Surprises Revealed by Bacterial Genome Sequences
In the past few years, the number of bacterial genomes sequenced or in the process of being sequenced has increased rapidly. The genome sequence has already been completed for several pathogenic bacteria, and a number of others are in progress. The genomes of these pathogens have revealed a number of suprises, as much by what has been found as by what has not been found.

Borrelia burgdorferi, the causative agent of Lyme disease, has a very interesting genome composed of a linear chromosome of approximately one megabase in size and numerous linear and circular plasmids with a combined size of more than 500 kilobases. Some Borrelia isolates contain up to twenty different plasmids. These plasmids have a copy number of approximately one per chromosome, and different plasmids may share regions of homologous DNA. Long term culture of B. burgdorferi can result in loss of some plasmids and inability to infect lab animals, suggesting that the plasmids may encode certain virulence factors required for infection. In addition, these plasmids contain genes that are usually found on the chromosome. It was expected that the genome sequence of this microbe would reveal numerous toxin and virulence genes and two-component signal transduction pathways. Instead, a large number of duplicated lipoproteins unique to Borrelia were discovered. Although the function of these lipoproteins is unknown, it is thought that they may be involved in antigenic variation and evasion of the immune system. No genes for cellular biosynthetic reactions, such as synthesis of amino acids, fatty acids, enzyme cofactors, and nucleotides were found, reminiscent of the genome of Mycoplasma genitalium, a distantly related pathogenic bacterium. The parallels between the B. burgdorferi and M. genitalium genomes extend to other aspects, such as transporters, limited metabolic capacity, and the lack of a respiratory electron transport chain.

The second pathogenic spirochete genome to be sequenced was that of Treponema pallidum, the causative agent of syphilis. The completion of the T. pallidum genome sequence was a major step forward for the study of this organism, since attempts to culture it in vitro have been unsuccessful, making it difficult to apply the traditional tools of microbiology. Like B. burgdorferi and M. genitalium, T. pallidum is metabolically crippled, lacking the enzymes for the biosynthesis of enzyme cofactors, fatty acids, and nucleotides. Instead, this obligate pathogen relies on its host for many of its needs. Approximately 5% of its genes encode transport proteins to obtain nutrients such as amino acids and carbohydrates from the host cell. Like B. burgdorferi and M. genitalium, the T. pallidum genome encodes for a large number of lipoproteins.

The genome sequence of Chlamydia trachomatis, an obligate intracellular pathogen that is the cause of the most common bacterial sexually transmitted disease in the United States, revealed several surprises. It was previously thought that Chlamydia, lacked peptidoglycan, the principle target of penicillin; yet penicillin was still able to inhibit chlamydial cell division. However, the genome sequence revealed that Chlamydia contains a full complement of peptidoglycan synthesis genes. Several genes thought to be present in all bacteria were not found. For example, a gene encoding FtsZ was not found. FtsZ is a protein previously thought to be required for septum formation during cell division in prokaryotes. Another surprising finding from the genome sequence was that Chlamydia appears to have acquired an unusual number of eukaryotic genes. Many of these genes more closely resemble those of plants than those of animals, leading to the speculation that the evolution of Chlamydia as an intracellular pathogen started with an opportunistic interaction with an amoebal host with "plant-like" genes. Perhaps the most unusual findings were from the genome sequence of Rickettsia prowazekii, the causative agent of louse-borne epidemic typhus. Like the other intracellular pathogens discussed above, R. prowazekii has a limited number of biosynthetic genes. The R. prowazekii genome has a large fraction (24%) of non-coding DNA sequences, compared to an average of 9% for other sequenced bacterial genomes. These non-coding regions are believed to contain gene remnants that have been degraded by mutation but have not yet been removed from the genome. This is thought to be an example of reductive evolution, the elimination of genes that are no longer essential. As genes essential for a free-living mode of existence are lost, the microbe becomes dependent on its host and obligate parasite. Another fascinating finding is that R. prowazekii is closely related to mitochondria. Phylogenetic analyses suggest that the Rickettsia and mitochondrial genomes descended independently from an alpha-proteobacterial ancestor, each undergoing a separate process of reductive evolution.

These are just a few examples of the surprising findings yielded by microbial genome sequences. Although genome sequencing has answered some questions, many new questions and avenues for research have been opened. Genome sequences can reveal much about an organism, and comparisons among microbial genome sequences may help define those genes that are required for a free-living versus intracellular mode of life.