Evolution of primate interferon-induced transmembrane proteins (IFITMs): a story of gain and loss with a differentiation into a canonical cluster and IFITM retrogenes

Abstract

Interferon-inducible transmembrane proteins (IFITMs) are a family of transmembrane proteins. The subgroup of immunity-related (IR-)IFITMs is involved in adaptive and innate immune responses, being especially active against viruses. Here, we suggest that IFITMs should be classified as (1) a canonical IFITM gene cluster, which is located on the same chromosome, and (2) IFITM retrogenes, with a random and unique location at different positions within the genome. Phylogenetic analyses of the canonical cluster revealed the existence of three novel groups of primate IFITMs (pIFITM) in the IR-IFITM clade: the prosimian pIFITMs(pro), the new world monkey pIFITMs(nwm) and the old world monkey pIFITMs(owm). Therefore, we propose a new nomenclature: IR-pIFITM1, IR-pIFITM2, IR-pIFITM3, IR-pIFITMnwm, IR-pIFITMowm, and IR-pIFITMpro. We observed divergent evolution for pIFITM5 and pIFITM10, and evidence for concerted evolution and a mechanism of birth-and-death evolution model for the IR-pIFITMs. In contrast, the IFITMs scattered throughout the genomes possessed features of retrogenes retrotransposed by class 1 transposable elements. The origin of the IFITM retrogenes correspond to more recent events. We hypothesize that the transcript of a canonical IFITM3 has been constantly retrotransposed using class 1 transposable elements resulting in the IFITM retro(pseudo)genes. The unique pattern of each species has most likely been caused by constant pseudogenization and loss of the retro(pseudo)genes. This suggests a third mechanism of evolution for the IR-IFITMs in primates, similar to the birth-and-death model of evolution, but via a transposable element mechanism, which resulted in retro(pseudo)genes.

Keywords: antiviral proteins; evolution; innate immunity; interferon-induced transmembrane proteins; primates; retrogene; transposable elements.

Figure 1

Gene synteny of primate IFITMs of the canonical cluster. The gene synteny of the primate IFITMs in the canonical cluster is displayed for the 26 analyzed primate species (right). IFITMs were colored following the grouping in the phylogenetic analyses (Figure 3). Arrows indicate gene orientation. Primate phylogeny (left) was constructed using timetree.org (Kumar et al., 2022). Gray: flanking genes, pink: IFITM5, purple: IFITM10, brown: IR-pIFITMpro, light orange: IR-pIFITMnwm, orange: IR-pIFITMowm, sand: IR-pIFITM1, yellow: IR-pIFITM3, light yellow: IR-pIFITM2 red: not considered in the analyses, e.g., partial mRNA, Chim: Chimeric genes (see below); pro: prosimians; nwm: new world monkeys; owm: old world monkeys.

Figure 2

General genomic arrangement of canonical IFITMs cluster and IFITMs retrogenes. Schematic representation of the general arrangement of the proposed canonical gene cluster and IFITM retrogenes. The distinction between the consistently arranged canonical IFITM cluster on one chromosome (Chr) and the IFITM retrogenes, which are randomly distributed throughout the genome, is shown. Arrows indicate gene orientation. Gray: flanking genes, pink: IFITM5, purple: IFITM10, orange: IR-IFITMs.

Figure 3

Phylogeny of IR-IFITM in 26 primate species based on AA sequences. The evolutionary history was inferred by using the Maximum Likelihood (ML) method. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The bootstrap value is shown next to the branches. Mouse Ifitms were used as outgroup. IR-pIFITM1, IR-pIFITM2, IR-pIFITM3 (Immunity-Related-primate), IR-pIFITMnwm (Immunity-Related-primate-new world monkey) IR-pIFITMowm (Immunity-Related-primate-old world monkey), and IR-pIFITMpro (Immunity-Related-primate-prosimian).

Figure 4

AA sequence characteristics of primate IFITM groups. Sequence logos were derived from the AA alignments of the primate IFITM groups (Supplementary Figures S6–S8) defined in Figure 3 (IR-pIFITM1, IR-pIFITM2, IR-pIFITM3, IR-pIFITMnwm, IR-pIFITMowm, and IR-pIFITMpro). (A) N-termini with variable lengths. (B) Highly conserved CD225 domains comprising IM1 domain and CIL. (C) C-termini including IM2 and the C-terminal domains with highly variability in length. Probability of residues is shown. Protein domains are indicated. Black: transmembrane/intramembrane domain, orange: topological domain. Logos were generated using WebLogo3 (Crooks et al., 2004).

Figure 5

Identification of IR-pIFITM3/1 and IR-pIFITMnwm/1 chimeras. Alignment of chimeric IR-pIFITMs of Theropithecus gelada (owm) (A) and Saimiri boliviensis (nwm) (B) with IR-pIFITM3/nwm and IR-pIFITM1. For Theropithecus gelada, the alignment was performed with the protein sequences from its closest relative Papio anubis as only the chimeric gene is present in the genome. For Saimiri boliviensis, X represents start of frameshift omitted to emphasize identity of C-terminus. Identity to IR-pIFITM3/nwm highlighted with yellow or light orange box, respectively, and identity to IR-pIFITM1 highlighted with sand box.

Figure 6

Hypothesis for the origin and pattern of the IFITM retrogenes. Schematic representation of our hypothesis: the transcript of a canonical IR-pIFITM3/nwm/pro is constantly retrotranspositioned by class 1 transposable elements originating the retro(pseudo)genes. The unique pattern of each species is caused by constant pseudogenization and loss of the retro(pseudo)genes. Evidence supporting the hypothesis are listed.