FIGURE 2.
Sequence alignments of eukaryotic domains related to bacterial TPP-dependent riboswitches. Base-paired stems are shaded in black and labeled as defined previously (Winkler et al. 2002a). The P3 sequences, which in eukaryotes are significantly expanded in length and number of base pairs, are represented as a stem-loop structure. The highly conserved nucleotide positions in bacteria that were used to search for eukaryotic domains are shaded gray. For each identified (ID) sequence, the position of the conserved CUGAGA sequence within the given GenBank entry is given along with the accession identification, sequence name, and gene identification. Additional protein annotations based on sequence similarity are shown in brackets. (Methods) Riboswitch-like domains were initially identified by sequence similarity to bacterial sequences (Eco2 and Cac) by a BLASTN search of GenBank using default parameters. These hits were verified and expanded by searching for degenerate matches to the pattern (CTGAGA [200] ACYTGA [5] <<< GNTNNNNC >>> [5] CGNRGGRA) using the program SequenceSniffer (unpublished algorithm). Angle brackets indicate base pairing, and bracketed numbers are variable gaps with constrained maximum lengths. All of the eukaryotic sequences have one or zero mismatches to this pattern except for one (Aor), which initially had three mismatches due to a single A insertion in the final search element. The presence of this mutation results in an inactive aptamer, whereas removal permits TPP binding (data not shown). Comparison of mRNA (M33643.1) and genomic (AB033416.1) sequences demonstrated that the F. oxysporum element is in an intron in the 5′ UTR of the sti35 gene. Other fungal sequences (Ncr, Aor, and Fso) are flanked by consensus splicing sequences.