Scientists Finish Sequencing Genome of Oral Pathogen

Antonie van Leeuwenhoek, the renowned “father of microbiology,” peered through a microscope and noticed an unusual thread-like oral spirochete, a type of free-living bacterium, that would later receive the name Treponema denticola ( T. denticola ). Now, more than 300 years later, a team of scientists reports online in the journal Proceedings of the National Academy of Sciences ( PNAS ) that it has finished assembling the complete 2.8 million bases, or units of DNA, of Van Leeuwenhoek's microbe.

The lead authors, Drs. Ian Paulsen and Rekha Seshadri at The Institute for Genomic Research (TIGR) in Rockville , Maryland , note that although microbial genomes are now routinely sequenced, this organism could prove particularly interesting. They state that T. denticola is associated with periodontal, or gum, disease, which affects an estimated 200 million Americans. Previous studies indicate T. denticola aggregates in the mouth with Porphyromonas gingivalis , which has long been suspected as one of the main causes of periodontal disease. Because the genome of P. gingivalis already has been fully sequenced, today's paper will allow scientists to more systematically study how these oral pathogens interact to cause disease. Such studies could provide precise molecular clues on where to target new and potentially more effective therapies to prevent periodontal disease.

In addition, the authors say T. denticola could serve as an ideal prototype organism to study the biology of spirochetes in general, which include human pathogens such as Treponema pallidum , which causes syphilis, and Borrelia burgdorferi , the source of Lyme disease. “Spirochetes are notoriously difficult to culture,” said Dr. Ian Paulsen, who led the sequencing project at TIGR. “With the full DNA sequence of T. denticola , scientists now have an excellent point of reference to study the biology of spirochetes, allowing them to define their basic biology, as well as compare the evolutionary adaptations that T. denticola and other organisms have made to survive in their own unique environment.”

The T. denticola sequence is publicly available at GenBank ( http://www.ncbi.nlm.nih.gov/Genbank/index.html ) under accession number AE017226 . The project was supported by NIH's National Institute of Dental and Craniofacial Research.

T. denticola inhabits the mouth as a member of the complex microbial ecosystem, called the oral biofilm. In this dynamic environment of over 500 known micro-organisms, scientists have long thought that the T. denticola genome might provide an interesting glimpse into the molecular dynamics of the oral biofilm and issues such as how bacteria attach in clusters, known as coaggregation, and exchange genetic information, called gene transfer.

As reported in PNAS , T. denticola appears to have lived up to its advance billing. The authors found that T. denticola contains a predicted total of 2,786 genes, or, as is now the term in genomic studies, Aopen reading frames likely to encode proteins,” or CDSs. Interestingly, about one in four of these CDSs is unique, meaning similar genes have not been seen previously in other organisms. Their uniqueness suggests that studying the genome of T. denticola could lead to novel insights into microbial biology in general. When compared to other sequenced bacteria, T. denticola, for example, has an abundance of genes encoding drug efflux pumps, special membrane pumps that the bacteria use for survival in the competitive biofilm. Further research is needed, but this advantage for T. denticola might one day also be a target for innovative therapies.

The genome of T. denticola is much larger than that of T. pallidum , the cause of syphilis, which contains circa 1 million bases, and the two share only about 25 percent of their genes. This led the scientists to believe T. denticola has both lost and gained genes during evolution. The lost genes appear to be involved in basic metabolic functions and transport, while the functions of the acquired genes are still largely unknown. “Sequencing the genome does not provide all the answers, but it leads you to the questions you should be asking. With the genomic information, you can do a systematic investigation of the different genes and discover why they are present in this specific organism,” Paulsen said.

The scientists also found that 618 of T. denticola 's genes are conserved, or shared, among other known spirochetes. These genes are mostly involved in survival and maintenance, such as energy metabolism and DNA repair. Some genes specific to spirochetes are not seen in other related micro-organisms, and may be fundamental to these organisms.

Sequencing the T. denticola genome proved, at times, to be rather complex and was aided by efforts at both TIGR and its collaborators. These collaborators included Drs. Steve Norris at the University of Texas in Houston and George Weinstock at Baylor College of Medicine in Houston .

Even with this team approach, the project took about 18 months to complete, with much of that time spent grappling with tough-to-sequence, high-repeat regions. “However, with the refined techniques of today,” added Paulsen, “generating a draft sequence of an organism like T. denticola could be done in one day, if we put all of our capacity on it.”