The nucleotide sequence of comC, the gene encoding the 17-residue competence-stimulating peptide (CSP) of Streptococcus pneumoniae (L. S. Håvarstein, G. Coomaraswamy, and D. A. Morrison, Proc. Natl. Acad. Sci. USA 92:11140-11144, 1995) was determined with 42 encapsulated strains of different serotypes. A new allele, comC2, was found in 13 strains, including the type 3 Avery strain, A66, while all others carried a gene (now termed comC1) identical to that originally described for strain Rx1. The predicted mature product of comC2 is also a heptadecapeptide but differs from that of comC1 at eight residues. Both CSP-1 and CSP-2 synthetic peptides were used to induce competence in the 42 strains; 48% of the strains became competent after the addition of the synthetic peptide, whereas none were transformable without the added peptides.Genetic transformation not only is a valuable tool for molecular genetic analysis of Streptococcus pneumoniae (pneumococcus) but also appears to play a significant role in the evolution of this species, as in the assembly of mosaic antibiotic resistance genes containing blocks of information from other bacteria (6, 17) and in mediating a rapid mixing of alleles among natural populations (4). Yet, although transformation has long been described as a characteristic of the pneumococci, as a practical matter most studies involving this process have focused on a few laboratory strains, mainly descended from a single unencapsulated subclone (R36A) (2), for which optimal media and protocols were developed. Indeed, it has never been established just what proportion of pneumococcal isolates is transformable. This fraction has been difficult to assess, both because the pneumococcal capsule reduces or abolishes competence for genetic transformation (3,5,7,14,20,25) and because the optimal conditions for competence vary between strains.Competence for transformation in pneumococcus is not constitutive but is regulated by a quorum-sensing pheromone signal (23, 24). It was previously shown that culture supernatants from one strain, Rx1 (16), activate some other strains to competence and can induce competence in some encapsulated strains but not in others, including the type 3 strain A66 (25), even though an unencapsulated derivative of that strain is transformable (22). Following the recent identification of a small peptide from strain Rx1 with competence-stimulating activity (a competence-stimulating peptide [CSP]) (12), we reinvestigated the paradoxical behavior of A66, as a pure pheromone might be more effective than the crude culture supernatants used previously, but the results were still negative. We now trace the unresponsive character of strain A66 to the competence pheromone regulatory circuit itself and show that it reflects allelic variation of the pheromone gene in different isolates of this species.Failure of A66 to respond to the CSP of Rx1. Strain Rx1 is descended from R36A, an unencapsulated transformable derivative of D39S, a type 2 clinical isolate that was employed in early studies o...