Table 3.
Classification of TRF4/TRF5-like family of nucleotidyltransferases
| Subfamily | Phyletic distribution | Prominent members1 | Known functions | Comments |
|---|---|---|---|---|
| classical TRF4/5 | all eukaryotes | TRF4 (Scer), TRF5 (Scer), cid14 (Spom), DmTRF4-1 (Dmel), DmTRF4-2 (Dmel), GLD-4 (Cele), ncPAP1 (Tbru) | snRNA polyadenylation [278], U14 snoRNA, U5 snRNA, pre- ribosomal rRNA degradation [279], intergenic transcript degradation [280], hypomodified tRNA degradation [281, 282], etc. | PAPD7-like and PAPD5-like assemblages formed via gene duplication event occurring in TRF4 during chordate evolution; Scer TRF4 and TRF5, meanwhile, result from an Scer-specific gene duplication event |
| **PAPD7-like | jawed vertebrates | PAPD7/POLS/TRF4- 1/LAK1/POLK/TRF4 (Hsap) | - | |
| **PAPD5-like | jawed vertebrates and Xenopus | PAPD5/TRF4-2(Hsap) | snoRNA adenylation [283], miRNA modification [206, 218] | |
| TUT1 | animals | TUT1/PAPD2/TUTase/U6- TUTase/STAR-PAP/Hs5 (Hsap) | Regulation of selected mRNAs [213, 284], U6 snRNA uridylyl transferase [214], miRNA modification [218] | TUT1 & MTPAP subfamilies form a monophyletic higher- order assemblage |
| MTPAP | animals | MTPAP/PAPD1/Hs4 (Hsap) | mt-mRNA polyA tail extension [215, 285], miRNA modification [218] | |
| ZCCHC6/ZCCHC11 repeat 2 subfamily | crown group eukaryotes | ZCCHC6/PAPD6/Hs2 (Hsap), ZCCHC11/PAPD3 (Hsap), cid- 1(Cele), pup-2 (Cele), cid11 (Spom), cid13 (Spom), cid1 (Spom) | checkpoint control [286, 287], mRNA polyuridylation [288], targets ribonucleotide reductase mRNA [289], histone mRNA uridylation [290], pre-miRNA polyuridylation [227, 290, 291] miRNA uridylation [207, 209, 210] | Repeat 1 subfamily associated with repeat 2 subfamily before divergence of nematodes. cid11, cid13 are closely related to the exclusion of other sequences, suggesting late gene duplication event in S. pombe. Repeat 2 subfamily and GLD-2/PAPD4 likely share a common ancestor which originally emerged as single copy in Naegleria or chromalveolate lineages. |
| ZCCHC6/ZCCHC11 repeat 1 subfamily | chordates, Strongylocentrotus, C. elegans | ZCCHC6/PAPD6/Hs2 (Hsap), ZCCHC11/PAPD3 (Hsap), cid-1 (Cele) | see above | |
| GLD-2/PAPD4 | animals | GLD-2 (Cele), PAPD4/Hs1 (Hsap), XGLD-2 (Xlae), mut-2 (Cele) | Cytoplasmic mRNA polyadenylation [292–294], miRNA adenylation [205], transposon silencing and RNAi [295, 296] | |
| basal ZCCHC6/ZCCHC11 repeat 2-like, GLD- 2/PAPD4-like subfamily | Naegleria, ciliates, stramenopiles, slime molds, possible apicomplexan representation | Rdn1 (Tthe), Rdn2 (Tthe) | endo-siRNA production [212, 297] | |
| AT3G56320-like2 | plants, Giardia, kinetoplastids, stramenopiles, Naegleria | AT3G56320 (Atha), KPAP2 (Tbru) | mitochondrial mRNA editing [298] | |
| RET1-like | kinetoplastids | RET1 (Ltar), RET2 (Ltar), TbTUT3(Tbru), TbTUT4 (Tbru), KPAP1 (Tbru) | mRNA, gRNA uridylation, mitochondrial mRNA editing [299–303], mitochondrial transcript polyadenylation [304] | Monophyletic kinetoplastid- specific expansion |
| MEE44-like2 | plants, slime molds, stramenopiles | MEE44 (Atha) | - | Arabidopsis deletion linked to embryonic arrest [305] |
| MUT68-like | plants | MUT68 (Crei) | adenylation of RISC-cleaved mRNA fragments [211], miRNA and siRNA uridylation [198] | |
| MEAT1-like | kinetoplastids | MEAT1 (Tbru) | mitochondrial mRNA editing [306] | |
| ncPAP2-like | kinetoplastids | ncPAP2 (Tbru) | nuclear adenylation [307] | |
| monkey king | insects | mkg (Dmel), mkg-p(Dmel) | - | previously described [308] |
| CG1091-like2 | insects | CG1091 (Dmel) | - | |
| PFD1045c-like2 | apicomplexa | PFD1045c (Pfal) | - | PFD1045c was identified as an erythrocyte membrane- associated antigen [217] |
| Paramecium expansion2 | Paramecium | -- | - | Paramecium lineage-specific expansion |
1
Several members of the TRF4/TRF5 family notably found in S. pombe and C. elegans failed to reliably fall within a clear, monophyletic assemblage, including the functionally characterized, telomeric repeat-adenylating cid12 [309, 310].
2
Indicates newly-characterized subfamily
**
differentiated lineages emerging after a duplication event split the classical TRF4/5 subfamily late in animal evolution.