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
1st M.Sc. Botany
Viruses, Bacteria, Eukaryotes
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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12. Functions of Supercoiling
• Genome packaging
• Genome Expression
• DNA/RNA synthesis
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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.
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14. Topoisomerases and supercoiling
Type I topoisomerases.
• Type II Topoisomerases
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• 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.
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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.
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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
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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
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19. Solenoid Fibre
• The beaded thread coils into the 30-nm chromatin fiber.
• The term solenoid itself defines the winding of the DNA helix.
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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
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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)
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22. DNA-Level Eukaryotic Genome Organisation
The majority of DNA in eukaryotes (97% in humans) can not code for protein or RNA.
1. Regulatory sequences are found in non-coding areas.
2. They are usually introns.
3. The genome contains several copies of repetitive DNA.
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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.
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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
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26. THANK YOU
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