Genome organization in virus,bacteria and eukaryotes.pptx

Genome organization in virus,bacteria and eukaryotes.pptx

1. GENOME ORGANIZATION Submitted to, Dr. Arya P. Mohan St. Teresa’s College, Ernakulam Submitted by, Cathy Surya 1 st M.Sc. Botany Viruses, Bacteria, Eukaryotes 1

2. GENOME Genome- Complete set of genetic information in an organism. Provides all of the information the organism requires to function . It includes structural genes, regulatory genes, non functional nucleotide sequences. Term genome coined by Hans Winkler (German botanist). The study of genomes - Genomics . The genome is stored in chromosomes. 2

3. Viral Genome organization Viruses are tiny infectious particles made up of nucleic acids and protein coat . Viruses are broadly divided into DNA viruses and RNA viruses. Both DNA and RNA genomes can be either double stranded or single stranded. They posses very few genes (4 to few hundred). Genomes can be seen as packaged in segments or as one piece, and present in both linear and circular forms. 3

4. The protein coat and envelope Called capsid. Can have different shapes. Build from subunits called capsomeres. Most complex capsids are found in phages . Envelope Some viruses have envelop which help to infect cells. It actually comes from host cell. Made up of host cell phospholipids and membrane proteins. Also made up of proteins and glycoproteins from viruses. 4

5. Viral Genome organization DNA VIRUSES RNA VIRUSES They are viruses that possess DNA as their genetic material. They are viruses that possess RNA as their genetic material. They encode for many proteins They encode for limited number of proteins The two types include – dsDNA and ssDNA viruses. The two types include – dsRNA and ssRNA viruses. They have a larger genome size. They have a comparatively smaller genome size. They show a low mutation rate. They show a higher mutation rate. Most DNA viruses are assembled in the nucleus. Most RNA viruses are assembled in the cytoplasm. 5

6. Prokaryotic Genome Organization Single, circular, double stranded DNA molecule. Usually each cell contain single copy of each chromosome. Genetic materials mostly concentrated- Nucleoid . Do not have introns and histone proteins. They are organized in operons. Bacteria like the Borrelia burgdorferi possess linear chromosome like eukaryotes. Besides the chromosomal DNA, some bacteria posses extra chromosomal DNA called plasmid . 6

7. Gene Expression in Prokaryotes (Operon ) Operon - Operons are segments of genetic material (DNA) which functions as regulated unit or units that can be switched on or switched off. It is a sequence of closely placed genes regulating a metabolic pathway in prokaryotes. Regulatory genes Two types Positive regulators, negative regulators (repressors). These regulators are DNA binding proteins that recognize specific sites at or near the genes they control. Structural genes - Sequences of DNA corresponding to the amino acids of a protein that will be produced. 7

8. Plasmid Extrachromosomal circular DNA Found in bacteria, yeast and fungi. Replicate autonomously. May contain resistance genes. It can be transferred from one bacterium to another. 8

9. Classification and types of plasmids Conjugative The sexual transfer of plasmids to another bacterium through pilus. Non conjugative They don’t initiate conjugation. They can only be transferred with the help of conjugative plasmids. 9

10. Supercoiling of the prokaryotic chromosome Twist Number of helical turns of one strand around the other. Writhe (Supercoiling) Number of times double helix cross over itself. Linking Number L= T+W Represents amount of tension in molecule. 10

11. Positive Supercoils Supercoils in left handed direction. Winding is more frequent. Overwinding. Harder to unwind. Negative Supercoils Supercoils in right handed direction. Winding less frequent. Underwinding 11

12. Functions of Supercoiling Genome packaging Genome Expression DNA/RNA synthesis 12

13. Proteins involved in the Supercoiling Multiple proteins act together to fold and condense prokaryotic DNA, one such protein is called HU ( Heat unstable protein) Other proteins are Integration host factor (IHF) Histone-like nucleoid structuring protein (H-NS) DNA topoisomerase I DNA gyrase etc. 13

14. Topoisomerases and supercoiling Type I topoisomerases. Type II Topoisomerases 14 Make double strand break. Requires energy. Can relieve both (+) and (-) supercoiling. DNA Gyrase (ATP dependent enzyme) GyrA and GyrB subunits Makes double stranded cuts in DNA Introduce more (-) supercoiling. Relieve torsional stress caused by supercoils. Make single strand break Work on both (+) and (-) supercoiling.

15. Events in Supercoiling HU protein binds DNA non specifically by the wrapping of the DNA around the protein with enzyme called topoisomerase I Introduces single stranded breaks. H-NS proteins bind with DNA. Half of the wrapping is constrained and unconstrained. Unconstrained DNA is free in the medium and causing tension to the rest part of the DNA. Later, RNA polymerase, mRNA molecules IHF (Integration Host Factor) binds to specific sequences within the genome and introduce additional bends . DNA topoisomerase I, DNA gyrase and other proteins helps to maintain the supercoils. 15

16. Genome organization in Eukaryotes Eukaryotic genomes are Linear, follow the Watson-Crick Double Helix structural mode Contained within chromosomes, bundles of DNA and proteins (Histone) known as nucleosomes. The protein-coding genes in eukaryotic genomes are organized in exons and introns. 16

17. Continuous… Two characteristics Eukaryotic genome is much larger than that of a prokaryotic cell. Many genes can only be expressed in certain types of cells due to cell specialization. Stages of Eukaryotic genome organization Nucleosome formation Solenoid fibre Chromatin fibre Chromatid and chromosome formation 17

18. The DNA forms a complex with proteins“ histone proteins ”, and the complex is known as Nucleosome . There are two molecules of each of four types of Histones namely H2A, H2B, H3 & H4. This give rise to a complex of 8 proteins named as “Histone octamer ”. Histones are mostly positively charged amino acids. DNA (negatively charged is attracted to Histones) The histone proteins forms a core of nucleosome DNA wrapped around these core by 1.65 times (less than 2 rounds). These nucleosomes forms a bead like structure. The nucleosome beads attached with each other through linker DNA (H1 protein is associated with linker DNA). Nucleosome formation 18

19. Solenoid Fibre The beaded thread coils into the 30-nm chromatin fiber. The term solenoid itself defines the winding of the DNA helix. 19

20. Chromatin composed of DNA and proteins (300nm diameter). Chromatin is the complex basis of DNA Chromatin is of two types Euchromatin Heterochromatin Chromatin Fibre 20

21. Chromatid and chromosome formation Next higher order chromatin structure is chromatid (700nm diameter). It is one of the two identical halves of a chromosome that has been replicated in preparation for cell division. The two “sister” chromatids are joined at a constricted region of the chromosome called the centromere. Parts of chromosome Two arms Centromere (Region holds chromatin) Telomere (End of chromosome) 21

22. DNA-Level Eukaryotic Genome Organisation The majority of DNA in eukaryotes (97% in humans) can not code for protein or RNA. Regulatory sequences are found in non-coding areas. They are usually introns. The genome contains several copies of repetitive DNA. 22

23. Highly Repetitive DNA -These are very short DNA sequences(<100bp) which are organized as long tandem repeats. Naturally these sequences are non-coding by nature. Satellite DNA – Highly repetitive, contains short repeated sequences. 23

24. 24 Interspersed repeat sequences scattered throughout the genome (“ability to jump from one place to another in the genome”).

25. References G. Ann, Genome Packaging in Prokaryotes: the Circular Chromosome of E. coli , 2008 Nature Education. Karp, G. (2013). Cell and Molecular Biology: Concepts and Experiments. NJ: John Wiley & Sons. Leslie A. Pray, Eukaryotic Genome Complexity, 2008 Nature Education. https://byjus.com/ https://www.jove.com/science-education 25

26. THANK YOU 26