Bacterial Genomes

Genomes

All living organisms contain DNA. This amazing macromolecule encodes all of the information needed to program the cell's activities including reproduction, metabolism and other specialized functions. DNA is comprised of two strands of deoxynucleotides. Each deoxynucleotide contains a phosphate, a 5-carbon sugar (2-deoxyribose) and one of four nitrogenous bases: adenine, cytosine, thymine or guanine. The phosphate and sugar make up the backbone of each strand of DNA, while the bases are responsible for holding the two strands together via hydrogen bonds in a structure called the double helix (see figure above). The order of the bases in a DNA strand contains the coded genetic information. All of the DNA found in an organism is collectively referred to as the genome. The human genome is comprised of 23 pairs of linear chromosomes, and approximately 3000 megabases (Mb) of DNA, while thegenome of the bacterium Escherichia coli consists of a single 4.6 Mb circular chromosome. By studying the genomes of bacteria we are able to better understand their metabolic capabilities, their ability to cause disease and also their capacity to survive in extreme environments.Many of the well-studied bacterial model organisms, such as E. coli, have a single circular chromosome. However, advances in molecular genetics have shown that bacteria possess more complex arrangements of their genetic material than just a single circular chromosome per cell. Some bacterial genomes are comprised of multiple chromosomes and/or plasmids and many bacteria harbor multiple copies of their genome per cell. The following are a few examples of bacteria with unusual

Genome Terminology

Kb/Mb - A kilobase (Kb) is 1000 bases of DNA, while a megabase (Mb) is 1,000,000 bases.
Circular Chromosome ·The DNA is arranged in a closed circle, which is negatively supercoiled allowing for the compact nature of many bacterial genomes.
Linear Chromosome · A non-closed chromosome, which has inverted repeats at the ends, similar to teleomeres in eukaryotic chromosomes.
Plasmid · Extra-chromosomal DNA which replicates independently of the chromosome and regulates its own replication.
Megaplasmid · A very large plasmid ranging in size from 100- 1700 Kb.

Deinococcus radiodurans

Genomes

Deinococcus radiodurans was first discovered in 1956 by Arthur W. Anderson. While inspecting spoiled meat, he noticed reddish colonies forming despite the fact that the meat had been sterilized with megarads of radiation! This radiation resistant organism was given the name Deinococcus radiodurans - which literally means "strange berry that withstands radiation." Deinococcus radiodurans is able to survive radiation exposure up to 1,500,000 rads! That is 3,000 times greater than the amount of radiation exposure that would kill a human. Ionizing radiation makes double-strand breaks in the DNA. Cells have mechanisms to repair these lesions but if too many breaks are made, stitching together the DNA in the right order can overwhelm the cell·s DNA repair mechanisms. Somehow, D. radiodurans has the ability to repair a shattered genome. The genome of D. radiodurans is unusual in that it is composed of two chromosomes, a megaplasmid and a small plasmid. In addition, when D. radiodurans cells divide they do not completely separate from one another immediately and so cells often exist as tetrads (see photo for example). While the mechanisms by which D. radiodurans is able to survive high doses of radiation are still under investigation, it is hypothesized that by having multiple copies of its genome and by genetic exchange between cells in a tetrad, D. radiodurans is able to deal with multiple DNA breaks induced by high levels of radiation.

Azotobacter vinelandii

Genomes

Azotobacter vinelandii is a large, soil-dwelling, obligate aerobic bacterium capable of fixing nitrogen. In addition, A. vinelandii can metabolize a large number of carbohydrates, organic acids and alcohols. The number of genomes in an individual cell is dependent upon the growth stage of the cells. During exponential growth, A. vinelandii cells contain 2 to 4 copies of their chromosome. However, during stationary phase, the number of chromosomes in an individual cell can increase to 50-100. This unique plasticity in genome copy number is not well understood, and continued research is required to better understand the advantage of accumulating many chromosomes in these cells during stationary phase.

Buchnera spp.

Genomes

These bacteria are intracellular symbionts of certain aphid species. This mutualistic relationship between aphid and bacterium evolved millions of years ago. Although closely related to E. coli, Buchnera has a genome approximately one-seventh the size of the E. coli genome. In one Buchnera species, the genome is composed of one 640 kilobase (Kb) chromosome and two plasmids, which encode the biosynthetic pathways for several amino acids. It has been shown that the number of genome copies in Buchnera cells is related to the developmental stage of their host aphid; as an aphid enters into adulthood, the genomic copy number in individual Buchnera cells increases. As the aphid host ages, the genomic copy number in Buchnera decreases. It has been proposed that this fluctuation in copy number may be due to the bacterium purging itself of genomes with deleterious mutations, ensuring only viable chromosomes are transmitted to the next generation of aphids.

Agrobacterium tumefaciens

Genomes
Genomes

These ubiquitous, gram-negative, motile, rod-shaped soil bacteria are the causative agent of crown-gall disease in plants. Agrobacterium tumefaciens is referred to as a natural genetic engineer, as it is capable of transferring DNA from itself into plant cells. The approximately 5.7 megabase (Mb) genome is comprised of a circular chromosome, a linear chromosome and two plasmids. One of the plasmids, referred to as the Ti plasmid for Tumor Inducing plasmid, is responsible for A. tumefaciens virulence.

Epulopiscium spp.

Genomes

Epulopiscium spp are intestinal symbionts of certain species of surgeon fish belonging to the family Acanthuridae. Some morphotypes of Epulopiscium can attain lengths greater than 0.5 mm! This image is of DAPI stained Epulopiscium cells. DAPI is a DNA-specific stain, and all of the blue that you see in these cells is actually DNA. Preliminary results using real-time PCR suggest that Epulopiscium may contain tens of thousands of copies of its genome. This copy number is unprecedented in bacteria and may represent a cellular adaptation which allows Epulopiscium to maintain such a large cell size. By having thousands of copies of its genome, Epulopiscium may be able to synthesize macromolecules close to where they are needed in the cell, overcoming the constraints imposed by the diffusion coefficients of small molecules and biomolecules.

References

Websites of interest