Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes

Abstract

Background: The poly(ADP-ribose) polymerase (PARP) superfamily was originally identified as enzymes that catalyze the attachment of ADP-ribose subunits to target proteins using NAD+ as a substrate. The family is characterized by the catalytic site, termed the PARP signature. While these proteins can be found in a range of eukaryotes, they have been best studied in mammals. In these organisms, PARPs have key functions in DNA repair, genome integrity and epigenetic regulation. More recently it has been found that proteins within the PARP superfamily have altered catalytic sites, and have mono(ADP-ribose) transferase (mART) activity or are enzymatically inactive. These findings suggest that the PARP signature has a broader range of functions that initially predicted. In this study, we investigate the evolutionary history of PARP genes across the eukaryotes.

Results: We identified in silico 236 PARP proteins from 77 species across five of the six eukaryotic supergroups. We performed extensive phylogenetic analyses of the identified PARPs. They are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes. The PARP superfamily can be subdivided into six clades. Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described.

Conclusions: Three main conclusions can be drawn from our study. First, the broad distribution and pattern of representation of PARP genes indicates that the ancestor of all extant eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins was similar to human PARP1 and likely functioned in DNA damage response. The second of the ancestral PARPs had already evolved differences in its catalytic domain that suggest that these proteins may not have possessed poly(ADP-ribosyl)ation activity. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.

Figure 1

The PARP gene family forms six clades. A. Graphical representation of the maximum-likelihood (ML) phylogenetic tree of all identified eukaryotic PARPs indicating the relationships between the six clades as defined in the text. The full tree can be found in Additional file 4. The tree was based on an alignment of the PARP catalytic domains (Additional file 3). B. Graphical representation of the ML phylogenetic tree of Clade 1 PARPs indicating the relationships between nine subclades as defined in the text. C. Graphical representation of the ML phylogenetic tree of Clade 2 indicating the relationships between the two subclades as defined in the text. D. Graphical representation of the ML phylogenetic tree of Clade 3 PARPs indicating the relationships between the six subclades as defined in the text. E. Graphical representation of the ML phylogenetic tree of Clade 5 PARPs indicting the relationship between the two subclades as defined in the text. F. Graphical representation of the maximum-likelihood (ML) phylogenetic tree of Clade 6 PARPs indicating the relationships between the six subclades as defined in the text. Numbers in the clades or subclades indicate the number of proteins in each. Colors and letters indicate the eukaryotic supergroup or groups represented. A, Amoebozoa; O, Opithokonts; E, Excavata; P, Plantae; C, Chromalveolates. Purple, Amoebozoa; red, Opithokonts; orange, Excavata; green, Plantae; blue, chromalveolates. Branch support values are indicated at the nodes as computed in PhyML using an aLRT non-parametric Shimodaira-Hasegawa-like (SH) procedure and a midpoint rooting method. Triangle and branch colors indicate either the presence of the HYE (red) or variant (blue) catalytic triad in each group. Branch lengths do not indicate genetic distance.

Figure 2

Phylogenetic distribution of the PARP family across eukaryotes. The topology of the schematic tree is based on recent evidence from single- and multi-gene phylogenetic analyses of eukaryotes or subgroups thereof. Some nodes, especially the deepest ones (e.g. monophyly of Excavates, Plantae or Chromalveolates + Rhizarians), remain controversial; these uncertainties do not affect the conclusions concerning the evolutionary history of the PARP family. Branch lengths do not reflect genetic distance. Presence or absence of PARP proteins are indicated by a red + or a blue -, respectively. For each species or group, PARP family members are listed with the clade numbers introduced in Figure 1. For an expanded phylogeny of the fungi, please see Figure 11. Accession numbers of the genes and details on the source of data for individual taxa is provided in Additional files 1 and 2. The six eukaryotic supergroups are indicated as follows: Amoebozoa, purple; Opisthokonta, red; Excavata, orange; Plantae, green; Rhizaria, black; Chromalveolates, blue. ND, no data; NA, not applicable; O, orphan PARPs, as discussed in the text; 3?, reflects the ambiguity of placement of the Tetrahymena proteins into this clade, as discussed in the text.

Figure 3

Phylogenetic analysis of Clade 1 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 5). Clade 1 proteins can be divided into nine subclades A-I, as indicated. Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 4

Schematic representation of domains found in PARP proteins. Proteins are arranged by clade as defined in Figure 1 and in the text (indicated on the left). The protein name is given on the right, with species in parenthesis. Numbers indicate amino acids. Protein domains are illustrated by coloured boxes and were defined according to Pfam 23.0. Although each protein is represented in scale, the proteins are not in scale between each other. vWA, von Willebrand factor type A; VIT, vault inter-alpha-trypsin domain; Ankyrin, ankyrin repeats; UBCc, ubiquitin conjugating enzyme catalytic domain; PfamB_2311, domain of unknown function found in Clade 6 PARPs; UIM, ubiquitin interaction motif; PARP catalytic, catalytic domain of PARPs, PARP Zn²⁺, DNA binding zinc finger; Macro, macro domain; WWE, WWE domain; SAM, sterile alpha domain; PRD, PARP regulatory domain; PADR1, domain of unknown function found in PARPs; BRCT, BRCA-1 C terminus domain; CCHH Zn²⁺, DNA binding zinc finger; RRM1, RNA-binding motif; FPE, Fungal PARP E2-like domain; WGR, domain defined by conserved Trp, Gly, and Arg residues; U-box, modified ring finger found in E3 ubiquitin ligases; SAP, DNA binding domain. Human, Homo sapiens; Dictyostelium, Dictyostelium discoideum; Arabidopsis, Arabidopsis thaliana; Magnaporthe, Magnaporthe grisea; Physcomitrella, Physcomitrella patens.

Figure 5

Phylogenetic analysis of Clade 2 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 7). Clade 2 proteins can be divided into two subclades as indicated. Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 6

Phylogenetic analysis of Clade 3 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 8). Clade 3 proteins can be divided into six subclades A-F as indicated. Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 7

Clade 3 PARPs have divergent catalytic domains. Alignment of the deduced amino acid sequences of part of the PARP catalytic domains from Clade 3 proteins. Species names and protein accession numbers are shown at left. Numbers indicate amino acid position within each PARP catalytic domain while the labels on the right indicate the subclade to which the sequences belong. Dots indicate gaps introduced to maximize the alignment; the black thick lines indicate missing amino acids introduced to allow representation of all three residues of the catalytic triad, indicated by the blue boxes (C1 = H; C2 = Y; C3 = E). Only one Clade 3 protein contains a glutamic acid residue at the third position, while another has a glutamine (both indicated with red asterisks). Most Clade 3 proteins have substituted aliphatic amino acids (no asterisk), while five have serine or threonine at the position of the glutamic acid (blue asterisks). The black box surrounds a short motif characteristic of Tetrahymena thermophila Clade 3 proteins. The black box labelled with an asterisk indicates a proline residue that is found in most of the Clade 3 proteins. Shaded sequences indicate proteins for which a 3D structure is available.

Figure 8

Phylogenetic analysis of Clade 4 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 9). Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 9

Phylogenetic analysis of Clade 5 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 10). Clade 5 proteins can be divided into two subclades, A-B, as indicated. Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 10

Phylogenetic analysis of Clade 6 PARP genes. The represented tree is a ML tree. This tree is based on a multiple alignment that includes the PARP catalytic domain (Additional file 11). Clade 6 can be divided into five subclades, A-E, as indicated. Branch supports as in Figure 1. Scale bar indicates genetic distance reflected in branch length.

Figure 11

Multiple independent losses of PARP genes have taken place in the fungal lineage. A. Phylogeny of the fungi. The topology of the schematic tree is based on a recent higher order examination of the fungi [159]. B. Simplified phylogeny of the Agarimycotina. This tree is based on that of [160]. C. Simplified phylogeny of the Saccharomycotina, based on that of [161]. Branch lengths are not proportional to genetic distance in any of the phylogenetic trees. Presence or absence of PARP proteins are indicated by a red + or a blue -, respectively. Groups in which some species have lost PARPs while others have retained them are indicated by a +/- symbol. For each species or group, PARP family members are listed with the clade numbers introduced in Figure 1. Accession numbers of the genes and details on the source of data for individual taxa is provided in Additional file 1 and Table 1. ND, no data.

Figure 12

General summary of the evolutionary hypothesis of the PARP enzyme family. A. Simplified phylogeny of the eukaryotes. The last common eukaryotic ancestor (LCEA) contained Clades 1 and 6 PARPs. Subsequently, Clade 6 PARPs were lost in two supergroups (Amoebozoa and Chromalveolates), while individual supergroups gained novel clades of PARPs. Branch lengths do not reflect genetic distance. B. Schematic representation of the domain structure of ancestral PARP proteins present in the LCEA. WGR, WGR domain; PRD, PARP Regulatory Domain; PARP, PARP catalytic domain; 2311, PfamB_2311.