The Pif1 family in prokaryotes: what are our helicases doing in your bacteria?

Abstract

Pif1 family helicases, which are found in nearly all eukaryotes, have important roles in both nuclear and mitochondrial genome maintenance. Recently, the increasing availability of genome sequences has revealed that Pif1 helicases are also widely found in diverse prokaryotes, but it is currently unknown what physiological function(s) prokaryotic Pif1 helicases might perform. This Perspective aims to briefly introduce the reader to the well-studied eukaryotic Pif1 family helicases and speculate on what roles such enzymes may play in bacteria. On the basis of our hypotheses, we predict that Pif1 family helicases are important for resolving common issues that arise during DNA replication, recombination, and repair rather than functioning in a eukaryotic-specific manner.

FIGURE 1:

Phylogenetic tree revealing the relationships between selected Pif1 and RecD helicases. Pif1 (solid boxes) and RecD (dashed boxes) protein sequences were aligned using CustalX (v. 2.0.12) by iterating each step of the alignment. The same program was used to both draw and bootstrap a neighbor-joining tree. TreeView (v. 1.6.6) was used to visualize the phylogenetic tree and root it with the outgroup (human β-actin, unpublished data). The scale bar indicates the number of substitutions per site. Red boxes indicate prokaryotes, blue boxes denote eukaryotes, the green box indicates a bacteriophage, and the purple boxes designate viruses. Ps, Psychrobacter sp. PRwf-1; Mp, Mucilaginibacter paludis DSM 18603; Bb, Borrelia burgdorferi N40; Ec, E. coli; Sa, Staphylococcus aureus; Da, Desulfobacterium autotrophicum HRM2; Ba, Bacteroides sp. 2_1_16; rV5, E. coli phage rV5; IIV3, Invertebrate Iridescent Virus-3; Hs, Homo sapiens; Bl, Bifidobacterium longum subsp. longum F8; Sc, S. cerevisiae; V99B1, Emiliania huxleyi virus 99B1; and Sp, Schizosaccharomyces pombe. Protein sequences are available upon request.

FIGURE 2:

Sequence conservation of helicase motifs in the Pif1 family and E. coli RecD proteins. The sequences of the conserved SFI helicase motifs I–VI, the Pif1/RecD-specific motifs A–C, and the Pif1 family signature sequence are shown (protein sequences were aligned as in Figure 1). Residues that are completely conserved in all six sequences are bold. Residues that are identical in ≥3 sequences are red, and conserved similarities (i.e., either similar to the red residues in the same column or ≥3 similar residues in the same column) are green. E. coli RecD does not display conservation of the Pif1 family signature sequence, so the residues aligned by ClustalX in this region are shown in lowercase. The amino acid similarity groups were defined as FYW, IVLM, RK, DE, GA, TS, and NQ. Here Bb indicates B. bacteriovorus instead of B. burgdorferi; the remaining abbreviations are the same as in Figure 1.