Fig. 1

LTR and non-LTR retrotransposons that target to tRNA genes. a. LTR retrotransposons. Ty1, Ty3, DGLT-A and Tj1 elements are depicted in dark green. The boxed black arrows represent the LTRs flanking the two ends of the elements. The first ORF of the Ty1 element encodes Gag and the second ORF encodes a polypeptide (Pol) which is further processed into protease (PR), integrase (IN), and reverse transcriptase (RT)/ ribonuclease H (RH). Ty3 differs in structure from Ty1 by swapping positions of IN and RT/RH. For both Ty1 and Ty3, the Pol polypeptide is generated by a + 1 translational frameshift 38 bp upstream of the 3’end of Gag [169,170,171]. The D. discoideum DGLT-A element contains one ORF that encodes for both Gag and Pol proteins. DGLT-A belongs to the Ty3-gypsy clade, signified by the arrangement of pol with IN after RT/RH [172]. S. japonicas Tj1 has a similar structural arrangement as Ty3 with GAG  and POL as two separate ORFs. The GAG ORF has a stop codon that is thought to be translationally suppressed to allow for translation of the POL ORF which lacks a start codon [121]. The length of each element is depicted by the scale at the bottom in kb. b. non-LTR retrotransposons. D. discoideum TRE5-A and TRE3-A, D. purpureum NLTR-A and P. pallidum NLTR-B are depicted in dark orange and all share a similar structural arrangement. All elements except NLTR-B have two ORFs flanked by untranslated regions (UTR), with TRE5-A and TRE3-A ending with an oligo(A) tail. The 5′ and 3’UTR of TRE5-A are arranged into A- and B-modules, and B- and C-modules respectively. The protein domain arrangement of TRE5-A and TRE3-A ORF2 is the same and encodes a protein containing an apurinic/apyrimidinic endonuclease (APE), RT, and zinc-finger (ZF) domain. Both TRE5-A and TRE3-A require a − 1 frameshift for translation of ORF2 [137, 173]. NLTR-A and NLTR-B have a similar arrangement to the TRE5-A and TRE3-A elements except that an RH domain substitutes for the ZF domain. In addition, NLTR-B has three separate ORFs for APE, RT and RH. It is not yet known if the 5′ and 3’ UTRs of NLTR-A and NLTR-B are arranged into modules. NLTR-A ORF1 overlaps with ORF2 by 13 bp but whether a frameshift occurs or not for translation of ORF2 is not yet known [124]. NLTR-B does not contain overlapping ORFs, however RT does not contain a start codon [124]. The length of each element is depicted by the scale at the bottom in kb