Prokaryote genome

Prokaryotic genome organization

1. PRESENTATION Genome Organization In Prokaryotes

2. Introduction The term “prokaryote” means “primitive nucleus”. Cells have no nucleus i.e., prokaryotic chromosome is dispersed within the cell and is not enclosed by separate membrane. Prokaryotes are monoploid i.e., they have only one set of genes. In most viruses and prokaryotes, the single set of genes is stored in a single chromosome. Prokaryotic genomes are exemplified by the E.coli chromosome. The bulk of the DNA in E. coli cells consists of a single closed-circular DNA molecule of length 4.6 million base pairs.

3. There are two very different groups of prokaryotes, distinguished from one another by characteristic genetic and biochemical features: the  B acteria , which include most of the commonly encountered prokaryotes such as the gram-negatives (e.g.  E.   coli ), the gram-positives (e.g.  Bacillus subtilis ), the cyanobacteria (e.g.  Anabaena ) and many more The A rchaea , which are less well-studied, and have mostly been found in extreme environments such as hot springs, brine pools and anaerobic lake bottoms.

4. PROKARYOTE GENOME SIZE Bacteria Size( Mbp ) Escherichia coli 4.64 Bacillus subtilis 4.20 Streptococcus 1.85 pyrogenes Mycobacterium 0.58 genitalium Archaea Size( Mbp ) Methanococcus 1.66 jannaschii Sulfolobus 2.25 solfactaricus Pyrococcus 1.75 furiosus

5. PROKARYOTIC CELL

6. Genome Organization Each bacterial chromosome is made by a single circular DNA molecule. Usually each cell contain one single copy of each chromosome. The genetic material can be seen as a fairly compact clump (or series of clumps) that occupies about a third of the volume of the cell named NUCLEOID. The DNA of these loops is not found in the extended form of a free duplex, but instead is compacted by association with proteins. Loop domain in bacterial genome contribute to the packaging. To fit the genome in a bacterial cell the DNA undergoes supercoiling.

7. The Genophore A   genophore  is the DNA of a prokaryote , 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 . The genophore is circular in most prokaryotes. The circular nature of the genophore allows replication to occur without telomeres. Genophores are generally of a much smaller size than Eukaryotic chromosomes and can be as small as 0.58 million 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.

8. Plasmid Besides chromosomes, some prokaryotes have smaller loops of DNA called  plasmids. M ay contain one or a few genes not essential for normal growth. Bacteria exchange these plasmids with other bacteria in a process known as  horizontal gene transfer (HGT) . E xchange of genetic material on plasmids provides microbes with new genes beneficial for growth and survival under special conditions. In some cases, genes obtained from plasmids may have clinical implications, encoding virulence factors that give a microbe the ability to cause disease or make a microbe resistant to certain antibiotics.

9. Nucleoid Nucleoid is composed of 60% DNA and small amount of RNA and protein. Proteins helping to maintain the supercoiled structure of the nucleic acid are known as  nucleoid proteins  or  nucleoid-associated proteins . T hese proteins often use mechanisms , such as DNA looping, to promote compaction. The nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural protein and RNA molecules as well as DNA supercoiling . The structure of the DNA in the nucleoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent influencing each other reciprocally.

10. DNA Supercoiling The term "supercoiling" means literally the coiling of a coil. DNA supercoiling is generally a manifestation of structural strain. Supercoiling occurs when the molecule relieves the helical stress by twisting around itself. Overtwisting leads to positive supercoiling, while undertwisting leads to negative supercoiling. If DNA is in the form of a circular molecule, or if the ends are rigidly held so that it forms a loop, then overtwisting or undertwisting leads to the supercoiled state.

11. Positive and Negative Supercoiling Positive supercoiling is the right-handed , double helical form of DNA. It is twisted tightly in a right handed direction until the helix creates knot. P ositive supercoiling is more condensed as the supercoil forms at the direction of DNA helix

12. Negative supercoiling is the left-handed, double helical form of DNA. Prokaryotes usually have negative supercoiled DNA. It is naturally prevalent as it prepares the molecule for processes that require separation of the DNA strands without the need of additional energy.

13. Enzymes Some enzymes like topoisomarase can relieve the stress. Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA. In prokaryotes, there are two major topoisomerases that act toward opposite direction. DNA gyrase is the only topoisomerase able to actively introduce negative supercoils into DNA molecules, in a reaction dependent upon ATP hydrolysis. In the absence of ATP, gyrase can relax supercoiled DNA . T opoisomerase I can relax negatively supercoiled DNA but not positively supercoiled DNA .

14. DNA supercoiling in prokaryotes and eukaryotes. Bacteria and some archaea have enzymes that allow them to introduce supercoils into DNA at the expense of ATP, which results in the formation of plectonemic structures.

15. DNA Loops DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons. In addition, instances of looped structures have been found in replication and in recombination in both prokaryotes and eukaryotes. The ability of DNA to form loops is affected by the distance between binding sites; by the DNA sequence, which determines deformability and bendability; and by the presence of other proteins that exert an influence on the conformation of a particular sequence. Alteration of the stability of DNA loops and/or protein- DNA binding by extra- or intracellular signals provides responsivity to changing metabolic or environmental conditions. The fundamental property of site-specific protein binding to DNA can be combined with protein-protein and protein-ligand interaction to generate a broad range of physiological states .

16. A model of the genome of E.coli . The chromosome is folded into ~100 loops which undergoes supercoiling. As a result, the chromosome becomes much shorter so that it is able to be packaged into the cell. When an endonuclease makes a cut in one strand of one domain only that becomes unfolded and enlarged while the other domains remains unaffected.

17. Comparison between Prokaryotic and Eukaryotic Chromosome Prokaryotic Chromosomes Many prokaryotes contain a single circular chromosome. Prokaryotic chromosomes are condensed in the nucleoid via DNA supercoiling and the binding of various proteins . Because prokaryotic DNA can interact with the cytoplasm, transcription and translation occur simultaneously. Most prokaryotes contain only one copy of each gene (i.e., they are haploid). Nonessential prokaryotic genes are encoded on extrachromosomal plasmids . Prokaryotic genomes are efficient and compact, containing little  repetitive and noncoding DNA. Eukaryotic Chromosomes Eukaryotes contain multiple linear chromosomes. Eukaryotic chromosomes are condensed in a membrane-bound nucleus via histones. In eukaryotes, transcription occurs in the nucleus, and translation occurs in the cytoplasm. Most eukaryotes contain two copies of each gene (i.e., they are diploid). Extrachromosomal plasmids are not commonly present in eukaryotes. Eukaryotes contain large amounts of noncoding and repetitive DNA . Introns are present.

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