Figure 2

Examples of conserved RNA structures found within coding sequences with covariant sites caused by different substitutions of the corresponding amino acids. The color scheme used for coloring the alignment indicates the number of different types of base pairs that support stabilizing selection on the structure. The transparency indicates the number of incompatible pairs (ranging from 0 to 2 going from dark to light). Red: one base pair type; ochre: two base pair types; green: three base pair types. (A) Section of conserved structure found within an alignment of four fungal species (S. bayanus, S. kudriavzeii, S. mikatae, S. cerevisiae) of the yeast gene YDL211C, for which the protein product is vacuolar localized. Substitution of the amino acid arginine (R) by histidine (H) at the opening base pairs is followed by a different usage of codons for cysteine (C) in the respective closing base pairs. (B) Section of conserved structure found within an alignment of four fungal species (A. gossypii, S. castelli, S. kluyveri, S. cerevisiae) of the yeast gene SAK1 (YER129W) involved in glucose metabolism. Substitution of the amino acid isoleucine (I) by valine (V) at the opening base pairs is followed by a different usage of codons for glutamic acid (E) in the closing base pairs. Another example of covariant sites is within the second stem where a different usage of codons for asparagine (N) at the opening base pairs follows a substitution of isoleucine (I) to valine (V) in the closing base pairs.