Comparative genomic analysis of the interferon/interleukin-10 receptor gene cluster

Abstract

Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components of the interferon gamma-receptor (IFNGR2) and of the IL-10 receptor (IL10R2). We report here the complete gene content of this GART-cytokine receptor gene cluster and the use of comparative genomic analysis to identify chicken IFNAR1, IFNAR2, and IL10R2. We show that the large-scale structure of this locus is conserved in human and chicken but not in the pufferfish Fugu rubripes. This establishes that the receptor components of these host defense mechanisms were fixed in an ancestor of the amniotes. The extraordinary diversification of the interferon ligand family during the evolution of birds and mammals has therefore occurred in the context of a fixed receptor structure.

Figure 1

Structure of the genomic loci downstream of the GART gene in human, chicken, and Fugu: Genes are indicated with their names, size, and orientation of transcription (arrows). Scale is indicated in each panel. (A) Human locus on chromosome 21. Arrowheads labeled Y represent processed pseudogenes. (rib. prot) Ribosomal protein S5. The orientation relative to the centromere (cen) and telomere (tel) is indicated. (EST) The presence of a spliced EST. Regions sequenced for this study: 5′ of IFNAR2 (accession no. AF039905), IL-10R2 to IFNAR1 (accession no. AF039904 ), IFNAR1 to IFNGR2 (accession no. AF039907), IFNGR2 to GART (accession no. AF039906). The accession number for C21orf4 cDNA is AF045606. (B) Chicken locus. The distance between IFNAR1 and GART has been measured by PFGE analysis (Fig. 5). Accession numbers are as follows: AF082664 (cDNA for cIFNAR1), AF082665 (cDNA for cIFNAR2), AF082666 (cDNA for cIL10R2), and AF082667 (CRII gene cluster). (C) Fugu locus (accession no. for the cosmid is AF083221): The question mark (?) represents a potential gene predicted with high confidence by both GRAIL (excellent exons) and GenScan (exon probability > 0.99).

Figure 2

Sequence alignment of the human C21orf4 with its related proteins in C. elegans and in yeast. Predicted transmembrane domains are indicated TM1–TM4. YOL129w is from S. cerevisiae, SPC8D2_2 is from S. pombe, and G_YK3109 is from C. elegans. Identical (*), similar (:), and related (.) residues are indicated.

Figure 3

Zoo blot hybridized at low stringency with a human IL10R2 probe. Murine, chicken, and zebrafish DNAs were digested either with BamHI or with HindIII, blotted to a nylon membrane, and hybridzed with a human IL10R2 probe. Sizes are indicated.

Figure 4

Sequence alignment of human IFNAR2 (A), IL10R2 (B), and IFNAR1 (C) to their chicken counterparts. Long overlines indicate leader peptides and transmembrane domains; short overlines represent links between SD100 domains. In the IFNAR1 alignment, (###) indicating the link between the two D200s highlights the duplication of the external domain. Identical (*), similar (:), and related (.) residues are indicated. Respective percents of identity for IFNAR2, IL10R2, and IFNAR1 are 28%, 42%, and 36%.

Figure 4

Sequence alignment of human IFNAR2 (A), IL10R2 (B), and IFNAR1 (C) to their chicken counterparts. Long overlines indicate leader peptides and transmembrane domains; short overlines represent links between SD100 domains. In the IFNAR1 alignment, (###) indicating the link between the two D200s highlights the duplication of the external domain. Identical (*), similar (:), and related (.) residues are indicated. Respective percents of identity for IFNAR2, IL10R2, and IFNAR1 are 28%, 42%, and 36%.

Figure 4

Sequence alignment of human IFNAR2 (A), IL10R2 (B), and IFNAR1 (C) to their chicken counterparts. Long overlines indicate leader peptides and transmembrane domains; short overlines represent links between SD100 domains. In the IFNAR1 alignment, (###) indicating the link between the two D200s highlights the duplication of the external domain. Identical (*), similar (:), and related (.) residues are indicated. Respective percents of identity for IFNAR2, IL10R2, and IFNAR1 are 28%, 42%, and 36%.

Figure 5

Physical linkage between the CRII gene cluster and the GART gene in chicken. DNAs from chicken embryonic fibroblasts was digested with MluI, NruI, XhoI, and SalI, electrophoresed, and blotted to a membrane. The same membrane was hybridized sequentially with a chicken IFNAR1 3′ probe (A) and, after stripping, with a chicken GART probe (B). Common bands are highlighted. Multiple NruI hybridizing fragments using probes devoid of NruI sites are attributable to partial methylation of the NruI sites.

Figure 6

A unique GART locus in Fugu. Fugu DNA was digested with HindIII and BamHI, electrophoresed, and transfered to a nylon membrane. The membrane was hybridized with the Fugu GART probe.