Bacterial Genome: The Nucleoid

Bacterial Genome
The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA,

multiple copies of which may exist at any time. The length of a genome varies widely , but is
generally at least a few million base pairs. A genophore is the DNA of a prokaryote. It is
commonly referred to as a prokaryotic chromosome. The irregularly-shaped region within a
prokaryote cell where the genetic material is localized is called nucleoid.
The 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. In the case of prokaryotic chromosomes, the smallest known is about 160
kB, while the largest is about 10,000 kB.
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. In contrast to histones, the DNA-binding proteins of the nucleoid do not
form nucleosomes, in which DNA is wrapped around a protein core. Instead, these proteins
often use other mechanisms, such as DNA looping, to promote compaction.
The Genophore
A genophore is the DNA of a prokaryote. It is 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, but a chromosome
is additionally compacted through the use of chromatin. The genophore is circular in most
prokaryotes, and linear in very few. The circular nature of the genophore allows replication to
occur without telomeres. Genophores are generally of a much smaller size than Eukaryotic
chromosomes. A genophore can be as small as 580,073 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.
DNA supercoiling
The nucleoid is composed of DNA in association with a number of DNA-binding proteins

that help it maintain its structure. The protein HU non-specifically binds to DNA and bends
it, with the DNA apparently wrapping around the HU protein. Another protein found on DNA
is IHF, whose sequence is reminiscent of that of HU and is therefore evolutionarily related. It
also facilitates bending of DNA, but it does so by binding to specific DNA sites. A third
protein, H-NS, binds to DNA non-specifically and is apparently involved in compacting
DNA structure. It is found throughout the nucleoid and is likely the major DNA-binding
protein that organizes the chromosome. The nucleoid also contains a large amount of RNA
polymerase and RNA, as well as small amounts of many different proteins that regulate the
expression of specific genes. These seem not to perform any structural role, but reflect the
importance of RNA transcription in the nucleoid in growing cells.
The DNA double helix typically has a bit of twisting tension in the opposite direction of the
helix ladder (the twists typically "unwind" the left-handed DNA helix). Negative
supercoiling, as it is called, is produced by the action of enzymes termed topoisomerases.
Figure. Chromosome structural organization. A model of the overall structure of the

bacterial chromosome. (A) The unfolded, circular chromosome of E. coli depicted as a single
line for simplicity, though of course it is a double-stranded helix. (B) The DNA folded into
chromosomal domains by protein-DNA associations. The proteins are depicted as the black
circles, interacting with both the DNA and with each other. Six domains are shown, but the
actual number for E. coli is about 50. (C) Supercoiling and other interactions cause the
chromosome to compact greatly.
Archaeal genome
 The genome of the archaea is mostly held in a single circular DNA molecule.
 This DNA is not associated with histone proteins, but does have unique DNA binding
proteins.
 The genomic chromosome is attached to the cell membrane at one point just as in
bacteria.
 However, this genome is smaller than typical bacteria, it has gene sequences closer to
similar genes in eukaryotes rather than those of bacteria.
 The archaea also show insertion sites in their gene sequences for transposable
elements (transposons).
 The transcription of genes in archaea is accomplished by an RNA polymerase that is
very, very similar to that of RNA polymerase II of eukaryotic cells rather than
bacterial RNA polymerase.
 Moreover, it binds at TATA sequences, just like RNA polymerase II of eukaryotes.
 In addition to the genomic chromosome, the archaea have some additional small
circular DNAs known as replicons.
 These replicons have additional genes that are essential to the life of the archaean.
 In binary fission, there is no synapsis of homologous chromosomes, because archaea
are fundamentally haploid (they have only the one set of chromosomes).
 During this process there is no genetic recombination (there is no exchange of DNA
between one molecule and another).
 Just like bacteria, archaea do have parasexual recombination.
 Archaea produce pili for conjugation.
 Their tRNAs have a number of features that differ from all other living things.
 The tRNA molecules are important in decoding the message of DNA and in building
proteins.
 There are even features of archaeal tRNA that are more like eukaryotic critters than
bacteria. The same is true of their ribosomes. While bacterial ribosomes are sensitive
to certain chemical inhibiting agents, archaeal and eukaryotic ribosomes are not
sensitive to those agents. This may suggest a close relationship between Archaea and
eukaryotes.
Cell partitioning
The stable maintenance of low-copy-number plasmids in bacteria is actively driven by
partition mechanisms that are responsible for the positioning of plasmids inside the
cell. Partition systems are ubiquitous in the microbial world and are encoded by many
bacterial chromosomes as well as plasmids. These systems, although different in
sequence and mechanism, typically consist of two proteins and a DNA partition site,
or prokaryotic centromere, on the plasmid or chromosome. One protein binds site-
specifically to the centromere to form a partition complex, and the other protein uses
the energy of nucleotide binding and hydrolysis to transport the plasmid, via
interactions with this partition complex inside the cell.
MukF are proteins involved in chromosome condensation, segregation and cell cycle
progression. MukE along with MukF interact with MukB in vivo forming a complex,
which is required for chromosome condensation and segregation in Escherichia coli.
The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other
prokaryotes where MukB is the homologue of SMC. ScpA and ScpB have little
sequence similarity to MukE or MukF, though they are predicted to be structurally
similar, being predominantly alpha-helical with coiled coil regions.
mukB mutants of Escherichia coli are defective in the correct partitioning of

replicated chromosomes. This results in the appearance of normal-sized anucleate
(chromosome-less) cells during cell proliferation. Based on the nucleotide sequence
of the mukB gene, the MukB protein of 177 kDa was predicted to be a filamentous
protein with globular domains at the ends, and also having DNA binding and
nucleotide binding abilities.
In C. crescentus, the genes encoding the chromosome partitioning proteins, Par A and
Par B, are essential. Deplition of Par B results in smooth filamentous cells in which
DNA replication continued. The formation of FtsZ at the midcell was blocked in cells
lacking Par B. Recent experiments have shown that Par A and Par B, the cellular
homologous of partitioning proteins found in some phage and unit-copy plasmids,
may have a role in partitioning bacterial chromosomes. It has been demonstrated that
mutants at three loci, par A, par B and cis acting loci par S (sopABC respectively, in F
factor) result in plasmid partitioning defect. Par A is an ATPase, whose activity is
stimulated by the presence of Par B bound to DNA. Lack of Par B blocks FtsZ ring
formation. Par B is required for either the synthesis of FtsZ or the assembly of FtsZ
ring,but not for division at previously exsisting sites.

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Bacterial Genome

The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA,

The nucleoid (meaning nucleus-like) is an irregularly-shaped region within the cell of a

The nucleoid is composed of DNA in association with a number of DNA-binding proteins

Figure. Chromosome structural organization. A model of the overall structure of the

mukB mutants of Escherichia coli are defective in the correct partitioning of

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