Prokaryotic Chromosomes

The genome of prokaryotes is usually made up of one ''chromosome'' and plasmids.

Chromosome consists of double–stranded circular DNA. Prokaryotes do not contain nucleus or
other membrane bounded organelles. The term "prokaryotes" actually means "before nucleus".
Chromosome is stored in a special area called nucleoid.

The genome of prokaryotes is often significantly larger than the cell itself though it is possible
that the genetic information fit into the cell. Prokaryotes do not contain histones (with a few
exceptions). Prokaryotes to compress their DNA using fiber rolled into small rolls –
supercoiling. The fibers are twisted so tightly that the final consequences loops overlap to form
one big ball. Distinguishes two types of collapse – positive (DNA turns are in the same direction
as the helix) or negative (DNA is coiled in the opposite direction than the helix). Most bacteria
during normal growth are negatively coiled.

Specific properties of prokaryotes

Prokaryotes reproduce asexually most often and are haploid (there is always only one copy of
the gene). Prokaryotes often contain several plasmids (extrachromosomal stored DNA molecule
– linear or circular). Unlike chromosomal DNA, plasmid DNA is typically smaller and encode
genes that are not necessary for survival. Often, however, give to the cell some advantage (eg
resistance to antibiotics). Replication of plasmids is independent of chromosomal replication.
Prokaryotes need to cram all their genes within one chromosome, so it doesn´t remain too much
space for the non–coding sequences. While in eukaryotes, the share of non–coding parts of DNA
is about 98%, in prokaryotes it is only 12%.
 Most prokaryotes contain one circular chromosome.
 DNA communicates with the cytoplasm – so it allows direct connection
to transcription and translation.
 Contain only one copy of the gene (haploid).
 Non-essential genes are stored outside of chromosome – in plasmids.
 Prokaryotic genome is very compact – contain very little non-coding DNA sequences.

Prokaryotic cells (bacteria) contain their chromosome as circular DNA. Usually the entire
genome is a single circle, but often there are extra circles called plasmids. The DNA is packaged
by DNA-binding protein. The bacterial DNA is packaged in loops back and forth and thus
formed bundled DNA is called the nucleoid. It concentrates the DNA in part of the cell, but it
is not separated by a nuclear membrane. The DNA does form loops back and forth to a protein
core, attached to the cell wall.

DNA domains
The DNA consists of 50–100 domains or loops, the ends of which are constrained by binding to
a structure which probably consists of proteins attached to part of the cell membrane. The loops
are about 50–100 kb in size.

Supercoiling of the genome

DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of
the strain on that strand. Supercoiling is important in a number of biological processes, such as
compacting DNA, and by regulating access to the genetic code, DNA supercoiling strongly
affects DNA metabolism and possibly gene expression.

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 or nucleus is
a difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. In
prokaryotes, plectonemic supercoils are predominant, because of the circular chromosome and
relatively small amount of genetic material.

Genomes can be negatively supercoiled, meaning that the DNA is twisted in the opposite
direction of the double helix, or positively supercoiled, meaning that the DNA is twisted in the
same direction as the double helix. Most bacterial genomes are negatively supercoiled during
normal growth

DNA-binding proteins
The most abundant of these are protein HU, a small basic (positively charged) protein. It’s binds
DNA nonspecifically by the wrapping of the DNA around the protein, and H-NS (formerly
known as protein H1), a monomeric neutral protein, which also binds DNA nonspecifically in
terms of sequence. These proteins are sometimes known as histone-like proteins, and have the
effect of compacting the DNA, which is essential for the packaging of the DNA into the
nucleoid, and of stabilizing and constraining the supercoiling of the chromosome and works with
an enzyme called topoisomerase I to bind DNA and introduce sharp bends in the chromosome,
generating the tension necessary for negative supercoiling. 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, much like eukaryotic chromosomes are wrapped around histones. Once the
prokaryotic genome has been condensed, DNA topoisomerase I, DNA gyrase, and other proteins
help maintain the supercoils.