Transfer RNA genes in pieces

Abstract

The short genes encoding transfer RNA (tRNA) molecules are highly conserved in both sequence and structure, reflecting the central role of tRNA in protein biosynthesis. The frequent occurrence of fragmented intron-containing tRNAs that require processing to form contiguous molecules is therefore surprising. Recent discoveries of permuted and split tRNA genes have added to the apparent creativity of nature regarding the organization of these fragmented genes. Here, we provide an overview of the various types of fragmented tRNA genes and examine the hypothesis that the integration of mobile genetic elements--including viruses and plasmids--established such genes in pieces.

Figure 1

Characteristics of the archaeal bulge–helix–bulge splicing motif. The colouring scheme in all three panels indicates the transfer RNA (tRNA; blue) and the intron (orange). Splice sites are indicated by arrows. (A) Schematic secondary structure of an intron-containing pre-tRNA. The conserved features of a tRNA are indicated, D and T indicate the D-loop and the T-loop respectively. (B) Crystal structure of a bulge–helix–bulge (BHB) motif taken from the complex structure with splicing endonuclease from Archaeoglobus fulgidus (Xue et al, 2006). (C) Sequence logo representation of 44 euryarchaeal (top) and 137 crenarchaeal (bottom) BHB motifs (extracted from Marck & Grosjean, 2003; Sugahara et al, 2007).

Figure 2

Schematic overview of pre-transfer RNA processing of unusual transfer RNA gene products. (A) Processing of single introns in members of the Archaea. The conserved structural bulge–helix–bulge (BHB) motif is recognized by the splicing endonuclease. (B) Processing of up to three introns in Thermofilum pendens. Two BHB motif-containing elements are spliced out leading to the formation of pre-transfer RNA (pre-tRNA) with a third intron. (C) Split tRNAs in Nanoarchaeum equitans are assembled by long reverse-complementary sequences. The helix–tRNA junctions fold into the BHB motif, which are recognized by the splicing endonuclease. (D) Permuted tRNAs in Cyanidioschyzon merolae show a splicing motif on folding of the reversed tRNA sequences. The circular product is probably processed by RNase P and RNase Z to yield the mature 5′ and 3′ termini.

Figure 3

Integration of archaeal viruses into transfer RNA genes and attachment sites. (A) Schematic presentation of a spindle-shaped virus (SSV) genome integrated in its host chromosome (Chr). The amino-terminus of the partitioned integrase gene (integrase N) restores the 3′ terminal portion of the targeted tRNA gene (orange) with its attachment site (att). A direct repeat of this sequence is present in the carboxy-terminal integrase fragment (integrase C). (B) Four examples of attachment sites of SSV viruses and the corresponding transfer RNA (tRNA) sequences of the Sulfolobus host. The secondary structure of the tRNA is indicated as helices (‘<' and ‘>' symbols) and unpaired bases (dots). The integration of SSV K1 mutates potential tRNA^Glu targets at four positions (yellow), which changes the identity of the tRNA species from Glu to Asp (modified from Wiedenheft et al, 2004).

Dieter Söll (left) & Lennart Randau