It took 44 scientists and technicians from 11 institutions in three countries to sequence the genome of Bacillus anthracis - the anthrax bacterium. Nature announced the long-awaited feat in its issue dated May 1, 2003, under the title: "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria." Its senior author is genomicist Claire Fraser, president of TIGR, The Institute of Genomic Research, in Rockville, Md., which honchoed the sequencing project. She chaired an international press briefing on Wednesday morning.
"What is being published in Nature on Thursday," Fraser told the press briefing, "is a description of the complete, fully annotated genome sequence of an Ames isolate of Bacillus anthracis. It's the first anthrax strain to be completely sequenced and analyzed."
"Ames" refers to the bacterial strain of A. anthracis harvested in 1881 from the anthrax-ridden carcass of a cow that went belly-up on a Texas ranch. In the intervening 40 years, that paradigmatic culture of the carnivorous anthrax bug has become the index-type bacterium at laboratories the world over.
TIGR compared the sequence of B. anthracis to the genomes of two almost-identical bacteria - Bacillus cereus and Bacillus thuringiensis (bt). The former is infamous as the author of severe food poisoning. The latter, bt, attacks insects, as B. anthracis does people. As such, bt provides the world with its near-universal insecticide.
A companion article in the same issue of Nature bears the title: "Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis." Its first author is genomicist Natalia Ivanova at Integrated Genomics in Chicago. B. cereus is closely related genetically to B. anthracis, and serves as a convenient pinch-hitter for the signal anthrax bacterium - as does bt.
A Tale of Two Plasmids - Virulent, Toxic
Inhalational anthrax is the lethal form of the bacterium, which led to five deaths and 17 injuries late in 2001 on the eastern seaboard of the U.S. The first death occurred in Florida. Coincident with this outbreak was a rash of sealed envelopes containing anthrax spores, which inundated post offices from New Jersey to Washington, D.C. The Ames strain of A. anthracis has now been indicted as genomically identical to the postal bioterror version.
TIGR's press briefing was attended by Maria Giovanni, assistant director for microbial genomics and advanced technologies at NIAID - the National Institute of Allergy and Infectious Diseases. This NIH agency was a principal sponsor of TIGR's anthrax sequencing program. "We are collaborating," Giovanni told the conference, "on developing diagnostics, therapeutic drugs and vaccines to control anthrax poisoning."
Aside from its two virulence and toxicity plasmids, the complete sequence of B. anthracis/Ames chromosome totaled some 5,227,293 base pairs. Housekeeping functions, such as DNA replication and fatty-acid metabolism, are overwhelmingly partitioned to the chromosome, whereas the two outlier plasmids have a greater proportion of transposons, genes involved in toxicity and genes without assigned function.
The plasmids encode 5,508 predicted protein-coding sequences. These differ in only 11 confirmed single nucleotide polymorphisms (SNPs) from the 2001 lethal Florida attack of Ames isolate. The TIGR co-authors found several chromosomally encoded proteins that might contribute to pathogenicity, and identified numerous surface proteins - possibly important targets for vaccines and drugs. Almost all of these proteins have homologues, which highlights the similarity of B. anthracis to near neighbors not associated with anthrax at all. Those two plasmids, of which the 300,000 bp carry virulence and toxicity genes, account for much of the lethal power of anthrax to kill animals, including humans.
Anthrax Put-Down: A Soil Bug Gone Bad'
Almost all potential chromosomal virulence-enhancing genes have homologues in Bacillus cereus. This suggests that they are not specifically associated with the unique pathogenicity of B. anthracis but are part of the common arsenal of the B. cereus group of bacteria.
Microbiologist Timothy Read, the Nature paper's lead author, bad-mouths anthrax as, "a soil bug gone bad." He added that the anthrax bacillus has "a large metabolic tool kit" - similar to that of other soil bacteria. "It gives the bacterium the versatility to import nutrients and respond to signals from its environment."
These attributes long ago turned the bug into a ready-made bioweapon. By deactivating its dangerous cells into inert spores, it can hole up in macrophages underground or in rotting flesh for decades, perhaps centuries. Then, when stimulated to germinate, it springs back to deadly inhalational life. Germination of the anthrax endospore is a key initial event in the B. anthracis infectious cycle. Protection of DNA during dormancy and efficient DNA repair during germination are believed to be important factors in endospore viability.
Over the last seven decades, the anthrax bacillus was developed and weaponized as a biowarfare/bioterror agent by several national programs, from Japan in the 1930s to Iraq in the 1980s.
TIGR's anthrax research project was supported by the U.S. Office of Naval Research, the U.S. Army Medical Research Institute of Infectious Diseases and the UK's Defense Sciences Technology Laboratory. (Fraser confirmed that TIGR continues to do some anthrax-related sequencing work for the FBI, but declined to comment on details.)
In addition to deciphering the complete genome of the Ames strain, TIGR now is sequencing several other strains and isolates of the anthrax bacterium for comparative genome studies that will help scientists explore the evolution and biology of B. anthracis. The genomic sequence, Fraser observed, will benefit research projects to find new drugs and vaccines as well as to improve anthrax detection and diagnosis.
"I don't think we want to be focusing solely on B. anthracis/Ames," she continued, "because - if we ever find ourselves in a situation where B. anthracis is used in another bioterror attack - there is no guarantee that the next time around it will be the Ames strain."
"Findings from this genome sequence analysis," the Nature paper concludes, "raise further questions about the biology of B. anthracis; for instance, what are the roles of putative virulence' genes in close relatives of B. anthracis that do not cause anthrax, and do they actually contribute to virulence in B. anthracis?"