Most of the prokaryotic chromosomes have single-stranded or a double-stranded DNA. They have a linear or a circular structure. A nucleoid is a dense clump in the bacterial and the archaeal cells. The viruses have a double-stranded or a single-stranded DNA or RNA. Most of the viruses possess a single chromosome with a segmented genome. Bacteria consist of one or few chromosomes. The DNA in the E. coli bacteria is in a supercoiled form. Its length is a thousand times that of its cell. If we try turning the one end of an E. coli DNA segment to the left in the opposite direction of the twists, the strands unwind a bit. A negative supercoil gets produced as a result of the force. Hence, think the DNA double helix to be a spiral staircase. It turns in a clockwise direction. A positive supercoil gets produced when you try turning the DNA by one or more complete turn. A class of enzymes known as topoisomerases controls the process of DNA supercoiling.
The enzyme creates or removes supercoiling in the duplex DNA by creating transitory breaks in the DNA strands. The supercoiling is a fundamental property of the DNA and the chromatin structures. The DNA gets organized in loop domains in the E. coli bacteria. The bacterial chromosomal DNA gets a thousandfold compact structure forming looped domains. In E. coli, each domain consists of a 40Kb loop coiled negatively. An E. coli genome consists of approximately a hundred domains. The nucleoid isolation studies revealed that the E. coli DNA does not freely rotate once a break gets introduced into the DNA. Introduction of breaks affects the rotation of the double helix. Hence, it also affects the supercoiling property of the DNA. There arises a loss of DNA supercoiling due to the breaks. It happens mainly because the DNA is not alone, but attached to proteins. The structure of an E. coli nucleoid seems to be very interesting. The supercoiled DNA loops radiate from the central protein core. The protein component consists of DNA gyrase and DNA topoisomerase-I. They help in maintaining the supercoiled state of the DNA. The E. coli consists of total 40 to 50 supercoiled DNA loops. Each loop consists of 100 Kb supercoiled DNA. It is the amount of DNA that unwinds after introducing a break.
Image: Packaging of prokaryotic chromosomes (Looped domains in E. coli)
The packaging proteins of the bacterial DNA:
The packaging of the DNA involves four main proteins. HU is the most abundant packaging protein. It is a histone-like protein. An E. coli cell consists of 60,000 HU proteins. The wrapping of the DNA among HU proteins determines the level of supercoiling.
Comparison studies distinguishing the relaxed DNA from the supercoiled DNA:
These studies compare the relationship between the binding of the trimethylpsoralen and the dosage of the radiation. Trimethylpsoralen is also known as Trioxysalen. It is a furanocoumarin and a psoralen derivative obtained from a plant source. It creates inter-strand crosslinks. The experiment involves photoactivation of DNA. A pulse of light with a wavelength of 360 nm participates in the photoactivation. Trimethylpsoralen binds to double-stranded DNA due to photoactivation. The rate of binding is directly proportional to the degree of torsional stress possessed by the molecule. Next, the assay involves measuring the degree of supercoiling. The E. coli cells get irradiated for introducing breaks in the DNA. The binding of the trimethylpsoralen depends on the radiation dose. The relation between the dose of radiation involves a direct proportion of the binding.
An advantage of an E. coli nucleoid organized in the domain is that it protects the nucleoid from complete damage occurring due to breaks. The presence of the domains is very important for the presence of the nucleoid. If there were no domains, the radiations would have destroyed the nucleoid completely.
Borrelia and Agrobacterium chromosomes:
Borrelia burgdorferi consists of an increased number of linear chromosomes. It is an organism causing Lyme disease. The linear molecules have free ends. These structures require terminal ends similar to telomeres. They protect the DNA from breaks. Borrelia and Agrobacterium DNA have real chromosome ends. The Borrelia also contains few circular molecules. Agrobacterium studies reveal the presence of one linear and one circular chromosome.
The core genome and the mobile elements Salmonella are good to study. All the Salmonella strains have a single chromosome with core genes.
Multipartite genome in bacteria:
The multipartite genomes are those genomes divided into two or more DNA molecules. For example, Vibrio cholera consists of two circular molecules with the main chromosome and a megaplasmid. In such cases of the multipartite genomes, the difference between the genuine part of the genome and the plasmid becomes difficult to identify. Certain bacteria consist of more than one chromosome with a larger primary chromosome and conserved housekeeping genes. Plasmids are known as small circular DNA capable of replicating autonomously. They coexist with the main chromosome. Multipartite genomes in the bacteria arise due to the origin of additional chromosomes. They arise due to single chromosome splitting, duplication or other factors.
References:
[1] Genes And Genomes, Maxine Singer, Paul Berg
[2] Genomes, T.A. Brown
[2] Genomes, T.A. Brown
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