Fig. 7
Comparison of catalytic efficiency of Gadiformes AIDs through Michaelis–Menten kinetics. A The catalytic rate of Gadiformes AIDs was compared to that of other AID orthologs through Michaelis–Menten kinetics. Thirty-six extant AID orthologs were expressed and purified as GST-tagged recombinant proteins. At least two independent protein preparations of each AID ortholog were incubated at their optimal pH and temperature with 0.03125–600 fmol range of TGCbub7 substrate. Each reaction was carried out in duplicate. For better visual representation, the data is graphed based on the AIDs’ activity level. A through D show AIDs with low to high activity levels. Data is represented as mean ± SEM (n ≥ 4). Abbreviations: Gm: Gadus morhua; Bs: Boreogadus saida; Ag: Arctogadus glacialis; Memrla: Merlangius merlangus; Ma: Melanogrammus aeglefinus; Pv: Pollachius virens; Ga: Gadiculus argenteus; Tmi: Trisopterus minutus; Bb: Brosme brosme; Mmol: Molva molva; Llo: Lota lota; Pp: Phycis phycis; Pb: Phycis blennoides; Mo: Malacocephalus occidentalis; Mb: Macrourus berglax; Bm: Bathygadus melanobranchus; Lla: Laemonema laureysi; Mmor: Mora mora; Tmu: Trachyrincus murrayi; Tsc: T. scabrous; Mma: Muraenolepis marmoratus; Mz: Melanonus zugmayeri; Mmerlu: Merluccius merluccius; Sc: Stylepnorus chordates; Cr: Cyttopsis roseus; Zf: Zeus faber; Tsu: Typhlichthys subterraneus; Pt: Percopsis transmontane; Pj: Polymixia japonica; Ss: Salmo salar; Dr: Danio rerio; Ol: Oryzias latipes; Tr: Takifugu rubripes; Ip: Ictalurus punctatus; Hs: Homo sapiens. B The relative catalytic efficiency (i.e., Kcat/Km) of AID orthologs to the value of this parameter for Ag-AID (AID with lowest non-zero catalytic efficiency). We did not detect any cytidine deaminase activity for Bs-AID and Mz-AID (labelled with red asterisks). C The average catalytic efficiency of AIDs according to their phylogenetic classifications. D Schematic representation of catalytic efficiency of AID orthologs. Red to green color change indicates low (0: Bs-AID and Mz-AID) to high (9.62E − 05: Dr-AID) catalytic efficiency (Table 1). NA indicates species without aicda gene. The dashed line represents the manual addition of Homo sapiens. The black triangle represents the collapsed phylogenetic node