The DNA sequence of the gene encoding the early and specific 46-kDa surface antigen (P46) of Mycoplasma hyopneumoniae has been determined. The P46 gene, encoding a putative lipoprotein, contained three TGA codons and a single CGG codon in a 1,257-bp open reading frame. Edman degradation of peptide fragments showed that at least one TGA codon encodes tryptophan and that the CGG codon, which has been reported to be nonsense or unassigned in other mycoplasmas, is used for arginine in M. hyopneumoniae.There has been increasing interest in the phylogenetics of mycoplasmas. A small AϩT-rich genome and a specific codon usage, which diverges from the universal genetic code, are unique features of these organisms. In several mycoplasma species, TGA is translated as tryptophan rather than a translational stop (3,19). Also, it was suggested that CGG, an arginine codon in the universal code, is an unassigned or nonsense codon in Mycoplasma capricolum (10, 11) but not in Mycoplasma pneumoniae (3,20). It is thus an ambiguous point in the genetic code of mycoplasmas.Mycoplasma hyopneumoniae is the pathogenic agent of mycoplasmal pneumonia of swine. The 46-kDa antigen (P46) of M. hyopneumoniae is one of the species-specific surface proteins. Recently, the enzyme-linked immunosorbent assay double sandwich method, using a monoclonal antibody which recognizes P46 of M. hyopneumoniae, was successfully applied to the diagnosis of mycoplasmal pneumonia of swine (6, 7). In this report, we describe cloning and the nucleotide sequence of the gene encoding P46 of M. hyopneumoniae and the properties of the gene. The data showed that at least one TGA codon encodes tryptophan and that a CGG codon is used for arginine in M. hyopneumoniae. This is different from M. capricolum, in which the CGG codon is nonsense or unassigned.Cloning of the P46 gene was accomplished by the following experiments. A gt11 genomic library of M. hyopneumoniae ATCC 25934 (strain J) was constructed and immunoscreened with swine hyperimmune serum against the same strain (21). Approximately 500 clones were immunologically reactive among 2 ϫ 10 7 plaques. Subsequently, specific antibodies against recombinant clones were prepared from the hyperimmune serum by epitope selection (18). Each selected antibody was used to probe the immunoblots of M. hyopneumoniae whole-cell proteins for identification of the recombinant products. As a result, two clones which encode almost the same region of P46, NRK02 and NRK03, were obtained.On the basis of the results of genomic Southern analysis with the DNA fragment inserted in NRK02 as a probe, it was suggested that a 5.0-kb HindIII fragment contained the fulllength P46 gene (data not shown). Therefore, a HindIII fragment library was constructed with pUC119 (17). A plasmid clone containing the complete P46 gene, designated pURR126, was obtained by colony hybridization. The sequence of the P46 gene in the HindIII insert was determined by the dideoxy-mediated chain-termination method (Fig. 1) (12).The sequencing result showed that there i...