We grouped the 207 tRNA-like pseudogenes identified by tRNAscan-SE into four classes: I) end-truncated tRNAs, II) insertion-disrupted tRNAs, III) ``non-maintained'' tRNAs, and IV) non-tRNA, polIII-like elements. Members of classes I and II show almost identical sequence similarity to legitimate tRNAs, with the exception of one contiguous insertion or deletion. About 16 tRNA families contained between one and three pseudogenes in these classes, most likely the result of recent and limited mutational events. Some of these predicted pseudogenes may still be functional - we cannot be certain without experimental characterization.
Class III pseudogenes appear to be derived from tRNAs, but show interspersed point mutations and single nucleotide insertions or deletions when compared to known tRNAs or other class III pseudogenes. Some of the multi-member groups of this type may be tRNA-derived SINE repetitive elements [Daniels & Deininger, 1985,Deininger, 1989]. Members of this class could almost be mistaken for legitimate tRNAs, except for the fact that they have reduced tRNA-like secondary structure, and the mechanism used by tRNA families to maintain sequence homogeneity appears to be absent. Lack of such a mechanism has allowed group members to drift by mutation independently, without evidence of structural conservation or covariation.
Figures 3.2 and 3.3 show two example alignments of class III elements. The first group of 12 pseudogenes have TTG in their anticodon positions, although comparison with a true Gln-TTG tRNA shows poor similarity (first sequence in Figure 3.2). Comparison to all other true tRNAs in C. elegans does not give any significant hits. It is formally possible this represents a tRNA family, but the lack of tRNA-like secondary structure and frequent point mutations relative to other members argues these are not functional molecules. Figure 3.3 shows another example of this type of element. The sequence in the anticodon position for this group is ATG (His). Interestingly, we found no legitimate tRNAs with this anticodon. Instead, the His-GUG is expected to read CAU codons, as per standard wobble rule [Crick, 1966]. As with the TTG pseudogenes, this group possesses weak tRNA secondary structure, as well as frequent base substitutions relative to other members in the group. We found at least three other large groups like these in our analyses.
Class IV pseudogenes contain strong RNA polymerase III internal promoter elements (A and B boxes), but show no recognizable similarity to other tRNAs or tRNA-like pseudogenes. Some members of class IV may in fact be unidentified pol-III transcribed RNA genes. Alternatively, these may be nonfunctional tRNAs that have drifted beyond obvious sequence similarity with their original families.