Chromosome, Prokaryotic

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, 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 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 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.

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.

see also Antibiotic Resistance; Archaea; Chromosome, Eukaryotic; Conjugation; Escherichia coli (E. coli bacterium); Eubacteria; Human Genome Project; Operon; Replication.

Ralph R. Meyer

Bibliography

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>.

Chromosomes, prokaryotic

The genetic material of microorganisms , be they prokaryotic or eukaryotic, is arranged in an organized fashion. The arrangement in both cases is referred to as a chromosome.

The chromosomes of prokaryotic microorganisms are different from that of eukaryotic microorganisms, such as yeast , in terms of the organization and arrangement of the genetic material. Prokaryotic DNA tends to be more closely packed together, in terms of the stretches that actually code for something, than is the DNA of eukaryotic cells. Also, the shape of the chromosome differs between many prokaryotes and eukaryotes . For example, the deoxyribonucleic acid of yeast (a eukaryotic microorganism) is arranged in a number of linear arms, which are known as chromosomes. In contrast, bacteria (the prototypical prokaryotic microorganism) lack chromosomes. Rather, in many bacteria the DNA is arranged in a circle.

The chromosomal material of viruses is can adopt different structures. Viral nucleic acid, whether DNA or ribonucleic acid (RNA ) tends to adopt the circular arrangement when packaged inside the virus particle. Different types of virus can have different arrangements of the nucleic acid. However, viral DNA can behave differently inside the host, where it might remain autonomous or integrating into the host's nucleic acid. The changing behavior of the viral chromosome makes it more suitable to a separate discussion.

The circular arrangement of DNA was the first form discovered in bacteria. Indeed, for many years after this discovery the idea of any other arrangement of bacterial DNA was not seriously entertained. In bacteria, the circular bacterial chromosome consists of the double helix of DNA. Thus, the two strands of DNA are intertwined while at the same time being oriented in a circle. The circular arrangement of the DNA allows for the replication of the genetic material. Typically, the copying of both strands of DNA begins at a certain point, which is called the origin of replication. From this point, the replication of one strand of DNA proceeds in one direction, while the replication of the other strand proceeds in the opposite direction. Each newly made strand also helically coils around the template strand. The effect is to generate two new circles, each consisting of the intertwined double helix.

The circular arrangement of the so-called chromosomal DNA is mimicked by plasmids . Plasmids exist in the cytoplasm and are not part of the chromosome. The DNA of plasmids tends to be coiled extremely tightly, much more so than the chromosomal DNA. This feature of plasmid DNA is often described as supercoiling. Depending of the type of plasmid, replication may involve integration into the bacterial chromosome or can be independent. Those that replicate independently are considered to be minichromosomes.

Plasmids allow the genes they harbor to be transferred from bacterium to bacterium quickly. Often, such genes encode proteins that are involved in resistance to antibacterial agents or other compounds that are a threat to bacterial survival, or proteins that aid the bacteria in establishing an infection (such as a toxin).

The circular arrangement of bacterial DNA was first demonstrated by electron microscopy of Escherichia coli and Bacillus subtilus bacteria in which the DNA had been delicately released from the bacteria. The microscopic images clearly established the circular nature of the released DNA. In the aftermath of these experiments, the assumption was that the bacterial chromosome consisted of one large circle of DNA. However, since these experiments, some bacteria have been found to have a number of circular pieces of DNA, and even to have linear chromosomes and sometimes even linear plasmids. Examples of bacteria with more than one circular piece of DNA include Brucella species, Deinococcus radiodurans, Leptospira interrogans, Paracoccus denitrificans, Rhodobacter sphaerodes, and Vibrio species. Examples of bacteria with linear forms of chromosomal DNA are Agrobacterium tumefaciens, Streptomyces species, and Borrelia species.

The linear arrangement of the bacterial chromosome was not discovered until the late 1970s, and was not definitively proven until the advent of the technique of pulsed field gel electrophoresis a decade later. The first bacterium shown to possess a linear chromosome was Borrelia burgdorferi.

The linear chromosomes of bacteria are similar to those of eukaryotes such as yeast in that they have specialized regions of DNA at the end of each double strand of DNA. These regions are known as telomeres, and serve as boundaries to bracket the coding stretches of DNA. Telomeres also retard the double strands of DNA from uncoiling by essentially pinning the ends of each strand together with the complimentary strand.

There are two types of telomeres in bacteria. One type is called a hairpin telomere. As its name implies, the telomers bends around from the end of one DNA strand to the end of the complimentary strand. The other type of telomere is known as an invertron telomere. This type acts to allow an overlap between the ends of the complimentary DNA strands.

Replication of a linear bacterial chromosome proceeds from one end, much like the operation of a zipper. As replication moves down the double helix, two tails of the daughter double helices form behind the point of replication.

Research on bacterial chromosome structure and function has tended to focus on Escherichia coli as the model microorganism. This bacterium is an excellent system for such studies. However, as the diversity of bacterial life has become more apparent in beginning in the 1970s, the limitations of extrapolating the findings from the Escherichia coli chromosome to bacteria in general has also more apparent. Very little is known, for example, of the chromosome structure of the Archae, the primitive life forms that share features with prokaryotes and eukaryotes, and of those bacteria that can live in environments previously thought to be completely inhospitable for bacterial growth .

See also Genetic identification of microorganisms; Genetic regulation of prokaryotic cells; Microbial genetics; Viral genetics; Yeast genetics