Two basic differences between prokaryotic and eukaryotic genome are noteworthy. First, all prokaryotic genomes are made up of a single DNA molecule, and all genetic information is encoded in this molecule only. In most eukaryotes, information is distributed in a number of DNA molecules termed as chromosomes. This is because the average size of genome is much less in bacteria (about 1000 times smaller) than average eukaryotic genome. It is highly unlikely that such a large DNA can be packed in a single molecule, which will create problems during packing and unwinding of DNA in eukaryotes. Prokaryotes, with higher genomic economy and much less junk DNA can store all the information in a single molecule. Second, difference lies in the manner of genomic organization. In eukaryotes, genome organization is hierarchical having different levels of genome organization. Prokaryotes, on the other hand organize their genome into domains of topologically isolated DNA loops connected to a central region by DNA binding proteins. The eukaryotic genetic material is protected from the cytosolic environment by binding with histone and non-histone proteins,
as well as by nuclear envelope. In prokaryotes, the organized DNA loops are in direct contact with the cytoplasm. Higher concentration of cellular proteins than DNA in cytosol helps in compaction of DNA through an energetically favourable process. It has been observed that nucleoid may contain more than one
topologically isolated domains of size about 10 Kb, maintained by DNA binding protcins. Twisting and turning of DNA double helix into several ioops arc achieved by help of DNA topoisomerases like DNA gyrase, Topo I and Topo IV in the model prokaryote E. coil that induce and relax negative supercoiling
respectively thereby making the prokaryotic genome underwound. Apart from the domain binding proteins, other proteins known as Structural Maintenance of Chromosome (SMC) proteins are involved in maintenance of nucleoid structure. Instead of being a highly compressed structure, bacterial nucleoid is
loosely compacted to provide easy access for replication and transcription.
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