Identification of Pif1 helicases with novel accessory domains in various amoebae

• Published in: Molecular phylogenetics and evolution Vol. 103; pp. 64 - 74
• Main Authors: Harman, Ashley, Manna, Sam
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2016
• Subjects: Amino Acid Sequence; Amoeba - classification; Amoeba - metabolism; Amoebozoa; Basidiomycota - enzymology; DNA Helicases - classification; DNA Helicases - genetics; DNA maintenance; DNA Replication; DNA Topoisomerases, Type I - classification; DNA Topoisomerases, Type I - genetics; DNA, Protozoan - chemistry; DNA, Protozoan - isolation & purification; DNA, Protozoan - metabolism; Gene Transfer, Horizontal; Horizontal gene transfer; Nucleic acid binding; Phylogeny; Pif1 helicase; Sequence Alignment; Sequence Analysis, DNA; Ubiquitination; Zinc Fingers - genetics; ORC; DNA maintenance; G4; UDGase; CUE; Ubiquitination; Nucleic acid binding; HGT; UBA; Smr; Amoebozoa; Pif1 helicase; Horizontal gene transfer
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2016.07.015

[Display omitted] •We have identified ten amoebal Pif1 helicases possessing novel accessory domains.•Domains are involved in ubiquitination, DNA replication or nucleic acid binding.•These proteins evolved via horizontal gene transfer, gene duplication and fusion.•Acanthamoeba accessory domains were acquired from fungi in two different phyla.•These domains have likely improved or expanded the roles of amoebal Pif1 helicases. Pif1 helicases are a conserved family of eukaryotic proteins involved in the maintenance of both nuclear and mitochondrial DNA. These enzymes possess a number of known and putative functions, which facilitate overall genome integrity. Here we have identified multiple subtypes of Pif1 proteins in various pathogenic and non-pathogenic amoeboid species which possess additional domains not present in other Pif1 helicases. These helicases each possess one of five different accessory domains, which have roles in ubiquitination, origin of DNA replication recognition or single-stranded nucleic acid binding activity. Using a robust phylogenetic approach we examined each Pif1 class, which revealed that gene duplication, fusion and horizontal gene transfer events have all contributed to the evolution of these enzymes. This study has identified the first collection of Pif1 helicases to contain additional domains, which likely confer novel enzymatic activity, or improve existing functionality. Furthermore, the potential functions of these helicases may shed further light on the overall role the Pif1 family plays in genome maintenance.