Despite the plethora of microbial genome papers, most do little more than catalog genes and analyze results, says Hervé Tettelin, a microbial genomics investigator at the Institute for Genomic Research, Rockville, Md. They normally are presented, he says, as underpinnings for further inquiry. But that was not the case when Tettelin and coworkers set out to sequence a serogroup B strain of Neisseria meningitides--their goal was to find vaccine candidates. The resulting Hot Paper "is the first case of a whole genome sequence coming out with a very direct application," he says.1
Neisseria meningitidis lives peacefully in the nasopharynx until unknown factors conspire to make it cross the endothelial cell barrier, where it causes septicemia. From there, it may work its way into the meninges, with meningitis as a possible result. It is primarily a pathogen in infants, responsible for up to 5,300 cases worldwide per year, with 5% to 15% of cases resulting in death.
Working on the assumption that vaccine candidates will code for surface proteins, the team used software to scan the genome for motifs. The scan revealed approximately 600 proteins, which were separated into four functional sets: nutrient acquisition, host colonization, immune-system evasion, and toxin production.
FINDING A CANIDATE Reported in a separate paper, colleagues of Tettelin at the Siena, Italy, facility of Emeryville, Calif.-based Chiron cloned and purified those 600 proteins and then tested them in immunized mice to retrieve antibodies.2 They narrowed the vaccine candidates to 25 proteins that were well expressed on the bacteria and readily recognized by antibodies on the surfaces of whole cells. In addition, these antibodies would kill cells when administered along with the human complement. A survey across strains of N. meningitidis serogroup B showed that seven proteins were 100% conserved. "So we had seven candidates that people could use [in vaccine research]... as opposed to none that had turned up after several decades of classical research," says Tettelin. Those candidates are now being evaluated at Chiron for protective immunity in mice, and although he won't provide details, "I can tell you that they're looking good," he says.
ISLANDS IN THE STRAND The team also looked for genes that might contribute to pathogenicity. "Nothing is known about what turns [any] commensal bug into a pathogen, so using the genomic sequence, we tried to characterize all of the genes that would possibly be involved in such processes as crossing the endothelium and getting into the blood," says Tettelin.
Although the scans did not pinpoint any particular genes, a separate analysis did provide tantalizing hints that pathogenicity might be a result of horizontal gene transfer. The team looked for atypical base compositions in the genome and found four islands that stood out. One of them was a capsule locus, which frequently has a different composition than the rest of the genome. The other three seem likely candidates for horizontal transfer, because they contain a relatively small amount of the DNA motifs that the bacteria use to identify their DNA, says Tettelin. It is not clear what those regions code for, but two appear to be related to virulence, while the other is composed of completely unknown genes. "To maintain it in your DNA, there must be a [selective] pressure," says Tettelin. "The genes in those islands allow the pathogen either to survive in its human host or to have a growth advantage over other organisms ... so that's why [horizontal transfer] regions are interesting to look at. That's the beauty of genomics. Now, if investigators are interested in virulence they can go and target those genes that they had no clue about before."
Tettelin's team is still not sure what those virulent genes do, and the answer could have important healthcare implications, as N. meningitidis lives harmlessly in the throat until some shift causes it to go on a virulent rampage. The next step, says Tettelin, is gene-expression profiling using microarrays to better understand what happens when the bacteria interact with host cells. A Nature Biotechnology paper that is currently in press will describe these results, he says.
Jim Kling (email@example.com) is a freelance writer in Washington, DC.
1. H. Tettelin et al., "Complete genome sequence of Neisseria meningitidis serogroup B strain MC58," Science, 287:1809-15, March 10, 2000. (Cited in 155 papers)
2. M. Pizza et al., "Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing," Science, 287:1816-20, 2000.