Table 1.
Phyletic distribution, relationships and shared sequence features of different JOR/JmjC families
| Family Name | Phyletic distribution | Additional comments | Clade synapomorphies |
|---|---|---|---|
| Histone demethylase clade | |||
| JMJD6a | An, Ch, Fu, Pl, My, Al, St, He, Kib | Conserved arginine just N-terminal to strand-1; sporadic fusions to F-box, AT-hook, Ankyrin repeats, C2, chromo and phospholipase domains. | (i) Two amino acid β bulge in connector between strands 2 and 3, (ii) Conserved asparagine residue in the middle of strand-3, (iii) HxxxN motif in strand-7 and (iv) Universally conserved C-terminal small residue (usually asparagine) displaced towards end of strand 8 in crystal structures. |
| JMJD4a | An, Ch, Fu, Pl, Ap, St, Ki | Conserved N[HR]NWhN motif in strand-8. | |
| Dictyostelium C-module binding factora | Fu, Am, He | Although the active site basic residue in strand-4 is lost, there is a highly conserved lysine residue before strand-8 that probably serves as an alternative active site residue; fusions to ZZ, CxxC, PHD, Bmb domains. | |
| Jumonji/JARID1/SMCX/KDM5a | An, Fu, My, Pl, Al, St, He | HxE in strand-2 catalytic site; Jumonji inactive; fusions to BRIGHT, PHD, SJA, C2H2 Zn-fingers and SANT domains. | |
| JMJD2/KDM4a | An, Ch, Fu, Plc, St, Ci, He | HxE in strand-2 catalytic site; A cysteine and histidine in insert between strand 4 and 5, and 2 cysteines after strand-8 form a Zn-binding cluster, Fused to PHD, TUDOR, C2H2, chromo, TAM/MBD and SET domains. | |
| JMJD3 (KDM6B)/UTX (KDM6A) | An, Ch, Fu, Ci | Basic residue in strand-4 is lost, there is a highly conserved lysine residue in strand-1 that probably serves as an alternative active site residue; HxE in strand-2 catalytic site; lacks asparagine of HxxxN motif, characteristic C-terminal domain with a C2C2 motif (treble clef fold); fused to N-terminal TPR repeats, expanded in Paramecium of which some inactive. | |
| Hairless/JMJD1 | An, Ba, Pl | Fused to an N-terminal ZZ finger, distinct N-terminal treble clef domain and CxC domains in plants. | |
| JMJD8 | An, Plc, St | Contain a HxH instead of a HxD in the catalytic site in strand-2. | |
| JHDM1/KDM2/PHF2/FBXL10 | An, Ch, Fu, St, Pl | HxxT instead of the HxxxN motif in strand-7; Fusions to CxxC, FBOX, LRR, PHD. | |
| Bacterial Histone-demethylase-like | Proteobacteria, Firmicutes, Bacteroidetes | See text and Figure 4 for gene neighborhoods and associations. | |
| yW hydroxylase/FIH1 clade | |||
| yW hydroxylase/peroxidasea | An, Ch, Fu, Plc, Ap, Ki, He | Conserved arginine in strand-N-5 and strand N-1; Fused to TYW3+TYW2, TYW4 and the kelch repeats of TYW4 in some species (Figure 1). | (i) Insert between strands N-3 and N-4, (ii) Highly conserved asparagine at beginning of strand-3 and (iii) Universally conserved C-terminal small residue (usually asparagine) in middle of strand 8 in structures. |
| FIH1a | An, Ch, My, Plc, St, He | Conserved HP motif in connector between strands 4 and 5; fusions to kelch repeats in Naegleria, and N-terminal P-loop sulfotransferase in Monosiga; expansion in Monosiga and stramenopiles. | |
| JMJD5a | An, Ch, Ba, Pl, My, Ap, St, He | Conserved glutamate in N-3 and aromatic between strands N-3 and N-4, DxxxP motif in Helix N-4; fusion to acetyltransferase in nematodes. | |
| Secreted JMD5-like family | An (lost in vertebrates, arthropods, nematodes) | Contains disulfide-bonding conserved cysteines and a unique N-terminal GHxxxhG-motif; three subfamilies each with lineage-specific expansions in various metazoans. | |
| JMJD7a | An, Ch, Fu, Pl, St, Ci, He | Conserved acidic N-terminal to strand-1; conserved asparagine in strand 1 shared with S. pombe Jmj4-like. | |
| Schizosaccharomyces pombe Jmj4-like | Fu, Ch, Plc, St, Ap | Conserved histidine in strands 3 and 8; Fused to TPR repeats and DNAJ in oomycetes; shares conserved asparagine in strand 1 with JMJD7. | |
| HSPBAP1 | An | Conserved histidine between strands 6 and 7; always a stand-alone DSBH domain. | |
| Bacterial yW hydroxylase/FIH1 | Widespread in bacteria, see supplement | See text and Figure 4 for gene neighborhoods and associations. | |
| MINA/No66 clade | |||
| MinA/No66a | An, Ch, Fu, Pl, My, Al, St, He, Kib | Expanded in Monosiga where it is fused to SH2, STY kinase, Ig-like domains, GCC repeat and cysteine containg extracellular domains. | Share a conserved C-terminal α-helical extension. |
| Bacterial MinA/No66-like/YxbC/YcfD | Wide-spread in bacteria, see supplement | Versions closer to eukaryotic homologs additionally share several conserved motifs, e.g. HxT motif in strand-8 and arginine between strands 6 and 7. |
aAncient eukaryotic JOR/JmjC lineages.
bSpecies abbreviations: Al, Alveolates; An, Animals; Ap, Apicomplexa; Ba, Basidiomycete fungi; Ch, Choanoflagellates; Ci, Ciliates; Fun, Fungi; He, Heterolobosea; Ki, Kinetoplastids; My, Mycetozoa; Pl, Plants; St, Stramenopiles.
cOnly present in chlorophyte algae.