Evolution and functional divergence of NLRP genes in mammalian reproductive systems

Abstract

Background: NLRPs (Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing Proteins) are members of NLR (Nod-like receptors) protein family. Recent researches have shown that NLRP genes play important roles in both mammalian innate immune system and reproductive system. Several of NLRP genes were shown to be specifically expressed in the oocyte in mammals. The aim of the present work was to study how these genes evolved and diverged after their duplication, as well as whether natural selection played a role during their evolution.

Results: By using in silico methods, we have evaluated the evolution and functional divergence of NLRP genes, in particular of mouse reproduction-related Nlrp genes. We found that (1) major NLRP genes have been duplicated before the divergence of mammals, with certain lineage-specific duplications in primates (NLRP7 and 11) and in rodents (Nlrp1, 4 and 9 duplicates); (2) tandem duplication events gave rise to a mammalian reproduction-related NLRP cluster including NLRP2, 4, 5, 7, 8, 9, 11, 13 and 14 genes; (3) the function of mammalian oocyte-specific NLRP genes (NLRP4, 5, 9 and 14) might have diverged during gene evolution; (4) recent segmental duplications concerning Nlrp4 copies and vomeronasal 1 receptor encoding genes (V1r) have been undertaken in the mouse; and (5) duplicates of Nlrp4 and 9 in the mouse might have been subjected to adaptive evolution.

Conclusion: In conclusion, this study brings us novel information on the evolution of mammalian reproduction-related NLRPs. On the one hand, NLRP genes duplicated and functionally diversified in mammalian reproductive systems (such as NLRP4, 5, 9 and 14). On the other hand, during evolution, different lineages adapted to develop their own NLRP genes, particularly in reproductive function (such as the specific expansion of Nlrp4 and Nlrp9 in the mouse).

Figure 1

Consensus phylogenetic tree of NLRPs reconstructed by the fusion of four separate methods (NJ, ME, MP and ML). A total of 83 NLRP protein sequences from 6 mammalian species (cattle, dog, human, chimpanzee, mouse and rat) are used with chicken as outgroup. A total of 122 amino acid sites are included in the analyses. The bootstrap values are labeled on the main branches for the four different methods (followed the order of NJ, ME, MP and ML methods). The symbol * means that the branch is not supported by the corresponding method.

Figure 2

Syntenic comparison of NLRP genes among the cattle, the dog, the human and the mouse. The NLRP genes are marked in red, the orthologues are indicated by discontinuous lines. The order of NLRPs in each genome is listed as following: The cattle: NLRP3 (chr 7); NLRP1 (chr 19); NLRP9, 13, 8 and 5 (chr 18); NLRP6 (Un.004.137); NLRP14 (chr 15). The dog: NLRP3 (chr 8); NLRP1 (chr 5); NLRP12, 2, 9, 13, 8 and 5 (chr 1); NLRP6 (chr 18); NLRP14 and 10 (chr 21). The human: NLRP3 (chr 1); NLRP1 (chr 17); NLRP12, 2, 9, 13, 8 and 5 (chr 19); NLRP6, NLRP14 and 10 (chr 11). The mouse: Nlrp3, 1a, 1b and 1c (chr 11); Nlrp12, 2, 4c, 4d, 4b, 9b, 4e, 5, 9c, 4a, 9a, 14, 10 and 6 (chr 7).

Figure 3

Segmental duplications of Nlrp4 duplicates and V1r genes in the mouse genome. Figure 3a Comparison of gene relationships in the phylogenetic tree and their genomic position. Left: Phylogenetic tree of mouse Nlrp4 duplicates (including pseudogenes) and its closely related Nlrp5 and Nlrp9 genes. A total of 439 nucleotide sites are included in the final dataset. Right: Phylogenetic tree of 25 mouse V1r proteins whose encoding genes are located in the same genomic region as Nlrp4 genes. A total of 271 amino acid sites are included in the final dataset. The statistical confidence of each branch was estimated by the bootstrap method with 1000 replications, and only the values ≥ 80% are labeled in the trees. Middle: Genomic organization of related Nlrp and V1r genes. Five putative regions (I - V) might be concerned in segmental duplication. Figure 3b A possible scenario of segmental duplication deduced from synteny combining phylogeny: Genomic region I (involving Nlrp4b) and region II (involving Nlrp4d) might have been resulted from an early duplication, and the subsequence duplication events have given birth to region III (involving Nlrp4a) and region IV (involving Nlrp4c). Region V might have been duplicated later, and in this genomic region, other more recent segmental duplications (concerning pseudogenized Nlrp4 copy and V1rd genes) have been undertaken several times. We note that the order of duplication events in this potential scenario is mainly based on the topology of Nlrp4 phylogenetic tree. There might be other alternative itinerary to explain the present complex pattern of this genomic region.