Figure 3

Dyad symmetry in repeat-coding (PARCEL) sequences. (A-B) Arrows depict tandem copies (1,2,3,...) of the canonical 25-amino acid (75-nucleotide) repeat representing the HMM logo in and Figure 2A. Bars below the arrows show locations and lengths of repeating palindromic motifs in relation to the HMM repeat-coding sequence. ORFs from the sources indicated at the left were used to derive the palindromic motifs shown, as described in Methods; these ORFs and features of the palidromes are detailed in Table 1 and Additional file 6. Lower case letters (a,b,c) indicate the single or multiple palindromic motifs derived from a particular source. Examples in (A) show repeating palindromic motifs with periodicities corresponding to the repeating HMM domains; those in (B) show longer palindromes spanning blocks of multiple HMM domains. The examples shown represent palindromic motifs derived from the sequences of individual ORFs, except in two cases indicated by asterisks (*): Mcc Kid (consensus) indicates palindromes generated from the composite of all HMM motif-containing ORFs in that genome; Mmm SC PG1 represents the palindrome derived from the composite sequences of two LPs shown previously to be expressed, LppQ and LppC. (C) The locations and lengths of palindromic motifs derived in the same manner from a region of CRISPR repeats are shown, corresponding to known palindromic DR repeats in the sequence (arrows), separated by spacer regions. (D) Cartoon illustrates the concept that multiple tandem palindromes of like sequence (stem-loops A through F) can form extended and diverse palindromic structures.