Comparative Genomic Analysis of Two Avian (Quail and Chicken) MHC Regions

Shiina, Takashi; Shimizu, Soichi; Hosomichi, Kazuyoshi; Kohara, Saori; Watanabe, Shinji; Hanzawa, Kei; Beck, Stephan; Kulski, Jerzy K.; Inoko, Hidetoshi

doi:10.4049/jimmunol.172.11.6751

Cited by 147 publications

(136 citation statements)

References 62 publications

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“…BLAST search approaches in chicken, turkey, quail, black grouse, and zebra finch failed to detect genes for immuno-and thymoproteasome, suggesting that they have been lost in the lineage of birds (Balakrishnan et al 2010;Chaves et al 2009;Shiina et al 2007;Shiina et al 2004;Sutoh et al 2012;Wang et al 2012). While the genes coding for the catalytic subunits β1i and β5i are present in the class II region of the human and murine MHC loci, sequence searches in chicken genome databases revealed that there are no LMP genes in the avian MHC region, and also the immune subunit β2i could not be identified.…”

Section: Introductionmentioning

confidence: 99%

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Erath

Groettrup

2014

Immunogenetics

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The proteasome is the main protein-degrading machine within the cell, producing ligands for MHC class I molecules. It is a cylindrical multicatalytic protease complex, and the catalytic activity is mediated by the three subunits β1, β2, and β5 which possess caspase-, trypsin-, and chymotrypsin-like activities, respectively. By stimulation with interferon (IFN)-γ the replacement of these subunits by β1i, β2i, and β5i is induced leading to formation of immunoproteasomes with altered proteolytic and antigen processing properties. The genes coding for these immunosubunits are restricted to jawed vertebrates but have so far not been found in the genomes of birds, e.g., chicken, turkey, quail, black grouse and zebra finch. However, the chicken genome sequences are not completely assigned; therefore, we investigated the presence of immunoproteasome on protein level. 20S proteasome was purified from the chicken brain, blood, spleen, and bursa of Fabricius, followed by separation via two-dimensional (2D) gel electrophoresis. We analyzed the protein spots derived from the spleen and brain by mass spectrometry and could identify all 14 proteasomal subunits, but there were no differences detectable in the spot patterns. Moreover, we stimulated the chicken spleen cells with phorbol 12-myristate 13-acetate (PMA) and ionomycin aiming at the induction of immunoproteasome, but in spite of the induction of proliferation and IFN-γ, no evidence for immunoproteasome formation in chicken could be obtained. This result was substantiated by the finding that 20S proteasomes isolated from immune and non-immune tissues showed very similar peptidolytic activities. Taken together, our results indicate that chicken lack immunoproteasomes also on protein level.

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Section: Introductionmentioning

confidence: 99%

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Erath

Groettrup

2014

Immunogenetics

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“…For example, Japanese quail have a series of duplications yielding seven MHC class I genes and at least four expressed genes (although only two appear to be classical class I MHC) (23)(24)(25). However, the Inoko group has since published that only one of these two expressed classical loci is highly expressed (26), much like the chicken.…”

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confidence: 99%

Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks

Fleming-Canepa

Jensen

Mesa

et al. 2016

The Journal of Immunology

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MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual. To determine whether expressed alleles correspond to UAA adjacent to TAP2 as in domestic ducks, we cloned and sequenced genomic UAA-TAP2 fragments from all mallards, which matched transcripts recovered and allowed us to assign most alleles as UAA. Allelic differences are primarily located in α1 and α2 domains in the residues known to interact with peptide in mammalian MHC class I, suggesting the diversity is functional. Most UAA alleles have unique residues in the cleft predicting distinct specificity; however, six alleles have an unusual conserved cleft with two cysteine residues. Residues that influence peptide-loading properties and tapasin involvement in chicken are fixed in duck alleles and suggest tapasin independence. Biased expression of one MHC class I gene may make viral escape within an individual easy, but high diversity in the population places continual pressure on the virus in the reservoir species.

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“…Gene duplication among MHC-I genes has also been observed in many other representative vertebrates such as Atlantic salmon , frogs (Kiemnec-Tyburczy et al, 2012), birds (Shiina et al, 2004), iguanas (Glaberman and Caccone, 2008), and saltwater crocodile (Jaratlerdsiri et al, 2012;2014). Meanwhile, we found two putative pseudogenes, which contain premature stop codons.…”

Section: Xiuyun Yuan Et Al Mhc Class I Exon 4 In Eremias Multiocellatamentioning

confidence: 75%

“…So far, data from the α3 domain are frequently used to recover evolutionary relationships among class I sequences across species because they are relatively conserved in comparison to the two peptide-binding domains (α1, α2), which are often under balancing selection. MHC class I has been wellstudied in mammals (Kelley et al, 2005), birds (Shiina et al, 2004), and fishes (Shand and Dixon, 2001;Kulski et al, 2002). However, there is still limited knowledge of the MHC in non-avian reptiles, particularly in the key group of squamates.…”

Section: Introductionmentioning

confidence: 99%

MHC Class I Exon 4 in the Multiocellated Racerunners (Eremias multiocellata): Polymorphism, Duplication and Selection

Yuan¹,

Zeng²,

Guo³

2014

AHR

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The major histocompatibility complex (MHC) is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-anddeath evolution, gene conversion, and concerted evolution. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. However, the investigation of this region in nonavian reptiles is still in its infancy. We present the first characterization of MHC class I genes in a species from the family Lacertidae. We assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 4 among 37 individuals of Eremias multiocellata from a population in Lanzhou, China. We generated 67 distinct DNA sequences using cloning and sequencing methods, and identified 36 putative functional variants as well as two putative pseudogene-variants. We found the number of variants within an individual varying between two and seven, indicating that there are at least four MHC class I loci in this species. Gene duplication plays a role in increasing copy numbers of MHC genes and allelic diversity in this species. The class I exon 4 sequences are characteristic of low nucleotide diversity. No signal of recombination is detected, but purifying selection is detected in β2-microglobulin interaction sites and some other silent sites outside of the function-constraint regions. Certain identical alleles are shared by Eremias multiocellata and E. przewalskii and E. brenchleyi, suggesting trans-species polymorphism. The data are compatible with a birth-and-death model of evolution.class II genes, have been the subjects of the majority of research in the fields of ecology and evolution (reviewed in Sommer, 2005; Milinski, 2006;Piertney and Oliver, 2006;Ujvari and Belov, 2011). This is because MHC includes the most polymorphic genes in vertebrate populations. Given the extraordinary richness and diversity of continuously evolving pathogens in the environment, it is not surprising that the MHC harbors the most polymorphic genes described thus far, with some loci, such as the human HLA-B locus, possessing more than 2000 alleles (de Bakker and Raychaudhuri, 2012). The number of genes in the MHC varies enormously between species, even between individuals of the same species (Malaga-Trillo et al., 1998;Figueroa et al., 2001). It has been noted that balancing selection is an evolutionary force that can maintain many haplotypes over long periods of evolutionary time. Genes that

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Comparative Genomic Analysis of Two Avian (Quail and Chicken) MHC Regions

Cited by 147 publications

References 62 publications

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

No evidence for immunoproteasomes in chicken lymphoid organs and activated lymphocytes

Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks

MHC Class I Exon 4 in the Multiocellated Racerunners (Eremias multiocellata): Polymorphism, Duplication and Selection

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