Comparison of two b1 alleles from within the A mating-type of the basidiomycete Coprinus cinereus

We cloned and sequenced the b1 specificity gene, b1-2, from the A43 mating-type locus of the basidiomycete Coprinus cinereus, to compare its molecular structure to a previously published allele. The b1-2 gene was identified and isolated using a transformation assay for A-activity. The nucleotide (nt) sequence was determined and compared to the published sequence for the b1 specificity gene of the A42 mating-type locus. Both genes map to the same physical location within the A mating-type locus and conserved structural organization is observed at both the genomic and the protein level. Sequence alignments show that the two alleles share 73% overall nt sequence identity for the open reading frames (ORFs) and 68% overall amino acid (aa) sequence identity for the deduced polypeptides. Allowing for conservative substitutions, the overall aa sequence similarity is 79%. Comparison of the deduced aa sequences reveals several conserved structural motifs, including a DNA-binding homeodomain, putative bipartite nuclear localization signal sequences, and four predicted dimerization motifs. Regions rich in Pro and hydroxylated aa (Ser and Thr) are also common to both alleles. Sequence similarity varies greatly along the length of the gene at both the nt and aa levels. In general, similarity increases progressively from the N- to the C-terminal end with variable patterns of similarity observed for individual exons and the predicted motifs they encode. The low sequence similarity observed in the N terminus suggests that variability in this region may be involved in non-self recognition. Differing levels of positional and compositional constraint are apparent for different functional domains.