SUBJECT

Molecular plant biology I

lecture

master

Faculty of Science

Biology MSc

2

Semester 2

Spring semester

1. Principle of molecular biology. Central dogma of molecular biology. Results of genome projects - the challenges of post-genomic era in molecular biology. From functional genomics to systems biology.

2. Genetic information of the plant cells and the encoding macromolecules. Distribution of genetic information in the plant cells between nuclear genom and the genomes of autonomous organelles (plastids, mitochondria). Organization levels of nuclear DNA from nucleosomes to chromosome. Role of histones. Functional organization of chromatin. Euchromatin, heterochromatin.

3. Factors affecting accessibility of DNA. Histone modifications, the histone code. Minor histone variants and their role in chromatin condensation and remodelling. ATP-dependent remodelling complex. Role of DNA methylation in chromatin condensation-decondensation. Propagation and epigenetic inheritance of inactive and active chromatin states. SiRNA-dependent regulation of changes in chromatin states.

4. The C-value. Correlation of genome size with organismic complexity, the C-value paradox. Reasons of high C-values of plant nuclear genomes. Polyploidy. Autopolyploidy, allopolyploidy. Repetitive DNA. Tandemly repeated sequences - satellite, minisatellite, microsatellite DNA, telomere DNA. The structural characteristics of the rDNA region and its importance in systematics.

5. Dispersedly repeated DNA sequences. Transposons. Structures of autonomous and non-autonomous elements and their transposition mechanisms. MITE elements, Helitrones. MULE elements. Types of retrotransposons. Structure of LTR retrotransposons and mechanism of transposition. Non-LTR retrotransposons. Structure and movements of SINE and LINE elements. Multigene families. Structures of sequenced plant genomes, function and distribution of genes. Mutational and selective evolutionary forces influencing genome size.

6. Structural organization and coding capacities of organellar genomes. Organization of plasid geneomes. Inverted repeats, small and large single copy regions. Gene content of the sequenced plastid genomes. Gene tranfer into the nucleus and mitochondria. Diversity of plastid genomes in selected organisms (Dinoflagellata, Cyanidium, Nephroselmis, Toxoplasma).

7. Multiple structural organization of plant mitochondrial genomes. Variability in size and arrangement. Master circle, subgenomic circles. The role of homologous recombination between direct repeats in yielding subgenomic circles. Gene transfer to the nucleus. Mitochondrial genome as an evolutionary mosaic.

8. Variability in size, and arrangement of genom organization in fungi. Multiplicity in C-values, gene content. Unique structures in organization at different structural levels. Srtucture of mitochondrial genomes in fungi.

9. Genetic transformation of plant genome. Plant cell- and tissue cultures and the ability of plant cells to regenerate into plants (totipotency, organogenesis, somatic embriogenesis). Procedures to introduce DNA into nuclear genome. Protoplast fusion, particle gun bombardment, electroporation. Agrobacterium-mediated transformation. Process of genetic colonization. Plant signals, and gene expression changes. Mechanism of transfer and insertion of T-DNA into plant nuclear genome. Genetic markers used in transformation.

10. First gerneration of transgenic plants. Engineering potentially useful agronomic traits. Herbicide tolerance, virus resistance, resistance to insect predation. Problems of expression of genes of procaryote origin in eukaryotes (codon bias, regulatory regions).

11. Second generation of transgenic plants. Engineering plants to accumulate novel products or display agronomically useful phenotypes. Modification of development, protein, carbohydrate, lipid metabolism

and production of secondary metabolites. Using transgenic plants for fitoremediation. Possibilities and problems of using multigenic constructions for transformation.

12. Third generation of transgenic plants. Bioreactor GM plants for production of vaccines, antibodies, special proteins and other metabolites of pharmaceutical importance. Prospects of genetic engineering of plastid genomes.

13. Replication of nuclear and organellar DNA. Components and function of replicases in prokaryotes and eukaryotes. Arrangement of the replication fork. Semidiscontinous replication, the Okazaki fragments. Role of helicases, primases, topoisomerases. Proofreading.

14. Mechanisms of DNA repair (photoreactivation, excision repair, mismatch repair, error-prone repair).

15. Bioinformatics in molecular biology. Database collections. Primary and secondary databases as resources for experimental and computational biologists in structural and functional genomics (sequence alignments, BLAST, construction of phylogenetic trees, etc.)

• Plant Biotechnology, Oxford University Press, 2007

• Buchanan, Gruissem, Jones: Biochemistry and molecular biology of plants, American Society of Plant Physiologists, Rockwill, Maryland, USA 2000

• Current reviews in Annual Review of Plant Sciences, - Biochemistry, - Cell Biology, - Genetics and Progress in Nucleic Acid Research and Molecular Biology