Adaptive functional divergence among triplicated alpha-globin genes in rodents

Abstract

The functional divergence of duplicated genes is thought to play an important role in the evolution of new developmental and physiological pathways, but the role of positive selection in driving this process remains controversial. The objective of this study was to test whether amino acid differences among triplicated alpha-globin paralogs of the Norway rat (Rattus norvegicus) and the deer mouse (Peromyscus maniculatus) are attributable to a relaxation of purifying selection or to a history of positive selection that has adapted the gene products to new or modified physiological tasks. In each rodent species, the two paralogs at the 5'-end of the alpha-globin gene cluster (HBA-T1 and HBA-T2) are evolving in concert and are therefore identical or nearly identical in sequence. However, in each case, the HBA-T1 and HBA-T2 paralogs are distinguished from the third paralog at the 3'-end of the gene cluster (HBA-T3) by multiple amino acid substitutions. An analysis of genomic sequence data from several rodent species revealed that the HBA-T3 genes of Rattus and Peromyscus originated via independent, lineage-specific duplication events. In the independently derived HBA-T3 genes of both species, a likelihood analysis based on a codon-substitution model revealed that accelerated rates of amino acid substitution are attributable to positive directional selection, not to a relaxation of purifying selection. As a result of functional divergence among the triplicated alpha-globin genes in Rattus and Peromyscus, the red blood cells of both rodent species contain a mixture of functionally distinct alpha-chain hemoglobin isoforms that are predicted to have different oxygen-binding affinities. In P. maniculatus, a species that is able to sustain physiological function under conditions of chronic hypoxia at high altitude, the coexpression of distinct hemoglobin isoforms with graded oxygen affinities is expected to broaden the permissible range of arterial oxygen tensions for pulmonary/tissue oxygen transport.

Figure 1.—

Genomic structure of the α-globin gene family in rodents.

Figure 2.—

Dot plot of the P. maniculatus BAC sequence (185 kb) against the rat chromosome 10 sequence (250 kb) with masked repeats.

Figure 3.—

Dot plot of a chromosomal fragment spanning the P. maniculatus α-globin gene cluster (40 kb) against the syntenic region of rat chromosome 10 sequence (50 kb) with masked repeats.

Figure 4.—

Maximum-likelihood phylogeny of rodent α-globin genes based on coding sequence. Bootstrap support values are based on 1000 replicates.

Figure 5.—

Phylogenetic relationships among rodent α-globin genes inferred from sequence matches in flanking regions as well as shared, derived SINE elements and pseudogene fragments that lie outside of gene conversion tracts. The reconstructed history of gene duplication and species divergence indicates that the HBA-T3 genes of Rattus and Peromyscus originated via independent, lineage-specific duplication events. Nodes with solid circles denote duplication events.

Figure 6.—

Structural alignment of mammalian α-globins. The A, B, E, F, G, and H α-helical domains are shaded, and the C helix is underlined.

Figure 7.—

Homology-based structural model of the P. maniculatus α-globin polypeptide, showing the location of 20 amino acid substitutions that are unique to the product of the HBA-T3 gene. Color coding of the ribbon diagram shows site-specific variation in conservation scores (see text for details). Residue positions in blue are invariant or nearly invariant across all mammals (and are therefore presumably subject to stringent functional constraints), whereas residue colors that are further toward the red end of the spectrum are more variable (and are therefore presumably subject to less stringent functional constraints).

Figure 8.—

Isoform differences in hydrogen-bond distance between the E7 residue side chain and the free atom of the bound dioxygen molecule. (A) Heme–ligand complex in the (E7)His-containing α-globin produced by the HBA-T1 and HBA-T2 genes of P. maniculatus. (B) Heme–ligand complex in the (E7)Gln-containing α-globin produced by the HBA-T3 gene of P. maniculatus.