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Prokaryotic Chromosome

genetic bacterial coli dna species

The bacterial or prokaryotic chromosome differs in many ways from that of the eukaryote. The term "eukaryote" comes from the Greek and means "true nucleus." Eukaryotic cells have a double membrane (the nuclear membrane) surrounding the nucleus, the organelle that contains several chromosomes. In contrast, the term "prokaryote" means "primitive nucleus," and, indeed, cells in prokaryotes have no nucleus. Instead, the prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane.

This dispersed chromosome is called the bacterial "nucleoid," which can be seen in electron micrographs of thin sections, as shown in Figure 2. Although bacteria (now called eubacteria) are highly diverse, the prototypical bacterial species is Escherichia coli, which has served as a model organism for genetic, biochemical, and biotechnological research for many decades.

The E. coli chromosome is a single circle.

Because the single DNA molecule forming the chromosome is so long (about 4.6 million base pairs), it is easily broken when researchers try to isolate it. However, in the early 1960s, the Australian biochemist John Cairns was able to gently lyse E. coli cells without breaking the chromosome. He was interested in chromosomal replication and had labeled the DNA with tritium (3H), a radioactive form of hydrogen. Autoradiograms of the DNA demonstrated that the bacterial chromosome is a circular molecule. While the vast majority of bacterial species possess a single unique chromosome, there are a few rare species, Figure 1. The circular genetic map of the Escherichia coli chromosome. The map is divided into 100 map units, and representative genes are shown. The lac operon is at approximately 8 minutes. The origin of replication (not shown) is at 83.5 minutes. Based on Ingraham, 2000. such as Vibrio cholerae (the agent that causes the disease cholera) and Deinococcus radiodurans, that have two different chromosomes.

It is also quite common for bacterial species to possess extrachromosomal genetic elements called plasmids. These are small, circular DNA molecules which, when present, vary in number from one to about thirty identical copies per cell. Plasmids include the fertility factor (F+ plasmid), described below, as well as plasmids that carry drug-resistance genes. Indeed, these drug-resistance plasmids may be passed from species to species and are a major problem in the spread of antibiotic resistance. Whereas most bacteria that contain plasmids have just a single kind of plasmid, some bacterial species simultaneously possess a number of different plasmids, each of which, in turn, is present in varying numbers within the bacterial cell.

The bacterial chromosome is condensed into chromosomal domains.

The bacterial chromosome must be tightly packed to fit into the small volume of the bacterial cell. Figure 3 shows the relative sizes of the unfolded chromosome and the E. coli cell. During the 1980s, techniques were developed to isolate intact bacterial nucleoids by gentle lysis, under conditions that prevented the DNA of the chromosome from uncoiling. These isolated Figure 2. A transmission electron microscope image of Escherichia coli magnified approximately 20,000 times. nucleoids were highly condensed into a very compact structure, as shown in Figure 4.

Compacting the DNA involves supercoiling, or further twisting the twisted chromosome. The chromosome's fifty or so DNA domains are held together by a scaffold of RNA and protein, and the entire nucleoid is attached to the cell membrane. This membrane attachment aids in the segregation of the chromosomes after they replicate in preparation for cell division. Bacteria lack the histone proteins that are found bound to the DNA and that form the nucleosomes of eukaryotic chromosomes. However, it is believed that polyamines (organic molecules with multiple NH2 amine groups) such as spermidine, as well as some basic proteins, aid in compacting the bacterial chromosome. These basic proteins have a net positive charge that bind them to the negative charge of the phosphates in the DNA backbone.

Replication of the circular chromosome begins at a single point, called OriC, and proceeds in both directions around the circle, until the two replication forks meet up. The result is two identical loops. Replication takes approximately forty minutes.

The E. coli genetic chromosome.

The field of bacterial genetics began in 1946, even before the structure of DNA was determined, with the discovery by the geneticists Joshua Lederberg and Edward Tatum at the University of Wisconsin of sex in bacteria, in the form of conjugational genetic exchange between E. coli bacteria. In the conjugation process, a fertility Figure 3. Relative size of an E. coli cell and its chromosome. factor (F plasmid) recombines with (splices itself into) the E. coli chromosome at a specific site. It then acts as a "molecular motor" to drive the transfer of the entire E. coli chromosome to a recipient (F) cell. The transferred molecule can then recombine with the host chromosome, increasing the genetic diversity of the host. Transferring the entire chromosome takes approximately one hundred minutes, and thus the genetic map is divided into one hundred minutes (which were later defined as one hundred map units). As more and more genetic markers were found and mapped, it became apparent that the genetic chromosome map formed a circle, as shown in Figure 1.

The DNA sequence of the E. coli chromosome.

E. coli was chosen as one of the genetic model organisms whose chromosome was to be sequenced as part of the Human Genome Project. Although it was not the first bacterial species to be completely sequenced, it was one of the most important ones. In 1997, Fredrick Blattner of the University of Wisconsin and colleagues published the sequence of 4,639,221 base pairs of the K-12 laboratory strain. E. coli is estimated to have 4,279 genes.

Many sets of genes on the E. coli chromosome are organized into operons. An operon is a set of functionally related genes that are controlled by a single promoter and that are all transcribed at the same time.

Comparative bacterial genomes.

As of June 2002, the genomes of sixty-five different bacterial species had been completely sequenced. Several of these are listed in Table 1, along with the genomes' size and number of genes. Many of the species sequenced are human pathogens. Having the DNA sequence will prove useful in designing drugs and antibiotics to combat infections and bacterial toxins. DNA sequences may be found on the Internet, at the Genome Web site of the National Center for Biotechnology Information.

Table 1.

Bacterial species Chromosome size (base pairs) Number of genes Year sequence completed
Haemophilus influenzae 1,830,138 1714 1995
Mycoplasma genitalium 580,074 480 1995
Synechocystis sp. 3,573,470 3167 1996
Mycoplasma pneumoniae 816,394 1054 1996
Helicobacter pylori 1,667,867 1576 1997
Escherichia coli 4,639,211 4279 1997
Bacillus subtilis 4,214,814 4112 1997
Borrelia burgdorferi 910,724 851 1997
Aquifex aeolicus 1,551,335 1529 1998
Mycobacterium tuberculosis 4,411,529 3927 1998
Treponema pallidum 1,138,011 1036 1998
Rickettsia prowazekii 1,111,523 835 1998
Chlamydia trachomatis 1,042,519 895 1998
Chlamydiophila pneumonia 1,230,230 1054 1999
Thermotoga maritima 1,860,725 1858 1999
Campylobacter jejuni 1,641,481 1654 2000
Neisseria meningitidis 2,272,351 2079 2000
Buchnera sp. 640,681 564 2000
Bacillus halodurans 4,202,353 4066 2000

Figure 4. Model of the condensed bacterial chromosome. The circular DNA molecule (a) is folded into several domains (b). Seven domains are shown, but in the cell there are approximately fifty. These domains are held together by RNA and proteins. The DNA is further condensed by supercoiling (c). If the DNA backbone is nicked by a nuclease, the DNA domain opens (d). Adapted from Pettijohn, David E., 1996.

Minimal-gene-set concept.

One of the interesting features of studying bacterial chromosomes has been the concept of the minimal number of genes a cellular life form would need to survive. (This excludes viruses and viroids, which need living cells of a host in which to carry out their life cycle.) We know from the sequence of the Mycoplasma genitalium chromosome, the smallest genome sequenced so far, that the upper limit of the minimal gene set is 480, as shown in Table 1. After the sequence of the Haemophilus influenzae chromosome was completed, a comparison of the genes that were identical (or highly conserved) in the two species led to an estimate of 256 as the minimal gene set. The National Institutes of Health scientist Eugene Koonin, with the availability of many more sequenced species, has also estimated a minimal size of about 250 genes. It may be possible in the future for scientists to construct a minimal life-form by removing nonessential genes from an organism such as M. genitalium.

Ralph R. Meyer


Berlyn, Mary K. B., K. Brooks Low, and Kenneth E. Rudd. "Linkage Map of Escherichia coli K-12." In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., Frederick C. Neidhardt, et al., eds. Washington, DC: ASM Press, 1996.

Ingraham, John L., and Catherine A. Ingraham. Introduction to Microbiology, 2nd ed. New York: Brooks/Cole, 2000.

Koonin, Eugene V. "How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept." Annual Review of Genomics and Human Genetics 1 (2000): 99-116.

Pettijohn, David E. "The Nucleoid." In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., Frederick C. Neidhardt et. al. eds. Washington, DC: ASM Press, 1996.

Internet Resource

Entrez-Genome. National Center for Biotechnology Information. <http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html>.

Artificial Chromosomes - Natural Chromosome Function, Yeast Artificial Chromosomes, Mammalian Artificial Chromosomes [next] [back] Eukaryotic Chromosome - Basic Organization, Higher-order Organization, Heterochromatin Versus Euchromatin, Cytological Features, Polytene Chromosomes

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over 9 years ago

I am looking for information on the membrane attachment of the nucleoid: what proteins form the complexes and where are they on the genome? I have been scouring journal articles but I don't know enough to know what I'm looking for yet!

Thanks in advance with luck...