This document summarizes key aspects of genome organization in prokaryotes. It notes that prokaryotes like E. coli have a single circular chromosome composed of DNA that is compacted into a nucleoid structure. The DNA is highly condensed via supercoiling facilitated by enzymes like topoisomerases. Prokaryotic genomes are also typically smaller than eukaryotic ones and can contain extra DNA on plasmids that are exchanged between bacteria.

1. PRESENTATION
Genome Organization In
Prokaryotes

2. INTRODUCTION
• The term “prokaryote” means “primitive nucleus”.
• Cells have no nucleus i.e., prokaryotic chromosome is
dispersed within the cell and is not enclosed by separate
membrane.
• Prokaryotes are monoploid i.e., they have only one set of
genes.
• In most viruses and prokaryotes, the single set of genes is
stored in a single chromosome.
• Prokaryotic genomes are exemplified by the E.coli
chromosome.
• The bulk of the DNA in E. coli cells consists of a single
closed-circular DNA molecule of length 4.6 million base
pairs.

3. There are two very different groups of prokaryotes, distinguished
from one another by characteristic genetic and biochemical
features:
A. the Bacteria, which include most of the commonly encountered
prokaryotes such as the gram-negatives (e.g. E. coli), the gram-
positives (e.g. Bacillus subtilis), the cyanobacteria
(e.g. Anabaena) and many more
B. The Archaea, which are less well-studied, and have mostly
been found in extreme environments such as hot springs, brine
pools and anaerobic lake bottoms.

4. PROKARYOTE GENOME SIZE
Bacteria Size(Mbp)
Escherichia coli 4.64
Bacillus subtilis 4.20
Streptococcus 1.85
pyrogenes
Mycobacterium 0.58
genitalium
Archaea Size(Mbp)
Methanococcus 1.66
jannaschii
Sulfolobus 2.25
solfactaricus
Pyrococcus 1.75
furiosus

5. PROKARYOTIC CELL

6. GENOME ORGANIZATION
• Each bacterial chromosome is made by a single circular DNA
molecule.
• Usually each cell contain one single copy of each chromosome.
• The genetic material can be seen as a fairly compact clump (or
series of clumps) that occupies about a third of the volume of the
cell named NUCLEOID.
• The DNA of these loops is not found in the extended form of a free
duplex, but instead is compacted by association with proteins.
• Loop domain in bacterial genome contribute to the packaging.
• To fit the genome in a bacterial cell the DNA undergoes
supercoiling.

7. THE GENOPHORE
• A genophore is the DNA of a prokaryote, commonly referred to as a
prokaryotic chromosome.
• The term “chromosome” is misleading, because the genophore lacks
chromatin.
• The genophore is compacted through a mechanism known as
supercoiling.
• The genophore is circular in most prokaryotes.
• The circular nature of the genophore allows replication to occur
without telomeres.
• Genophores are generally of a much smaller size than Eukaryotic
chromosomes and can be as small as 0.58 million base pairs
(Mycoplasma genitalium).
• Many eukaryotes (such as plants and animals) carry genophores in
organelles such as mitochondria and chloroplasts. These organelles are
very similar to true prokaryotes.

8. PLASMID
• Besides chromosomes, some prokaryotes have smaller
loops of DNA called plasmids.
• May contain one or a few genes not essential for normal
growth.
• Bacteria exchange these plasmids with other bacteria in a
process known as horizontal gene transfer (HGT).
• Exchange of genetic material on plasmids provides
microbes with new genes beneficial for growth and
survival under special conditions.
• In some cases, genes obtained from plasmids may have
clinical implications, encoding virulence factors that give
a microbe the ability to cause disease or make a microbe
resistant to certain antibiotics.

9. NUCLEOID
• Nucleoid is composed of 60% DNA and small amount of RNA and
protein.
• Proteins helping to maintain the supercoiled structure of the nucleic
acid are known as nucleoid proteins or nucleoid-associated proteins.
• These proteins often use mechanisms, such as DNA looping, to
promote compaction.
• The nucleoid forms by condensation and functional arrangement
with the help of chromosomal architectural protein and RNA
molecules as well as DNA supercoiling.
• The structure of the DNA in the nucleoid appears to vary
depending on conditions and is linked to gene expression so that the
nucleoid architecture and gene transcription are tightly
interdependent influencing each other reciprocally.

10. DNA SUPERCOILING
The term "supercoiling" means literally the coiling of a coil.
• DNA supercoiling is generally a manifestation of structural strain.
• Supercoiling occurs when the molecule relieves the helical stress by
twisting around itself. Overtwisting leads to positive supercoiling, while
undertwisting leads to negative supercoiling.
• If DNA is in the form of a circular molecule, or if the ends are rigidly
held so that it forms a loop, then overtwisting or undertwisting leads to
the supercoiled state.

11. POSITIVE AND NEGATIVE SUPERCOILING
• Positive supercoiling is the
right-handed, double helical
form of DNA. It is twisted
tightly in a right handed
direction until the helix creates
knot.
• Positive supercoiling is more
condensed as the supercoil
forms at the direction of DNA
helix

12. • Negative supercoiling is the
left-handed, double helical
form of DNA.
• Prokaryotes usually have
negative supercoiled DNA.
It is naturally prevalent as it
prepares the molecule for
processes that require
separation of the DNA
strands without the need of
additional energy.

13. ENZYMES
• Some enzymes like topoisomarase can relieve the stress.
• Topoisomerases are enzymes that participate in the overwinding
or underwinding of DNA.
• In prokaryotes, there are two major topoisomerases that act
toward opposite direction. DNA gyrase is the only topoisomerase
able to actively introduce negative supercoils into DNA
molecules, in a reaction dependent upon ATP hydrolysis. In the
absence of ATP, gyrase can relax supercoiled DNA.
• Topoisomerase I can relax negatively supercoiled DNA but not
positively supercoiled DNA.

14. DNA supercoiling in
prokaryotes and
eukaryotes. Bacteria and
some archaea have
enzymes that allow them
to introduce supercoils
into DNA at the expense
of ATP, which results in
the formation of
plectonemic structures.

15. DNA LOOPS
• DNA-looping mechanisms are part of networks that regulate all aspects of
DNA metabolism, including transcription, replication, and recombination.
• DNA looping is involved in regulation of transcriptional initiation in
prokaryotic operons.
• In addition, instances of looped structures have been found in replication
and in recombination in both prokaryotes and eukaryotes. The ability of
DNA to form loops is affected by the distance between binding sites; by
the DNA sequence, which determines deformability and bendability; and
by the presence of other proteins that exert an influence on the
conformation of a particular sequence.
• Alteration of the stability of DNA loops and/or protein-DNA binding by
extra- or intracellular signals provides responsivity to changing metabolic
or environmental conditions. The fundamental property of site-specific
protein binding to DNA can be combined with protein-protein and
protein-ligand interaction to generate a broad range of physiological
states.

16. A model of the genome of E.coli.
The chromosome is folded into
~100 loops which undergoes
supercoiling. As a result, the
chromosome becomes much
shorter so that it is able to be
packaged into the cell. When an
endonuclease makes a cut in one
strand of one domain only that
becomes unfolded and enlarged
while the other domains remains
unaffected.

17. COMPARISON BETWEEN PROKARYOTICAND
EUKARYOTIC CHROMOSOME
PROKARYOTIC CHROMOSOMES
• Many prokaryotes contain a single
circular chromosome.
• Prokaryotic chromosomes are
condensed in the nucleoid via DNA
supercoiling and the binding of various
proteins.
• Because prokaryotic DNA can interact
with the cytoplasm, transcription and
translation occur simultaneously.
• Most prokaryotes contain only one copy
of each gene (i.e., they are haploid).
• Nonessential prokaryotic genes are
encoded on extrachromosomal
plasmids.
• Prokaryotic genomes are efficient and
compact, containing little repetitive and
noncoding DNA.
EUKARYOTIC CHROMOSOMES
• Eukaryotes contain multiple linear
chromosomes.
• Eukaryotic chromosomes are
condensed in a membrane-bound
nucleus via histones.
• In eukaryotes, transcription occurs in
the nucleus, and translation occurs in
the cytoplasm.
• Most eukaryotes contain two copies
of each gene (i.e., they are diploid).
• Extrachromosomal plasmids are not
commonly present in eukaryotes.
• Eukaryotes contain large amounts of
noncoding and repetitive DNA.
Introns are present.

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