169.
  7. Beridze T., Turishcheva M.S., Tsirekidze N. On the tertiary structure of satellite DNA. Abstracts of 7-th European Congress on Biotechnology, 1995 LUP 24.
  8. Tabidze V., Beridze T. Fine Structural Features of A.porrum Chloroplast DNA tRNA-gly, tRNA-arg and CF1 -ATPase ?-subunit genes: comparison with corresponding DNA sequences from monocot and dicot plants. Bulletin Georgian Academy Sciences, 1996, 153,113-115.
  9. Fann  Y., Kovarik A., Hemleben V.,  Tsirekidze N.,Beridze TSequence and Structure of Satellite DNAs of Citric Plants. Theor.Applied.Genet. 2001,103,1068-1073.
  10. .BeridzeT.G.,Tsirekidze N.I., Turishcheva M.SStructure of Highly Reiterated  DNA. In Materials of International Symposium  "Problems of Biochemistry, Radiation and Space biology", Moscow-Dubna, 1997, 14.
  11. Beridze TStructure and Organization of Plant Heterochromatic DNA. Abstracts,. XVI International Botanical Congress.St.Louis, USA. Symposium – Repetitive DNA in higher Plants. Organizers: V.Hemleben, T.Beridze 1999, 3,15,2.
  12. Tabidze V.,Steinmetz A., Beridze TFlower-specific cDNA  clone from sunflower encode a novel cytochrome P-450. Russian Journal of Plant Physiology (Moscow), 2001 48,1-5.
  13. Datukishvili N. T., Tarkhnishvili G. M., Mikeladze D. G.,  Beridze T. G., Sanadze G. A. Isolation and purification of protein responsible for the conversion of dimethylallylpyrophosphate from poplar leaves into isoprene. Russian Journal of Plant Physiology Moscow, 2001, 48.
  14. Devdariani, T., Beridze T., Devdariani I., Tabidze, V. On the influence of some carcinogenic polycyclic aromatic hydrocarbons on protein synthesis in plants. Bulletin of the Georgian Academy of Sciences. 2002, 165,  563-566 .
  15. Tabidze V.,  Gamkrelidze M., Gotsiridze V., Glonti T., Beridze T. Microsatellite  analysis of  Vitis vinifera L.Georgian  cultivars. Bulletin of the Georgian Academy of Sciences, 2006,174,333-336.

International Grants

  1. 1995 DAAD University of Tubingen ( www.daad.ge).
  2. 2000   DAAD   Ueberregionale Programme der  Entwicklungszusammenarbeit( www.daad.ge).
  3. INTAS 97-31424 Molecular mechanisms of regulation of chloroplast gene expression during early chloroplast differentiation.  (  www.intas.be).
  4. 4.2000-2002 ISTC G-284.   Biotransformation of  Carcinogens( www.istc.ru). 
  5. Soros foundation travel grant. International Botanical Congress. St. Louis, USA.
  6. GEB2-3326-TB-03 Genetic Diversity of Cultivated And Wild.  Varieties of Vitis Vinifera In The Caucasian Area (www.grdf.ge).

Participation in international conference

XVI International Botanical Congress.St.Louis, USA, Symposium – Repetitive DNA in higher Plants. Organizers: V.Hemleben, T.Beridze1999.
International Symposium  "Problems of Biochemistry, Radiation and Space biology", Moscow-Dubna, 1997, 2001.

Tabidze Vazha

1948 - Born
1971  -Tbilisi State University
1981– Candidate of Biological Sciences
2003 - Doctor of Biological Sciences

Selected Publications

  1. Tabidze V., Beridze T.  Fine Melting Curves of Chloroplast DNA of Higher Plants. Plant  SciensLetter, 1979,  16,  157-164.
  2. Steinmetz A., Baltz R., Domon C., Dudareva N., Evrard J – L., Krauter R., Mandel C.,Tabidze V.  Flower-specific genes in sunflower. Biotechnol.& Biotehnol.E.,. 1993, 7, 16-20.
  3. Tabidze V., Kartvelishvili M., Jincharadze A., Beridze N. Unlike other monocotyledonous  plants  such  as wheat and rice the region containing the tRNA-Gly(UCC), tRNA-Arg(UCU) and CF1 ATPase ?-subunit genes has not  undergone recombination in the leek chloroplast DNA. Plant Science, 1994, 100, 165-169.
  4. Tabidze V., Beridze T. Fine structural features of Allium porrum chloroplast DNA tRNA-Gly, tRNA-Arg  and  CF1 ATPase ?-subunit genes: Comparison with Corresponding DNA Sequences from Monocot and Dicot Plants. Bulletin of the Georgian Academy of Sciences, 1996, 153, 113-115.
  5. Tabidze V., Chiaureli N., Sakvarelidze L. Flower-specific cytochrome P450  from the sunflower: structural similarity with the  plant cytochrome P450. Bulletin of the Georgian Academy of Sciences, 2000, 162, 556-557.
  6. Devdariani T., Dolidze T., Tabidze V.  Peptide Conjugates of Benz(a)Pyrene in Plants. Bulletin of the Georgian Academy of  Sciences,  2002, 165, 354-357.
  7. Devdariani, T., Beridze T., Devdariani I., Tabidze, V. On the influence of some carcinogenic polycyclic aromatic hydrocarbons on protein synthesis in plants. Bulletin of the Georgian Academy of Sciences,  2002, 165, 563-566.
  8. Sakvarelidze L., Tabidze V. Sequence-dependent  bending  in  chloroplast DNA. Bulletin of the Georgian Academy of  Sciences,  2002, 166, 334-336.
  9. Devdariani T., Dolidze T., Tabidze V., Devdariani I. Influence of carcinogenic benz(a)pyrene on some enzymatic systems of plants. Bulletin of the Georgian Academy of Sciences, 2002, 166, 337-340.
  10.  Nowak K., Tabidze V.,  McCarty R. The C-terminal domain of the  e subunit of  the ATP synthase is not required for ATP synthesis.   Biochemistry USA.  2002, 41, 15130-15134
  11. Tabidze V.,  Gamkrelidze M., Gotsiridze V., Glonti T., Beridze T. Microsatellite analysis of  Vitis vinifera L.Georgian  Cultivars. Bulletin of the Georgian Academy of Sciences, 2006,174,333-336.

International Grants

  1. 19961997P 1 0247.Johns Hopkins University, Baltimore, USA. C.A.S.T  Post-Doctoral Fellowship.
  2. 2000-2002: INTAS 97-31424 Molecular mechanisms of regulation of chlo­ro­­plast gene expression during early chloroplast differentiation.  (www.intas.be).
  3. 2000-2002. ISTC G-284.   Biotransformation of  Carcinogens( www.istc.ru). 
  4. 1999. Soros foundation travel grant. International Botanical Congress. St. Louis, USA.
  5. 2004. GEB2-3326-TB-03. Genetic Diversity of Cultivated And Wild Varieties of Vitis Vinifera in the Caucasian Area ( www.grdf.ge).
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