An improved genetic tool suitable for routine markerless allelic exchange in Bacillus anthracis has been constructed. Its utility was demonstrated by the introduction of insertions, deletions, and missense mutations on the chromosome and plasmid pXO1 of the Sterne strain of B. anthracis.Bacillus anthracis, a gram-positive, spore-forming bacterium, is the causative agent of anthrax. Full virulence requires the production of a toxin and the formation of a protective capsule. The primary genes involved in the production of these two virulence factors are contained within two large nonessential plasmids, pXO1 and pXO2 (13). Distributed elsewhere on the two plasmids and on the chromosome are genes involved in regulating the expression of anthrax toxin, the capsule, and a number of other genes potentially involved in virulence (2, 6, 11). The entire genomic sequence of the Ames strain of B. anthracis has recently been determined, enabling the identification of interesting, potentially virulence-related genes by reverse genetics (19).The ideal mutation to initially introduce in such "genomemining" studies is an in-frame deletion of the candidate gene. Such a mutation avoids problems with polarity and other effects on the expression of surrounding genes, which accompany either insertion or less-precise deletion mutations and which can complicate interpretation. In addition, the ability to readily introduce missense mutations, which enables a determination of the effects of single-amino-acid substitutions, is necessary for more-sophisticated genetic analyses of structure-function relationships. Both of these types of desirable mutations are "markerless" in that they are not necessarily associated with a phenotype that can be selected or screened for during genetic manipulation (e.g., antibiotic resistance in the case of an insertion mutation). For B. anthracis, markerless gene replacements for some loci have been reported (3), but the methods by which these mutations have been isolated can be time and labor-intensive. This is due to the lack of a counterselection scheme, in which, by selecting for the loss of a plasmid vector, one can select for the second of two successive crossovers between such a vector and the chromosome in order to achieve gene replacement.An alternative to counterselection schemes involves the use of the intron-encoded homing restriction enzyme I-SceI. The ability of this enzyme, which recognizes an 18-bp sequence, to cleave an introduced site that is essentially unique in a genome has been exploited in the promotion of homologous recombination in organisms as diverse as bacteria, Drosophila, and other higher eukaryotes (4,20,22). In one case, the use of I-SceI in promoting allelic exchange in Escherichia coli has been reported (17). In such a scheme, the integration of a suicide plasmid by a cloned region of homology containing the desired genetic change results in one of the two crossovers required to effect allelic exchange. To promote the second, the synthesis of the I-SceI enzyme results in cl...