description of genome organization in prokaryotes

1. GENOME ORGANIZATION IN
PROKARYOTES
D.INDRAJA

2. Gene:
It is a unit of heridity which is transferred from a parent to offspring
and held to determine some charecteristic to offspring
Genome:
The entire set of genetic information in an organism
It is encoded in DNA or RNA in case of many viruses
It includes different types of genes they are
Structural genes:
DNA segments that code for some specific RNAs or proteins encode
for mRNAs, tRNAs, SnRNAs
Functional sequences:
The sequences that are regulatory elements such as initiation site,
promoter site, operator site
Non functional sequences:
It includes introns and repetetive sequences

3. Nucleoid
• The nucleoid (meaning nucleus-like) is an irregularly-shaped
region within the cell of a prokaryote that contains all or most of
the genetic material. In contrast to the nucleus of a eukaryotic
cell, it is not surrounded by a nuclear membrane. The genome of
prokaryotic organisms generally is a circular, double-stranded
piece of DNA, of which multiple copies may exist at any time.
The length of a genome varies widely, but is generally at least a
few million base pairs.

4. • The nucleoid can be clearly visualized on an electron micrograph at
high magnification, where it is clearly visible against the cytosol.
Sometimes even strands of what is thought to be DNA are visible. The
nucleoid can also be seen under a light microscope.by staining it with
the Feulgen stain, which specifically stains DNA. The DNA-
intercalating stains DAPI and ethidium bromide are widely used for
fluorescence microscopy of nucleoids.
• Experimental evidence suggests that the nucleoid is largely composed
of about 60% DNA, plus a small amount of RNA and protein. The
latter two constituents are likely to be mainly messenger RNA and the
transcription factor proteins found regulating the bacterial genome.
Proteins helping to maintain the supercoiled structure of the nucleic
acid are known as nucleoid proteins or nucleoid-associated
proteins, and are distinct from histones of eukaryotic nuclei.

5. • The prokaryotic chromosome structure was derived from studies of
E.coli a bacterium that line in human colon in large intestine and
commonly used E.coli in laboratory cloning experiment
• As the DNA of E.coli is larger than the size of the cell it gets problem
for packaging the problem is overcomed by supercoiling of DNA.

6. SUPER COILING
A double helix of DNA undergoes additional twisting in the same
direction or in the opposite direction from the turns in the original
helix.supercoiling results when DNA is subject to same form of
structural strain. A strain is introduced in the DNA to induce
supercoiling
• Positive super coiling  twisting in lefthanded fashion
• Negative super coiling  twisting in right handed fashion

7. Genomes can be negatively supercoiled or positively supercoiled,
Most bacterial genomes are negatively supercoiled during normal
growth.
Proteins involved in super coiling:
During the 1980s and 1990s, researchers discovered that multiple
proteins act together to fold and condense prokaryotic DNA. In
particular, one protein called HU, which is the most abundant
protein in the nucleoid, works with enzyme called topoisomerase I
to bind DNA and introduce sharp bends in the chromosome,
generating the tension necessary for negative supercoiling. Recent
studies have also shown that other proteins, including integration
host factor (IHF), can bind to specific sequences within the genome
and introduce additional bends . The folded DNA is then organized
into a variety of conformations that are supercoiled and wound
around tetramers of the HU protein

8. Acessing super coiled genes:
• Because there is no nuclear membrane to separate prokaryotic
DNA from the ribosomes within the cytoplasm, transcription and
translation occur simultaneously in these organisms.
• The nucleoid usually appears as an irregularly shaped mass within
the prokaryotic cell, but it becomes spherical when the cell is
treated with chemicals to inhibit transcription or translation.
Moreover, during transcription, small regions of the chromosome
can be seen to project from the nucleoid into the cytoplasm , where
they unwind and associate with ribosomes, thus allowing easy
access by various transcriptional proteins . These projections are
thought to explain the mysterious shape of nucleoids during active
growth. When transcription is inhibited, however, the projections
retreat into the nucleoid, forming spherical shape.

9. The Importance of DNA supercoiling
DNA supercoiling is important for DNA packaging within all cells.
Because the length of DNA can be thousands of times that of a cell,
packaging this genetic material into the cell is difficult .
Supercoiling of DNA reduces the space and allows for much more
DNA to be packaged. In prokaryotes, plectonemic supercoils are
predominant, because of the circular chromosome and relatively
small amount of genetic material.

10. GENOME ORGANIZATION
• Genome organization in prokaryotes takes place by FOLDED
GENOME MODEL
• In folded genome model the large DNA molecule in E.coli
chromosome is organized in to 50 to 100 loops each of which is
negatively supercoiled
• RNA and proteins are both components of folded genome which
can be partially relaxed by treatment with either DNAse or
RNAse
• DNAse  removes supercoiling
• RNAse  removes folding

12. VARIATIONS IN PROKARYOTIC GENOME
STRUCTURE
• While most prokaryotes, like E. coli, contain a single circular
DNA molecule that makes up their entire genome
Exceptions
 Vibrio cholerae cholera - 2 circular chromosomes
one for metabolism and virulence and another for remaining
essential genes
 Borrelia burgdorferi Lyme disease - 11 copies of a single
linear chromosome
It cannot supercoil its linear chromosomes into a tight ball within
the nucleoid; rather, these strands are diffused throughout the
cell This organism is transmitted through the bite of deer ticks
 Archaea, a taxonomic domain composed of single-celled,
nonbacterial prokaryotes share many similarities with
eukaryotes, can be negatively supercoiled, positively
supercoiled, or not supercoiled at all. It is important to note that
archaeans are the only group of prokaryotes that use eukaryote-
like histones.