Genome Organisation

1. A N U B H A K U M A R I
A S S I S T A N T P R O F E S S O R
D E P A R T M E N T O F B I O T E C H N O L O G Y
A N N A D A C O L L E G E
H A Z A R I B A G H J H A R K H A N D
BACTERIAL, VIRAL GENOME
ORGANISATION

2. GENEORGANISATION
• The word “genome,” coined by German botanist
Hans Winkler in 1920, was derived simply by
combining gene and the final syllable of
chromosome.
• An organism’s genome is defined as the complete
haploid genetic complement of a typical cell.
• In diploid organisms, sequence variations exist
between the two copies of each chromosome
present in a cell.
• The genome is the ultimate source of information
about an organism.

3. PROKARYOTESANDEUKARYOTES
GENOME
Prokaryotes Eukaryotes
Single cell Single or multi cell
No nucleus Nucleus
One piece of circular DNA Chromosomes
No mRNA post transcriptional
modification
Exons/Introns splicing

4. CHROMOSOMEDIFFERENCE
[PROKARYOTICANDEUKARYOTICCELL]
 PROKARYOTIC CELL
 Lacksamembrane bound nucleus.
 Circular DNAand supercoiled domain.
 Histones not present.
 Prokaryotic genomes generally contains one largecircular
piece of DNArefered to asaCHROMOSOME.
 Somebacteria have linear chromosome.
 Many bacteria have small circular DNAstr. CalledPLASMIDS
which can be swapped between neighbours and across
bacterial species.

5. Procaryotic genomes
 Generally 1 circular chromosome (dsDNA)
 Usually without introns
 Relatively high gene density (~2500 genes per mm
of E. coli DNA)
 length of E.coli genome: 1.7 mm
 Often indigenous(natural) plasmids are present

6. Plasmids
Extra chromosomal circular DNAs
 Found in bacteria, yeast and other fungi
 Size varies form ~ 3,000 bp to 100,000 bp.
 Replicate autonomously (origin of replication)
 May contain resistance genes
 May be transferred from one bacterium to another
 May be transferred across kingdoms
 Multicopy plasmids (~ up to 400 plasmids/per cell)
 Low copy plasmids (1 –2 copies per cell)
 Plasmids may be incompatible with each other
 Are used as vectors that could carry a foreign gene of
interest (e.g. insulin)
-lactamase
ori
foreign gene

7. PLASMID
o The term plasmid was first
introduced by the American
molecular biologist Joshua
Lederberg in 1952.
o A plasmid is separate form,
and can replicate
independently of, the
chromosomal DNA.
o Plasmid size varies from 1 to
over 1,000 (kbp).

8. Classification and typesof
PLASMID
•Plasmids can be broadly classified into
conjugative plasmids and non-conjugative
plasmids.
•In the complex process of conjugation,plasmid
may be transferred from one bacterium to
another via sexpili encoded by someof
the tragenes(transfer operon).
•Non-conjugative plasmids are incapable of
initiating conjugation, hence they canbe
transferred only with the assistance ofconjugative
plasmids.

9. Another way to classify plasmids isby
function. There are five mainclasses:
• Fertility F-plasmids, which contain tra genes.Theyare capable
of conjugation and result in the expression ofsexpili.
• Resistance(R)plasmids, which contain genesthat provide
resistance against antibiotics or poisons.
• Colplasmids, which contain genesthat code
for bacteriocins(p), proteins that can kill other bacteria.
• Degradative plasmids, which enable the digestion ofunusual
substances, e.g. toluene(aromatic hydrocarbon) and salicylic
acid(aromatic acid)
• Virulence plasmids, which turn the bacterium intoapathogen.

10. Bacterial genes
 Most do not have introns
 Many are organized in operons: contiguous
genes, transcribed as a single polycistronic
mRNA(bac and chloroplast mrna), that encode
proteins with related functions
Polycistronic mRNA encodes several proteins

11. Viral genomes
Viral genomes: ssRNA, dsRNA, ssDNA, dsDNA, linear or ciruclar
Viruses with RNA genomes:
•Almost all plant viruses and some bacterial and animal viruses
•Genomes are rather small (a few thousand nucleotides)
Viruses with DNA genomes (e.g. lambda = 48,502 bp):
•Often a circular genome.
Replicative form of viral genomes
•all ssRNA viruses produce dsRNA molecules
•many linear DNA molecules become circular
Molecular weight and contour length:
• duplex length per nucleotide = 3.4 Å
• Mol. Weight per base pair = ~ 660

12. VIRALGENOME
A virus has either a DNA or an
RNAgenome and is called aDNAvirus or an
vast majorityRNA virus, respectively.
The of viruses
viruses havetendto
RNA genomes. Plant
have single-stranded
RNA genomes and bacteriophages tend to
havedouble-stranded DNAgenomes.

13. Mitochondrial genome (mtDNA)
 Multiple identical circular chromosomes
 Size ~15 Kb in animals
 Size ~ 200 kb to 2,500 kb in plants
 Over 95% of mitochondrial proteins are encoded in
the nuclear genome.
 Often A+T rich genomes.
 Mt DNA is replicated before or during mitosis

15.  Mitochondrial DNA contains 37 genes, all of which are
essential for normal mitochondrial function. Thirteen of
these genes provide instructions for making enzymes
involved in oxidative phosphorylation. Oxidative
phosphorylation is a process that uses oxygen and simple
sugars to create adenosine triphosphate (ATP), the cell's
main energy source.
 The remaining genes provide instructions for making
molecules called transfer RNA (tRNA) and ribosomal
RNA (rRNA), which are chemical cousins of DNA. These
types of RNA help assemble protein building blocks
(amino acids) into functioning proteins.

16. Chloroplast genome (cpDNA)
 Multiple circular molecules
 Size ranges from 120 kb to 160 kb
 Similar to mtDNA
 Many chloroplast proteins are encoded in the
nucleus (separate signal sequence)

17. “Cellular” Genomes
VirusesProkaryotes Eukaryotes
Viral genome Bacterial
chromosome
Plasmids
Chromosomes
(Nuclear genome)
Mitochondrial
genome
Chloroplast
genome
Genome: all of an organism’s genes plus intergenic DNA
Intergenic DNA = DNA between genes
Capsid
Nucleus

18. Size of genomes
Epstein-Barr virus 0.172 x 106
E. coli 4.6 x 106
S. cerevisiae 12.1 x 106
C. elegans 95.5 x 106
A. thaliana 117 x 106
D. melanogaster 180 x 106
H. sapiens 3200 x 106

19. KARYOTYPE
o The study of chromosomes, their structure and
their inheritance is known as Cytogenetics.
o Each species has a characteristic number of
chromosomes and this is known as karyotype.

21. GENES–GENETICINFORMATION
• One gene : one enzyme
hypothesis: summarizes
that a gene is a stretch of
DNA coding for one or
more isoforms of a single
enzyme.(Beadle 1941)
• One gene : one
polypeptide hypothesis: a
gene is responsible for the
production of a single
polypeptide.(Beadle 1945)