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Fig. 12 | BMC Evolutionary Biology

Fig. 12

From: Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers

Fig. 12

Ohnologs of APLF. a Domains and interactions of H. sapiens APLF assigned using Uniprot Q81W19 as template with domain annotation and function refined with reference to [60,83,84,93,119]. b Domain models and phylogenetic relationship of the two pairs of A. vaga APLF ohnologs, with cladograms showing the relationship of gene copies and ohnologs. c Alignment of the tandem PBZ domains. Each PBZ domain has a conserved C(M/P)Y and CRY motif, highlighted in aqua along with nearby conserved residues, and these form a basic, hydrophobic pocket for ADP-ribose binding. APLF binds multiple ADP-ribose residues within PAR, and Y381/Y386 and Y423/Y428 are critical for interactions with the adenine ring, and R387/R429 coordinate the interactions with the phosphates [91]. All are marked with (*). The Y423F difference in D is found in some other metazoans. The C and D ohnologs substitute Q for P in the first PBZ domain, which would not be expected to maintain the characteristics of the basic, hydrophobic binding pocket. Both also terminate before the final H of the second PBZ domain, which undoubtedly alters the domain’s binding properties. d Alignment of the Ku80 Binding Domain (KBD) regions. Copies A, C and D retain R184 and W189, the residues found critical for Ku binding in mammals [117]; copy A lacks one of the conserved positively charged residues found in most KBD domains. e Differential expression of all four paralogs entering and recovering from desiccation, compared to hydrated controls. Values are log2 fold change of normalized counts, significance test values are listed in Additional file 1

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