Bacterial Nucleoid

The Nucleoid (Bacterial Chromosome)

Eukaryotic cells possess two or more chromosomes contained within a membrane-bound organelle called nucleus which lacks in prokaryotes. Exceptionally, membrane-bound DNA-containing regions have been found in two bacterial genera, namely, Pirellula and Gemmata. Pirellula has a single membrane that surrounds a region called pirellulosome which contains a fibrillar nucleoid and ribosome-like particles. The nuclear body of Gemmata obscuriglobus is delimited by two membranes.

However, the prokaryotes possess a single chromosome located in an irregular discrete region, namely, nucleoid (nuclear body, chromatin body, nuclear region are the other names used). Usually the bacteria (prokaryotes) contain single, circular, ds-DNA chromosome, but some have a liner DNA chromosome. Recently it has been discovered that some bacteria (e.g., Vibro cholerae possess more than one bacterial chromosome.

Nucleoids have been isolated intact and free from membranes. When chemically analysed, they are found composed of about 60% DNA, 30% RNA and 10% protein (mostly RNA polymerase) by weight. The DNA is looped and coiled extensively with the aid of RNA and nucleoid proteins which are different from the histone proteins occurring in eukaryotic nuclei and are recognized by different names such as HU, NS and DNA-binding protein-II. However, following two features of bacterial DNA are particularly distinctive:

(i) Lack of histone proteins. Contrary to the eukaryotic organisms in which the DNA is packaged by wrapping if around special beads of protein called histones to form structure called nucleosome, the monerans (prokaryotes) have no histone proteins and no nucleosome. (Ingle, 1986).

(ii) Lack of introns. Eukaryotic DNA, which codes for protein is interrupted by noncoding    sequences (introns). The latter are absent in bacteria (Ingle, 1986).

The closed circular DNA of E. coli (a rod-shaped cell about 2-6 μm long) measures approximately 1400μm having molecular weight 3 x 10⁹ daltons. Obviously, it is extremely efficiently packaged to fit within the nucleoid. The DNA is looped and coiled extensively with the aid of RNA and nucleoid proteins, as stated earlier. Worcel and Bury (1972) have proposed the structure of the coiled DNA of E. coli and showed as seven loops, each twisting into a superhelix

Diagrammatic representation of coiling and supercoiling of bacterial (E.coli) DNA (after Worcel and Burgi, 1972)

1.	Unfolded circular DNA	6.	Super-coiled
2.	Coiled	7.	DNA
3.	DNA	8.	Super Coiling
4.	Loop       5. RNA	9.	Superhelix

Electron microscopic studies have often shown that the bacterial chromosome is in contact with either the mesosome or plasmamembrane. This shows that the membranes may be involved in the separation of DNA into daughter cells during division. The nucleoid is observed as a coral-like (coralline) structure the branches of which spread and occupy most of the cytoplasmic part of the cell.

Plasmids

In addition to the nucleoid, bacterial cytoplasm normally contains one or more circular molecules of ds-DNA called plasmids (linear plasmids are also known). Naturally occurring plasmids vary in size from approximately 1 to more than 1000 kilobase pairs. The typical ds-DNA circular plasmid is less than 1/20 the size of the bacterial chromosome. Plasmids, the extra-chromosomal genetic materials, existing independently of the bacterial chromosome and are present in many bacteria (they are also present in some yeasts and other fungi). They replicate autonomously as they possess their own replication origins.

Because of the small size of plasmid DNA relative to the bacterial chromosome, the whole replication process takes place very quickly, perhaps in 1/10 or less of the total time of cell division cycle. Plasmids have relatively few genes, generally less than 30 and their genetic information is not essential for the bacteria because the latter lacking them function normally. Those plasmids that can reversibly integrate into the bacterial chromosome are called episomes. The plasmids share many characteristics with viruses.

Types of Plasmids.
(a) F-Plasmids tor F-factors)

These are the first described plasmids that play major role in conjugation in bacteria. It is a circular ds-DNA molecule of 99,159 base pairs. The genetic map of the F-plasmid is shown in One region of the plasmid contains genes involved in regulation of the DNA replication (rep genes), the other region contains transposable elements (IS3 Tn 1000, IS3 and IS2 gene involved in its ability to function as an episome, and the third large region, the tra region, consist of tra genes and possess ability to promote transfer of plasmids during conjugation. Example F-­plasmid of E. coli.

(b) R-Plasmids

These are the most widespread and well studied group of plasmids conferring resistance (hence called resistant plasmids) to antibiotics and various other growth inhibitors. R-plasmids typicallyhave genes that code for enzymes able to destroy and modify antibiotics.

Genetic Map of the F (Fertility Plasmid of Escherichia Coli. tea region contains tra genes involves in conjugative transfer; Ori T sequences is the origin of transfer during conjugation; transposable element region responsible for functioning as episome, and the rep genes regulate DNA replication.

Genetic map of the resistance plasmid R100. Cat = Chloramphenicol resistance gene; str = Streptomycin resistance gene; sul = sulfonamide resistance gene, mer = mercury ion resistance gene, IS = insertion sequences

They are not usually integrated into the host chromosome. Some R-plasmids possess only a single resistant gene whereas others can have as many as eight. Plasmid R 100, for example, is a 94.3 kilobase-pair plasmid that carries resistant genes for sulfonamides streptomycin and spectinomycin, chloramphenicol, tetracyclin etc. It also carries genes conferring resistance to murcury. Many R­-plasmids are conjugative and possess drug-resistant genes as transposable elements, they play an important role in medical microbiology as their spread through natural populations can have profound consequences in the treatment of bacterial infections.

(c) Virulence-Plasmids

These confer pathogenesity on the host bacterium. They make the bacterium more pathogenic as the bacterium is better able to resist host defence or to produce toxins. For example, Ti-plasmids of Agrobacterium tumefaciens induce crown gall disease of angiospermic plants: enterotoxilgenic strains of E. coli cause travelers diarrhea because of a plasmid those codes for an enterotoxin which induces extensive secretion of water and salts into the bowel.

(d) Col-Plasmids

These plasmids carry genes that confer ability to the host bacterium to kill other bacteria by secreting bacteriocins, a type of proteins. Bacteriocins often kill cells by creating channels in the plasmamembrane thus increasing its permeability. They also may degrade DNA or RNA or attack peptidoglycan and weaken the cell-wall. Bacteriocins act only against closely related strains. Col E1 plasmid of E. coli code for the synthesis of bacteriocin called colicins which kill other susceptible strains of E. coli.

Col plasmids of some E. coli code for the synthesis of bacteriocin, namely cloacins that kill Enterobacter species. Lactic acid bacteria produce bacteriocin NisinA which strongly inhibits the growth of a wide variety of gram (+) bacteria and is used as a preservative in the food industry.

(e) Metabolic Plasmids

Metabolic plasmids (also called degradative plasmids) possess genes to code enzymes that degrade unusual substances such as toluene (aromatic compounds), pesticides (2, 4-dichloro­phenoxy acetic acid) and sugars (lactose). TOL (= pWWO) plasmid of Pseudomonas putida is an example. However, some metabolic plasmids occurring in certain strains of Rhizobium induce nodule formation in legumes and carry out fixation bf atmospheric nitrogen