Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals

Abstract

TRIM5alpha provides a cytoplasmic block to retroviral infection, and orthologs encoded by some primates are active against HIV. Here, we present an evolutionary comparison of the TRIM5 gene to its closest human paralogs: TRIM22, TRIM34, and TRIM6. We show that TRIM5 and TRIM22 have a dynamic history of gene expansion and loss during the evolution of mammals. The cow genome contains an expanded cluster of TRIM5 genes and no TRIM22 gene, while the dog genome encodes TRIM22 but has lost TRIM5. In contrast, TRIM6 and TRIM34 have been strictly preserved as single gene orthologs in human, dog, and cow. A more focused analysis of primates reveals that, while TRIM6 and TRIM34 have evolved under purifying selection, TRIM22 has evolved under positive selection as was previously observed for TRIM5. Based on TRIM22 sequences obtained from 27 primate genomes, we find that the positive selection of TRIM22 has occurred episodically for approximately 23 million years, perhaps reflecting the changing pathogenic landscape. However, we find that the evolutionary episodes of positive selection that have acted on TRIM5 and TRIM22 are mutually exclusive, with generally only one of these genes being positively selected in any given primate lineage. We interpret this to mean that the positive selection of one gene has constrained the adaptive flexibility of its neighbor, probably due to genetic linkage. Finally, we find a striking congruence in the positions of amino acid residues found to be under positive selection in both TRIM5alpha and TRIM22, which in both proteins fall predominantly in the beta2-beta3 surface loop of the B30.2 domain. Astonishingly, this same loop is under positive selection in the multiple cow TRIM5 genes as well, indicating that this small structural loop may be a viral recognition motif spanning a hundred million years of mammalian evolution.

Figure 1. Evolutionary Dynamics of the TRIM6/34/5/22 Cluster

(A) The cluster of TRIM5-related genes on human chromosome 11p is compared to the cow and dog clusters. In all three species the cluster is flanked by olfactory receptors (OR). Dark green genes are predicted TRIM5 pseudogenes. The human TRIM5 pseudogene (TRIMP1) is supported by mRNA AF230412 [21] and actually combines a region of TRIM34 with a region within TRIM5. The remnants of two exons of the dog TRIM5 gene are indicated as “ex2” and “ex8.” Expression evidence is listed below validated genes. See Appendix S1 for all dog and cow sequences. Genes not shown to scale. (B) A neighbor-joining tree based on RBCC protein domains shows the evolutionary relationship of predicted and validated genes. Cow TRIM5–5 is not included because it encodes only a coiled-coil domain. The only known pig TRIM5 gene is included. Colors correspond to those used in (A).

Figure 2. Natural Selection of Cow TRIM5 Genes

(A) The four full-length cow TRIM5 genes or predicted ORFs (TRIM5–1, TRIM 5–3, TRIM 5–4, and TRIM 5–6) were analyzed for signatures of positive selection with PAML as described in the Methods section. Three different likelihood ratio tests between models allowing positive selection (M2 or M8) or only neutral/negative selection (M1, M7, or M8A) support the positive selection model (p-values all < 0.001), regardless of the model of codon frequency used (f3x4 or f61). With the f61 model, 4.8% of codons fall into a dN/dS category of 7.4. For more information on the codon evolution and frequency models, see the legend to Table 1. (B) A tree of the four cow TRIM5 paralogs illustrates evolution since the divergence of these genes from their single common gene ancestor. dN/dS was calculated for each branch, and the actual numbers of replacement and synonymous DNA changes are given in parentheses (R:S). For instance, 22 replacement DNA changes and only three synonymous DNA changes have accumulated in the TRIM5–3 sequence since the duplication that gave rise to it and to TRIM5–6. On each branch are listed values for the whole gene (top), and values calculated for the B30.2 domain alone (bottom, red). It appears that one more synonymous change occurred in the B30.2 domain of TRIM5–3 than in the entire gene. While all synonymous changes in this lineage do occur in the B30.2, the estimate differs slightly depending on the dataset (3.2 in the full-gene analysis and 3.7 in the B30.2-only analysis) due to slightly different likelihood optima being reached. These values round to the integers “3” and “4.” The asterisk on TRIM5–3 denotes that this gene was previously found to act as a retroviral restriction factor [36,43]. As with all highly related gene families, especially those arrayed in tandem, it is possible that gene conversion has obscured true phylogenetic relationships.

Figure 3. Disparate Evolution of TRIM5 and TRIM22 in Primates

Branch values of dN/dS for the TRIM22 and TRIM5 genes are shown on the cladogram, along with numbers of replacement and synonymous changes (in parentheses, R:S) that occurred along each primate lineage. NWM (A) were analyzed separately from OWM+HOM (B). On the OWM+HOM cladogram, branches with the top ten values of dN/dS are highlighted in red. Branches with dN/dS of infinity (dS = 0) are included in the top ten if the ratio of R:S is greater than or equal to 4:0, since this ratio compares approximately to R:S ratios of the other top branches.

Figure 4. Expression Patterns of Human TRIM22 and TRIM5α

Primers were designed to amplify ∼600 bp of the coiled-coil / B30.2 region of TRIM5α and TRIM22 transcripts. These primers were used to amplify cDNA from 31 human tissues.

Figure 5. TRIM22 Amino Acid Sites Identified as Evolving under Positive Selection

(A) A diagram of TRIM22 illustrates the amino acid positions highlighted as being subjected to positive selection (p > 0.95). Thirteen OWM and HOM sequences were analyzed for the first six coding exons (exons 2–7), with titi monkey included as an outgroup. For the large eighth exon, which encodes the B30.2 domain, six additional OWM and hominoid sequences were included in the analysis (listed in [C]). (B, C) Sequence is shown for the TRIM22 coiled-coil domain (B) and the first five beta-strands of the B30.2 domain (C). TRIM22 residues with strong support (p > 0.95) for positive selection are shown in blue highlight, with the symbols from (A) above the alignment. The human TRIM5α sequence is aligned, with residues previously found to be under positive selection [16] indicated in blue highlight. Residues indicated with asterisks are conserved with human TRIM5α. In (C), sequence motifs predicted to form beta strands are underlined (see Methods). Block arrows represent consensus beta strand positions, which are supported by crystallographic evidence for related B30.2 proteins [50,51]. The four cow TRIM5 paralogs are aligned under the human sequence, with the single residue found to be under positive selection in a separate analysis of these genes highlighted in blue. The outlined box indicates an additional site identified when pig is included as an outgroup (several other sites are also identified in that analysis). Exact TRIM5-TRIM22 sequence alignment is somewhat uncertain in the region of the TRIM5α “patch” of positive selection (black horizontal bar and [16]) located in the β2-β3 loop.