Rapid evolution of BRCA1 and BRCA2 in humans and other primates

Abstract

Background: The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers.

Results: To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection.

Conclusions: While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.

Figure 1

Evolution of BRCA1 over the course of primate speciation. A. dN/dS values for each branch of the primate phylogeny were calculated using the free-ratio model in PAML [13]. Branches exhibiting dN/dS values > 1 are shown in bold italics. Dashes (-) represent branches where zero synonymous substitutions are predicted to have occurred. On these branches, dS = 0 and dN/dS can therefore not be calculated. In these instances, the numbers of non-synonymous (N) and synonymous (S) substitutions predicted to have occurred along each branch are indicated in parentheses (N:S). Of these, branches that experienced 4 or more non-synonymous substitutions are in bold italics. Asterisks indicate new sequences generated in this study. B. The human, bonobo, and chimpanzee clade was isolated and dN/dS values were calculated using the one-ratio and two-ratio models in PAML. The two-ratio model was a better fit as determined by the likelihood ratio test shown in the box. ω0 is the calculated dN/dS for all branches under the one-ratio model, or for background branches under the two-ratio model, and ω1 is the dN/dS for the isolated branches in the two-ratio model.

Figure 2

BRCA1 evolution in the human, bonobo, and chimpanzee clade. A. dN/dS values for BRCA1 were calculated on each branch of the primate tree using the free-ratio model in PAML. dN/dS values > 1 are shown in bold italics. The numbers of non-synonymous (N) and synonymous (S) substitutions predicted to have occurred along each branch are indicated in parentheses (N:S). The asterisk represents the last common ancestor of humans, bonobos, and chimpanzees. MYA, million years ago. B. The number of human-specific non-synonymous (N) and synonymous (S) substitutions in BRCA1 and other genes encoding BRCA1-interacting proteins. The length of each gene is shown in kilobases (kb). Non-synonymous and synonymous substitutions are shown as number of substitutions per kilobases (N/kb and S/kb, respectively). An “enrichment ratio” of N/kb over S/kb was also calculated. C. A domain diagram of BRCA1 is shown with the RING domain, coiled-coil domain (C-C), and BRCT domains indicated. On this are superimposed all of the non-synonymous substitutions predicted to have occurred in the tree shown in panel A since the divergence of humans, bonobos, and chimpanzees from their last common ancestor (asterisk in A). Vertical lines indicate substitutions specific to humans, lines with white circles are substitutions specific to bonobos, and lines with grey circles are substitutions specific to chimpanzees. Lines with black circles indicate substitutions common to both bonobos and chimpanzees.

Figure 3

Specific codons in BRCA1 have experienced positive selection during primate speciation. A. Shown are the ten codons that have evolved under positive selection (dN/dS > 1) in primates with a P > 0.85. Codons with a P > 0.95 are indicated with asterisks. The amino acids encoded at these positions in human BRCA1 are shown, along with those found in hominoids, old world monkeys, and new world monkeys. In addition, human SNPs and disease mutations also found at these sites are listed. X refers to a single nucleotide mutation that results in a termination codon. B. A domain diagram of BRCA1 is shown with the RING domain, coiled-coil domain (CC), and BRCT domains. The triangles at the bottom represent sites of positive selection (grey - P > 0.85, black - P > 0.95). The 12 most common human variants recorded in the BIC are shown at the top of the diagram as stars. The black stars indicate disease-causing mutations, white stars represent variants with no known clinical significance, and grey stars are those with unknown significance.

Figure 4

Codons in exon 11 of BRCA2 that have experienced positive selection in primates. A. 5 codons in exon 11 of BRCA2 were found to be under positive selection in primates. All sites had a P > 0.95 (indicated with asterisks) except for S1008 (P = 0.9). The amino acid encoded by human BRCA2 at each of these codons is shown. The amino acids encoded by hominoids, old world monkeys, and new world monkeys are also shown. Human SNPs and disease mutations deposited to the BIC are listed at the bottom. B. A domain diagram of BRCA2 is depicted with the 8 BRC repeats, helical DNA binding domain (helical DBD), OB folds, and nuclear localization signals (NLS). Only exon 11 was sequenced in this study (section in white). The sites of positive selection are represented as triangles at the bottom of the diagram. The 11 most common protein-altering variants in the BIC are marked as stars at their respective locations at the top. Black stars correspond to disease-causing mutations, white stars are variants with no known clinical significance, and grey stars are positions with unknown significance.

Figure 5

The sites of positive selection lying within the BRC repeats of BRCA2 are located adjacent to the Rad51 binding region. A. The 8 BRC repeats of the human BRCA2 protein were aligned using ClustalX. The red and peach colored boxes are the motifs within the BRC repeats thought to facilitate binding with Rad51 [20]. Residues 1008, 1225, and 1426 are colored in green, orange, and yellow, respectively. All three sites lie just adjacent to the FxxA motif which interacts with two hydrophobic pockets in the Rad51 oligomer. B. The co-crystal structure of BRC4 (blue) in complex with Rad51 (grey) is shown (PDB ID 1N0W [19]). The FxxA motif is depicted in red. Residues 1008, 1225, and 1426 are shown in green, orange, and yellow, respectively.