Worm Breeder's Gazette 11(5): 59

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PAT Element Sequence Suggesting a Retroid Transposition Mode

Yves de Chastonay, Heinz Felder, Christopher Link, Fritz Muller and Heinz Tobler

Figure 1

The PAT elements of Panagrellus redivivus, described earlier (de 
Chastonay et al., WBG 11,4), code for a major transcript (about 900nt 
long) which maps to the preferentially deleted portion of PAT entities.
Sequence analysis of this region has revealed the presence of a 
single, COOH terminal cysteine motif, thought to be exclusively 
characteristic of retroid GAG proteins.
Longer exposition of Northern blots lights up further PAT specific 
signals, the most noteworthy of which is an approx.  1800nt band 
mapping slightly downstream of the putative GAG gene.  A 587 amino 
acid ORF, as deduced from nucleic acid studies, is found in the 
corresponding region.  ORF2, as we refer to it here, contains a YXDD 
box and neighboring motifs typical for reverse transcriptase (RT).  
The RT region is COOH terminally followed by a tether and an RNaseH 
motif.  Analysis of sequences further downstream suggests the presence 
of an endonuclease, albeit lacking a metal binding domain.  No 
protease like motif was found in either of these ORFs.
PAT ORFs 1 and 2 are on the same reading frame, but they have no 
overlap and the transcripts detected on Northern blot are discrete.  
Hence, ratio of GAG to Pol is not regulated by a translational frame-
shifting mechanism but, rather, seems to be regulated at the 
transcriptional level.  The strong transcription rate of ORF1 is 
paralleled by the presence of a TATA and a CAAT box, while the latter 
regulatory signal is not found preceding the weakly transcribed, 
putative Pol gene (ORF2).  Two further ORFs (i.e., 3 and 4) are 
located further downstream, but neither one has an apparent trans-
membrane domain, as one would expect from a putative Env gene of 
infectious retroids.
These structural features put together incite us to classify PAT 
elements as retrotransposons, and optimal alignments with published RT 
sequences, as well as the order of functional domains in ORF2, seem to 
assign PAT to the Gypsy group of retroid elements.  As described (WBG, 
op.  Cit.), however, PAT has a split DR structure, the only precedent 
of this being the Toc-1 element of Chlamydomonas reinhardtii (Day et 
al.  EMBO J.  7,1917-1927,1988).  We therefore propose to dub these 
elements 'Para-retrotransposons', 'para' reflecting the positions of 
DRs if a transposition intermediate of these elements was circular.
[See Figure 1]

Figure 1