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Arnaiz-Villena A, Suarez-Trujillo F, Juarez I, Rodríguez-Sainz C, Palacio-Gruber J, Vaquero-Yuste C, Molina-Alejandre M, Fernández-Cruz E, Martin-Villa JM. Evolution and molecular interactions of major histocompatibility complex (MHC)-G, -E and -F genes. Cell Mol Life Sci 2022; 79:464. [PMID: 35925520 PMCID: PMC9352621 DOI: 10.1007/s00018-022-04491-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Abstract
Classical HLA (Human Leukocyte Antigen) is the Major Histocompatibility Complex (MHC) in man. HLA genes and disease association has been studied at least since 1967 and no firm pathogenic mechanisms have been established yet. HLA-G immune modulation gene (and also -E and -F) are starting the same arduous way: statistics and allele association are the trending subjects with the same few results obtained by HLA classical genes, i.e., no pathogenesis may be discovered after many years of a great amount of researchers’ effort. Thus, we believe that it is necessary to follow different research methodologies: (1) to approach this problem, based on how evolution has worked maintaining together a cluster of immune-related genes (the MHC) in a relatively short chromosome area since amniotes to human at least, i.e., immune regulatory genes (MHC-G, -E and -F), adaptive immune classical class I and II genes, non-adaptive immune genes like (C2, C4 and Bf) (2); in addition to using new in vitro models which explain pathogenetics of HLA and disease associations. In fact, this evolution may be quite reliably studied during about 40 million years by analyzing the evolution of MHC-G, -E, -F, and their receptors (KIR—killer-cell immunoglobulin-like receptor, NKG2—natural killer group 2-, or TCR-T-cell receptor—among others) in the primate evolutionary lineage, where orthology of these molecules is apparently established, although cladistic studies show that MHC-G and MHC-B genes are the ancestral class I genes, and that New World apes MHC-G is paralogous and not orthologous to all other apes and man MHC-G genes. In the present review, we outline past and possible future research topics: co-evolution of adaptive MHC classical (class I and II), non-adaptive (i.e., complement) and modulation (i.e., non-classical class I) immune genes may imply that the study of full or part of MHC haplotypes involving several loci/alleles instead of single alleles is important for uncovering HLA and disease pathogenesis. It would mainly apply to starting research on HLA-G extended haplotypes and disease association and not only using single HLA-G genetic markers.
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Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain.
| | - Fabio Suarez-Trujillo
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Ignacio Juarez
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Carmen Rodríguez-Sainz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Palacio-Gruber
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Christian Vaquero-Yuste
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Marta Molina-Alejandre
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Eduardo Fernández-Cruz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Manuel Martin-Villa
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
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2
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Evolution of HLA-F and its orthologues in primate species: a complex tale of conservation, diversification and inactivation. Immunogenetics 2020; 72:475-487. [PMID: 33184728 PMCID: PMC7725694 DOI: 10.1007/s00251-020-01187-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
HLA-F represents one of the nonclassical MHC class I molecules in humans. Its main characteristics involve low levels of polymorphism in combination with a restricted tissue distribution. This signals that the gene product executes a specialised function, which, however, is still poorly understood. Relatively little is known about the evolutionary equivalents of this gene in nonhuman primates, especially with regard to population data. Here we report a comparative genetic analysis of the orthologous genes of HLA-F in various great ape, Old World monkey (OWM), and New World monkey (NWM) species. HLA-F-related transcripts were found in all subjects studied. Low levels of polymorphism were encountered, although the length of the predicted gene products may vary. In most species, one or two transcripts were discovered, indicating the presence of only one active F-like gene per chromosome. An exception was provided by a New World monkey species, namely, the common marmoset. In this species, the gene has been subject to duplication, giving rise to up to six F-like transcripts per animal. In humans, great apes, and OWM, and probably the majority of the NWM species, the evolutionary equivalents of the HLA-F gene experienced purifying selection. In the marmoset, however, the gene was initially duplicated, but the expansion was subjected afterwards to various mechanisms of genetic inactivation, as evidenced by the presence of pseudogenes and an array of genetic artefacts in a section of the transcripts.
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Arnaiz-Villena A, Juarez I, Suarez-Trujillo F, López-Nares A, Vaquero C, Palacio-Gruber J, Martin-Villa JM. HLA-G: Function, polymorphisms and pathology. Int J Immunogenet 2020; 48:172-192. [PMID: 33001562 DOI: 10.1111/iji.12513] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/04/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
HLA-G immune modulatory genes and molecules are presently being studied by a widespread number of research groups. In the present study, we do not aim to be exhaustive since the number of manuscripts published every year is overwhelming. Instead, our aim is pointing out facts about HLA-G function, polymorphism and pathology that have been confirmed by several different researchers, together with exposing aspects that may have been overlooked or not sufficiently remarked in this productive field of study. On the other hand, we question whether performing mainly studies on HLA-G and disease associations is going to give a clear answer in the future, since 40 years of study of classical HLA molecules association with disease has still given no definite answer on this issue.
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Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Ignacio Juarez
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Fabio Suarez-Trujillo
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Adrián López-Nares
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Christian Vaquero
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Jose Palacio-Gruber
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Jose M Martin-Villa
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, Wright SI, Weigel D. Long-term balancing selection drives evolution of immunity genes in Capsella. eLife 2019; 8:e43606. [PMID: 30806624 PMCID: PMC6426441 DOI: 10.7554/elife.43606] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.
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Affiliation(s)
- Daniel Koenig
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Jörg Hagmann
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Rachel Li
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Felix Bemm
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Tanja Slotte
- Department of Ecology,Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Barbara Neuffer
- Department of BiologyUniversity of OsnabrückOsnabrückGermany
| | - Stephen I Wright
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoCanada
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
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Lugo JS, Cadavid LF. Patterns of MHC-G-Like and MHC-B Diversification in New World Monkeys. PLoS One 2015; 10:e0131343. [PMID: 26121030 PMCID: PMC4486459 DOI: 10.1371/journal.pone.0131343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/01/2015] [Indexed: 11/29/2022] Open
Abstract
The MHC class I (MHC-I) region in New World monkeys (Platyrrhini) has remained relatively understudied. To evaluate the diversification patterns and transcription behavior of MHC-I in Platyrrhini, we first analyzed public genomic sequences from the MHC-G-like subregion in Saimiri boliviensis, Ateles geoffroyi and Callicebus moloch, and from the MHC-B subregion in Saimiri boliviensis. While S. boliviensis showed multiple copies of both MHC-G-like (10) and –B (15) loci, A. geoffroyi and C. moloch had only three and four MHC-G-like genes, respectively, indicating that not all Platyrrhini species have expanded their MHC-I loci. We then sequenced MHC-G-like and -B cDNAs from nine Platyrrhini species, recovering two to five unique cDNAs per individual for both loci classes. In two Saguinus species, however, no MHC-B cDNAs were found. In phylogenetic trees, MHC-G-like cDNAs formed genus-specific clusters whereas the MHC-B cDNAs grouped by Platyrrhini families, suggesting a more rapid diversification of the former. Furthermore, cDNA sequencing in 12 capuchin monkeys showed that they transcribe at least four MHC-G-like and five MHC-B polymorphic genes, showing haplotypic diversity for gene copy number and signatures of positive natural selection at the peptide binding region. Finally, a quantitative index for MHC:KIR affinity was proposed and tested to predict putative interacting pairs. Altogether, our data indicate that i) MHC-I genes has expanded differentially among Platyrrhini species, ii) Callitrichinae (tamarins and marmosets) MHC-B loci have limited or tissue-specific expression, iii) MHC-G-like genes have diversified more rapidly than MHC-B genes, and iv) the MHC-I diversity is generated mainly by genetic polymorphism and gene copy number variation, likely promoted by natural selection for ligand binding.
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Affiliation(s)
- Juan S. Lugo
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Luis F. Cadavid
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail:
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Cao YH, Fan JW, Li AX, Liu HF, Li LR, Zhang CL, Zeng L, Sun ZZ. Identification of MHC I class genes in two Platyrrhini species. Am J Primatol 2015; 77:527-34. [PMID: 25573376 DOI: 10.1002/ajp.22372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 11/22/2014] [Accepted: 11/30/2014] [Indexed: 11/07/2022]
Abstract
The major histocompatibility complex is a diverse gene family that plays a crucial role in the adaptive immune system. In humans, the MHC class I genes consist of the classical loci of HLA-A, -B, and -C, and the nonclassical loci HLA-E, -F, and -G. In Platyrrhini species, few MHC class I genes have been described so far and were classified as MHC-E, MHC-F, and MHC-G, with MHC-G possibly representing a classical MHC class I locus while there were arguments about the existence of the MHC-B locus in Platyrrhini. In this study, MHC class I genes were identified in eight common marmosets (Callithrix jacchus) and two brown-headed spider monkeys (Ateles fusciceps). For common marmosets, 401 cDNA sequences were sequenced and 18 alleles were detected, including 14 Caja-G alleles and 4 Caja-B alleles. Five to eleven Caja-G alleles and one to three Caja-B alleles were detected in each animal. For brown-headed spider monkeys, 102 cDNA sequences were analyzed, and 9 new alleles were identified, including 5 Atfu-G and 4 Atfu-B alleles. Two or three Atfu-G and two Atfu-B alleles were obtained for each of animal. In phylogenetic analyses, the MHC-G and -B alleles from the two species and other Platyrrhini species show locus-specific clusters with bootstrap values of 86% and 50%. The results of pairwise sequence comparisons and an excess of non-synonymous nucleotide substitutions in the PBR region are consistent with the suggestion that Caja-G and Atfu-G may be classical MHC class I loci in the Platyrrhini species… But it appears that MHC-B locus of the two Platyrrhini species shares features with both classical and nonclasical MHC class I loci. Our results are an important addition to the limited MHC immunogenetic information available for the Platyrrhini species.
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Affiliation(s)
- Yu-Hua Cao
- Laboratory Animal Center of the Academy of Military Medical Science, Beijing, China; College of Life Sciences of Tarim University, Alaer, China
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8
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Pratheek BM, Nayak TK, Sahoo SS, Mohanty PK, Chattopadhyay S, Chakraborty NG, Chattopadhyay S. Mammalian non-classical major histocompatibility complex I and its receptors: Important contexts of gene, evolution, and immunity. INDIAN JOURNAL OF HUMAN GENETICS 2014; 20:129-41. [PMID: 25400340 PMCID: PMC4228563 DOI: 10.4103/0971-6866.142855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The evolutionary conserved, less-polymorphic, nonclassical major histocompatibility complex (MHC) class I molecules: Qa-1 and its human homologue human leukocyte antigen-E (HLA-E) along with HLA-F, G and H cross-talk with the T-cell receptors and also interact with natural killer T-cells and other lymphocytes. Moreover, these nonclassical MHC molecules are known to interact with CD94/NKG2 heterodimeric receptors to induce immune responses and immune regulations. This dual role of Qa-1/HLA-E in terms of innate and adaptive immunity makes them more interesting. This review highlights the new updates of the mammalian nonclassical MHC-I molecules in terms of their gene organization, evolutionary perspective and their role in immunity.
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Affiliation(s)
- B M Pratheek
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Tapas K Nayak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Subhransu S Sahoo
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | | | - Soma Chattopadhyay
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Ntiya G Chakraborty
- Department of Medicine, University of Connecticut Health Center, Farmington, USA
| | - Subhasis Chattopadhyay
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
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Castelli EC, Ramalho J, Porto IOP, Lima THA, Felício LP, Sabbagh A, Donadi EA, Mendes-Junior CT. Insights into HLA-G Genetics Provided by Worldwide Haplotype Diversity. Front Immunol 2014; 5:476. [PMID: 25339953 PMCID: PMC4186343 DOI: 10.3389/fimmu.2014.00476] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Human leukocyte antigen G (HLA-G) belongs to the family of non-classical HLA class I genes, located within the major histocompatibility complex (MHC). HLA-G has been the target of most recent research regarding the function of class I non-classical genes. The main features that distinguish HLA-G from classical class I genes are (a) limited protein variability, (b) alternative splicing generating several membrane bound and soluble isoforms, (c) short cytoplasmic tail, (d) modulation of immune response (immune tolerance), and (e) restricted expression to certain tissues. In the present work, we describe the HLA-G gene structure and address the HLA-G variability and haplotype diversity among several populations around the world, considering each of its major segments [promoter, coding, and 3′ untranslated region (UTR)]. For this purpose, we developed a pipeline to reevaluate the 1000Genomes data and recover miscalled or missing genotypes and haplotypes. It became clear that the overall structure of the HLA-G molecule has been maintained during the evolutionary process and that most of the variation sites found in the HLA-G coding region are either coding synonymous or intronic mutations. In addition, only a few frequent and divergent extended haplotypes are found when the promoter, coding, and 3′UTRs are evaluated together. The divergence is particularly evident for the regulatory regions. The population comparisons confirmed that most of the HLA-G variability has originated before human dispersion from Africa and that the allele and haplotype frequencies have probably been shaped by strong selective pressures.
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Affiliation(s)
- Erick C Castelli
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Jaqueline Ramalho
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Iane O P Porto
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Thálitta H A Lima
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Leandro P Felício
- Biological Sciences Institute, Federal University of Goias , Goiânia , Brazil
| | - Audrey Sabbagh
- UMR 216, Institut de Recherche pour le Développement, MERIT , Paris , France ; Faculté de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité , Paris , France
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
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10
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Major histocompatibility complex I mediates immunological tolerance of the trophoblast during pregnancy and may mediate rejection during parturition. Mediators Inflamm 2014; 2014:579279. [PMID: 24812442 PMCID: PMC4000645 DOI: 10.1155/2014/579279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 02/16/2014] [Accepted: 02/18/2014] [Indexed: 12/30/2022] Open
Abstract
During pregnancy in larger mammals, the maternal immune system must tolerate the fetus for months while resisting external infection. This tolerance is facilitated by immunological communication between the fetus and the mother, which is mediated by Major Histocompatibility Complex I (MHC I) proteins, by leukocytes, and by the cytokines secreted by the leukocytes. Fetal-maternal immunological communication also supports pregnancy by inducing physiological changes in the mother. If the mother “misunderstands” the signal sent by the fetus during pregnancy, the fetus will be miscarried or delivered preterm. Unlike any other maternal organ, the placenta can express paternal antigens. At parturition, paternal antigens are known to be expressed in cows and may be expressed in horses, possibly so that the maternal immune system will reject the placenta and help to expel it. This review compares fetal-maternal crosstalk that is mediated by the immune system in three species with pregnancies that last for nine months or longer: humans, cattle, and horses. It raises the possibility that immunological communication early in pregnancy may prepare the mother for successful expulsion of fetal membranes at parturition.
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11
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The repertoire of MHC class I genes in the common marmoset: evidence for functional plasticity. Immunogenetics 2013; 65:841-9. [PMID: 24018468 DOI: 10.1007/s00251-013-0732-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/24/2013] [Indexed: 12/23/2022]
Abstract
In humans, the classical antigen presentation function of major histocompatibility complex (MHC) class I molecules is controlled by the human leukocyte antigen HLA -A, HLA-B and HLA-C loci. A similar observation has been made for great apes and Old World monkey species. In contrast, a New World monkey species such as the cotton-top tamarin (Saguinus oedipus) appears to employ the G locus for its classical antigen presentation function. At present, little is known about the classical MHC class I repertoire of the common marmoset (Callithrix jacchus), another New World monkey that is widely used in biomedical research. In the present population study, no evidence has been found for abundant transcription of classical I class genes. However, in each common marmoset, four to seven different G-like alleles were detected, suggesting that the ancestral locus has been subject to expansion. Segregation studies provided evidence for at least two G-like genes present per haplotype, which are transcribed by a variety of cell types. The alleles of these Caja-G genes cluster in separate lineages, suggesting that the loci diversified considerably after duplication. Phylogenetic analyses of the introns confirm that the Caja-G loci cluster in the vicinity of HLA-G, indicating that both genes shared an ancestor. In contrast to HLA-G, Caja-G shows considerable polymorphism at the peptide-binding sites. This observation, together with the lack of detectable transcripts of A and B-like genes, indicates that Caja-G genes have taken over the function of classical class I genes. These data highlight the extreme plasticity of the MHC class I gene system.
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12
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Ward JM, Vallender EJ. The resurgence and genetic implications of New World primates in biomedical research. Trends Genet 2012; 28:586-91. [PMID: 23099234 PMCID: PMC3500444 DOI: 10.1016/j.tig.2012.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/04/2012] [Accepted: 09/19/2012] [Indexed: 11/30/2022]
Abstract
There has been a recent resurgence of interest in New World monkeys within the biomedical research community, driven by both the sequencing of the common marmoset (Callithrix jacchus) genome and a growing demand for alternatives to Old World primates. New World monkeys offer attractive advantages over Old World species, including cheaper and simpler husbandry, while still maintaining a greater evolutionary proximity to humans compared with other animal models. Although numerous commonalities across primate species exist, there are also important genetic and reproductive differences that can and should play a critical role in selecting appropriate animal models. Common marmosets in particular have significantly reduced diversity at the major histocompatibility complex (MHC) loci and are born as hematopoietic chimeras. New World primates can make ideal translational models for research, but scientists must necessarily incorporate complete understandings of their genetic and phenotypic differences from humans and other model organisms.
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Affiliation(s)
- Joshua M. Ward
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA
| | - Eric J. Vallender
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA
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Kiemnec-Tyburczy KM, Richmond JQ, Savage AE, Lips KR, Zamudio KR. Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication. Heredity (Edinb) 2012; 109:146-55. [PMID: 22549517 DOI: 10.1038/hdy.2012.22] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Comparative studies of major histocompatibility complex (MHC) genes across vertebrate species can reveal the evolutionary processes that shape the structure and function of immune regulatory proteins. In this study, we characterized MHC class I sequences from six frog species representing three anuran families (Hylidae, Centrolenidae and Ranidae). Using cDNA from our focal species, we amplified a total of 79 unique sequences spanning exons 2-4 that encode the extracellular domains of the functional alpha chain protein. We compared intra- and interspecific nucleotide and amino-acid divergence, tested for recombination, and identified codon sites under selection by estimating the rate of non-synonymous to synonymous substitutions with multiple codon-based maximum likelihood methods. We determined that positive (diversifying) selection was acting on specific amino-acid sites located within the domains that bind pathogen-derived peptides. We also found significant signals of recombination across the physical distance of the genes. Finally, we determined that all the six species expressed two or three putative classical class I loci, in contrast to the single locus condition of Xenopus laevis. Our results suggest that MHC evolution in anurans is a dynamic process and that variation in numbers of loci and genetic diversity can exist among taxa. Thus, the accumulation of genetic data for more species will be useful in further characterizing the relative importance of processes such as selection, recombination and gene duplication in shaping MHC loci among amphibian lineages.
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Affiliation(s)
- K M Kiemnec-Tyburczy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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Mee ET, Greenhow J, Rose NJ. Characterisation of Mhc class I and class II DRB polymorphism in red-bellied tamarins (Saguinus labiatus). Immunogenetics 2011; 63:619-26. [PMID: 21681586 DOI: 10.1007/s00251-011-0546-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/01/2011] [Indexed: 12/12/2022]
Abstract
The infection of red-bellied tamarins (Saguinus labiatus) with GB virus B (GBV-B) is an important surrogate model of hepatitis C virus infection in man. To fully exploit the value of this model, we have characterised MHC class I G and class II DRB alleles in eight tamarins representing a cross-section of a UK breeding colony. The results indicated a high degree of classes I and II DRB allele sharing. Each animal transcribed three to four putative surface-expressed class I alleles and two to four class II DRB alleles. Most animals also transcribed at least one class I allele predicted to result in a C-terminal truncated protein. These results represent the first description of MHC polymorphism in this species and provide a foundation for characterisation of MHC diversity in breeding populations of red-bellied tamarins. The data will facilitate the identification of associations between MHC polymorphism and control of viral infections, and detailed dissection of cellular immune responses against GBV-B.
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Affiliation(s)
- Edward T Mee
- Division of Retrovirology, National Institute for Biological Standards and Control, Health Protection Agency, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK.
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15
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Goyos A, Sowa J, Ohta Y, Robert J. Remarkable conservation of distinct nonclassical MHC class I lineages in divergent amphibian species. THE JOURNAL OF IMMUNOLOGY 2010; 186:372-81. [PMID: 21115732 DOI: 10.4049/jimmunol.1001467] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nonclassical MHC class Ib (class Ib) genes are heterogeneous genes encoding molecules that are structurally similar to classical MHC class Ia molecules but with limited tissue distribution and polymorphism. Mammalian class Ib genes have diverse and often uncharacterized functions, and because of their rapid rate of evolution, class Ib phylogeny is difficult to establish. We have conducted an extensive genomic, molecular, and phylogenetic characterization of class Ib genes in two Xenopodinae amphibian species of different genera that diverged from a common ancestor as long ago as primates and rodents (∼65 million years). In contrast with the unsteadiness of mammalian class Ib genes, our results reveal an unusual degree of conservation of most Xenopodinae class Ib gene lineages, including a novel monogenic lineage represented by the divergent Xenopus laevis XNC10 gene and its unequivocal Silurana (Xenopus) tropicalis orthologue, SNC10. The preferential expression of this gene lineage by thymocytes themselves from the onset of thymic organogenesis is consistent with a specialized role of class Ib in early T cell development and suggests such a function is conserved in all tetrapods.
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Affiliation(s)
- Ana Goyos
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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16
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Donadi EA, Castelli EC, Arnaiz-Villena A, Roger M, Rey D, Moreau P. Implications of the polymorphism of HLA-G on its function, regulation, evolution and disease association. Cell Mol Life Sci 2010; 68:369-95. [PMID: 21107637 PMCID: PMC3021195 DOI: 10.1007/s00018-010-0580-7] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 10/22/2010] [Indexed: 12/27/2022]
Abstract
The HLA-G gene displays several peculiarities that are distinct from those of classical HLA class I genes. The unique structure of the HLA-G molecule permits a restricted peptide presentation and allows the modulation of the cells of the immune system. Although polymorphic sites may potentially influence all biological functions of HLA-G, those present at the promoter and 3′ untranslated regions have been particularly studied in experimental and pathological conditions. The relatively low polymorphism observed in the MHC-G coding region both in humans and apes may represent a strong selective pressure for invariance, whereas, in regulatory regions several lines of evidence support the role of balancing selection. Since HLA-G has immunomodulatory properties, the understanding of gene regulation and the role of polymorphic sites on gene function may permit an individualized approach for the future use of HLA-G for therapeutic purposes.
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Affiliation(s)
- Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, 14049-900 Ribeirão Preto, SP, Brazil.
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17
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Parga-Lozano C, Reguera R, Gomez-Prieto P, Arnaiz-Villena A. Evolution of major histocompatibility complex G and C and natural killer receptors in primates. Hum Immunol 2009; 70:1035-40. [PMID: 19651181 DOI: 10.1016/j.humimm.2009.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 07/25/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
Abstract
Major histocompatibility complex (MHC)-G and -C molecules bear ligands to natural killer immunoglobulin receptors (KIR). MHC-G evolution in primates shows some anomalies. In New World monkeys MHC-G molecules show a high polymorphism and most likely are classical antigen presenters; they also cluster closer to MHC-E in a relatedness dendrogram. Their genes lack intron 2 deletion, which is typical of all other primates in regard to MHC-G. Medium-sized Eurasian-African monkeys (Cercopithecinae) show stop codons in exon 3: only MHC-G isoforms without exon 3 are possible. Big apes such as the orangutan, gorilla, and chimpanzee as well as human beings show limited HLA-G polymorphism. HLA-C has not been found in medium-size Eurasian-African monkeys, but we have found MHC-C DNA sequences in more evolutionary ancient New World monkeys. Taking into account that the KIR inhibitory receptors signal is dominated by MHC-C in human beings, this suggests that both MHC-C molecules and their ligands within natural killer lymphocyte KIR also exist in the most evolutionary ancient apes (New World monkeys were present on Earth before 40 million years ago), as KIR receptors also appeared before 130 million years ago in evolution. Indeed, KIR receptor genes have recently been found in a New World monkey.
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Affiliation(s)
- Carlos Parga-Lozano
- Department of Immunology, University Complutense, The Madrid Regional Blood Center, Madrid, Spain
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18
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Blokhuis JH, van der Wiel MK, Doxiadis GGM, Bontrop RE. Evidence for balancing selection acting on KIR2DL4 genotypes in rhesus macaques of Indian origin. Immunogenetics 2009; 61:503-12. [PMID: 19506858 DOI: 10.1007/s00251-009-0379-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
The interaction of killer-cell immunoglobulin-like receptors (KIR) and their respective major histocompatibility complex (MHC) ligands can alter the activation state of the natural killer (NK) cell. In both humans and rhesus macaques, particular types of non-classical MHC class I molecules are predominantly expressed on the trophoblast. In humans, human leukocyte antigen G has been demonstrated to act as a ligand for KIR2DL4, present on all NK cells, whereas Mamu-AG may execute a similar function in rhesus macaques. During primate evolution, orthologues of KIR2DL4 appear to have been highly conserved, suggesting strong purifying selection. A cohort of 112 related and unrelated rhesus macaques of mostly Indian origin were selected to study their KIR2DL4 genes for the occurrence of polymorphism. Comparison of the proximal region provided evidence for strong conservative selection acting on the exons encoding the Ig domains. As is found in humans, in the Indian rhesus macaque population, two different KIR2DL4 entities are encountered, which differ for their intra-cellular signalling motifs. One genotype contains a complex mutation in the distal region of exon 9, which negates a serine/threonine kinase site. Furthermore, both allelic entities are present in a distribution, which suggests that balancing selection is operating on these two distinct forms of KIR2DL4.
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Affiliation(s)
- Jeroen H Blokhuis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 139, Rijswijk, 2288 GJ, The Netherlands.
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19
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Abstract
The major histocompatibility complex (MHC)-F class Ib locus shows a limited polymorphism, and the function of its mainly intracellular protein is not clear. We have identified human leukocyte antigen (HLA)-F orthologous DNA sequences in Pongidae in order to study the MHC-F gene evolution and its products' function. HLA-F orthologous complementary DNA transcripts are found in chimpanzee and in the new primate species studied (bonobo, gorilla and orangutan). Analyses of the predicted amino acid sequences and their comparison with other primate MHC-F proteins show that MHC-F may be a protein with a typical class I structure and that the key residues of the peptide-binding region are highly conserved in MHC-F in all studied primates species. Thus, MHC-F conservation along the primate evolution suggests an important role in cellular physiology. It is possible that the MHC-F protein could be involved, together with MHC-G and MHC-E, in the natural killer cell activity regulation, although rhesus macaque cannot express complete surface MHC-G orthologue molecules.
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Affiliation(s)
- J Moscoso
- Department of Immunology, The Madrid Regional Blood Center, Universidad Complutense, Madrid, Spain
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20
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Rölleke U, Flügge G, Plehm S, Schlumbohm C, Armstrong VW, Dressel R, Uchanska-Ziegler B, Ziegler A, Fuchs E, Czéh B, Walter L. Differential expression of major histocompatibility complex class I molecules in the brain of a New World monkey, the common marmoset (Callithrix jacchus). J Neuroimmunol 2006; 176:39-50. [PMID: 16750573 DOI: 10.1016/j.jneuroim.2006.04.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 04/06/2006] [Accepted: 04/10/2006] [Indexed: 11/18/2022]
Abstract
It has been supposed that central nervous neurons do not express MHC class I molecules. However, recent studies clearly demonstrated functional MHC class I expression in the rodent brain. In the present study, we have extended these studies and investigated the presence of MHC class I transcripts and proteins in the brain of a non-human primate species, the common marmoset monkey (Callithrix jacchus). Using in-situ hybridization, we found strong expression of MHC class I transcripts in neocortex, hippocampal formation, substantia nigra and nucleus ruber. In-situ hybridization with emulsion autoradiography demonstrated MHC class I mRNA in distinct pyramidal neurons of cortex and hippocampus, in granule neurons of the dentate gyrus, in dopaminergic neurons of substantia nigra and in motor neurons of nucleus ruber. Immunocytochemistry confirmed MHC class I protein expression in these neurons. Two monoclonal antibodies, MRC-Ox18 and HB115, reacted differentially with MHC class I proteins on neuronal and non-neuronal cells, respectively. Interestingly, in marmoset monkeys that were immunosuppressed with FK506 (tacrolimus), expression of neuronal MHC class I proteins, which could be detected with MRC-Ox18, was either very low (neocortex, nucleus ruber, substantia nigra) or absent (hippocampus). In contrast, class I expression in endothelial cells, which was detected by HB115, was not affected by immunosuppression. Our data show that selected neurons in the brain of a non-human primate express MHC class I molecules and that this expression can be modulated by immunosuppression.
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Affiliation(s)
- Ulrike Rölleke
- Department of Primate Genetics, German Primate Center, Göttingen, Germany
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21
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Bontrop RE. Comparative genetics of MHC polymorphisms in different primate species: duplications and deletions. Hum Immunol 2006; 67:388-97. [PMID: 16728259 DOI: 10.1016/j.humimm.2006.03.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Indexed: 11/25/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) play a crucial role in the activation of adaptive (antigen-dependent) immune responses. In this paper similarities and dissimilarities among the MHCs of different primate species and their functional implications are reviewed. The human HLA system represents the most thoroughly investigated MHC of any contemporary living primate species, and so it will serve as a reference.
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Affiliation(s)
- Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, GH Rijswijk, The Netherlands.
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22
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Joly E, Rouillon V. The orthology of HLA-E and H2-Qa1 is hidden by their concerted evolution with other MHC class I molecules. Biol Direct 2006; 1:2. [PMID: 16542007 PMCID: PMC1403747 DOI: 10.1186/1745-6150-1-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 01/31/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whether MHC molecules undergo concerted evolution or not has been the subject of a long-standing debate. RESULTS By comparing sequences of eight functional homologues of HLA-E from primates and rodents with those of MHC class Ia molecules from the same eight species, we find that different portions of MHC class I molecules undergo different patterns of evolution. By focusing our analyses sequentially on these various portions, we have obtained clear evidence for concerted evolution of MHC class I molecules, suggesting the occurrence of extensive interallelic and intergenic exchanges. Intra-species homogenisation of sequences is particularly noticeable at the level of exon 4, which codes for the alpha3 domain, but our results suggest that homogenisation also concerns certain residues of the alpha1-alpha2 codomain that lie outside the antigen recognition site. CONCLUSION A model is presented in which Darwinian selective pressures due to pathogens could, at the same time, favour diversification of MHC class Ia molecules and promote concerted evolution of separate loci by spreading advantageous motifs arising by mutations in individual MHC molecules to other alleles and to other loci of the MHC region. This would also allow MHC molecules to co-evolve with the proteins with which they interact to fulfil their functions of antigen presentation and regulation of NK cell activity. One of the raisons d'être of the MHC may therefore be to favour at the same time both diversification of MHC class Ia molecules and homogenisation of the whole pool of MHC class I molecules (Ia and Ib) involved in antigen presentation. REVIEWERS This article was reviewed by Stephan Beck, Lutz Walter and Pierre Pontarotti.
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Affiliation(s)
- Etienne Joly
- Equipe de Neuro-Immuno-Génétique Moléculaire, IPBS, UMR CNRS 5089, 205 route de Narbonne, 31077 Toulouse Cedex, France
| | - Virginie Rouillon
- Equipe de Neuro-Immuno-Génétique Moléculaire, IPBS, UMR CNRS 5089, 205 route de Narbonne, 31077 Toulouse Cedex, France
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23
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Rojo R, Castro MJ, Martinez-Laso J, Serrano-Vela JI, Morales P, Moscoso J, Zamora J, Arnaiz-Villena A. MHC-F DNA sequences in bonobo, gorilla and orangutan. ACTA ACUST UNITED AC 2005; 66:277-83. [PMID: 16185322 DOI: 10.1111/j.1399-0039.2005.00477.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC)-F class Ib locus shows a limited polymorphism, and the function of its mainly intracellular protein is not clear. We have identified human leucocyte antigen (HLA)-F orthologous DNA sequences in Pongidae in order to study the MHC-F gene evolution and its products' function. HLA-F orthologous cDNA transcripts are found in chimpanzee and in the new primate species studied (bonobo, gorilla and orangutan). Analyses of the predicted amino acid sequences and their comparison with other primate MHC-F proteins show that MHC-F may be a protein with a typical class I structure and that the key residues of the peptide-binding region (PBR) are highly conserved in MHC-F in all studied primates species. Thus, MHC-F conservation along the primate evolution suggests an important role in cellular physiology. It is possible that the MHC-F protein could be involved, together with MHC-G and MHC-E, in the natural killer (NK) cell activity regulation, although rhesus macaque does not express MHC-G and MHC-E orthologues. The evolutionary pathway of the six-base-pair deletion at exon 2 existing in some primates is put forward.
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Affiliation(s)
- R Rojo
- Department of Inmunologia, H. 12 Octubre, H. Clinico San Carlos, Universidad Complutense, Madrid, Spain
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24
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Abstract
Spondyloarthropathy is a common occurrence in Old World primates, with only limited presence in New World monkeys. Clearly distinguished from rheumatoid arthritis, this erosive arthritis afflicts 20% of great apes, baboons, and rhesus macaques and had been increasing in frequency. Habitat-dependent infectious agent diarrhea-induced reactive arthritis is implicated on a background of genetic predisposition. A gorilla-derived therapeutic preventative approach has possible application in human clinical medicine.
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Affiliation(s)
- Bruce M Rothschild
- Arthritis Center of Northeast Ohio, 5500 Market Street, Youngstown, OH 44512, USA.
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25
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Sawai H, Kawamoto Y, Takahata N, Satta Y. Evolutionary relationships of major histocompatibility complex class I genes in simian primates. Genetics 2005; 166:1897-907. [PMID: 15126407 PMCID: PMC1470823 DOI: 10.1534/genetics.166.4.1897] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
New World monkeys (NWMs) occupy a critical phylogenetic position in elucidating the evolutionary process of major histocompatibility complex (MHC) class I genes in primates. From three subfamilies of Aotinae, Cebinae, and Atelinae, the 5'-flanking regions of 18 class I genes are obtained and phylogenetically examined in terms of Alu/LINE insertion elements as well as the nucleotide substitutions. Two pairs of genes from Aotinae and Atelinae are clearly orthologous to human leukocyte antigen (HLA) -E and -F genes. Of the remaining 14 genes, 8 belong to the distinct group B, together with HLA-B and -C, to the exclusion of all other HLA class I genes. These NWM genes are classified into four groups, designated as NWM-B1, -B2, -B3, and -B4. Of these, NWM-B2 is orthologous to HLA-B/C. Also, orthologous relationships of NWM-B1, -B2, and -B3 exist among different families of Cebidae and Atelidae, which is in sharp contrast to the genus-specific gene organization within the subfamily Callitrichinae. The other six genes belong to the distinct group G. However, a clade of these NWM genes is almost equally related to HLA-A, -J, -G, and -K, and there is no evidence for their orthologous relationships to HLA-G. It is argued that class I genes in simian primates duplicated extensively in their common ancestral lineage and that subsequent evolution in descendant species has been facilitated mainly by independent loss of genes.
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Affiliation(s)
- Hiromi Sawai
- Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
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26
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Sawai H, Kawamoto Y, Takahata N, Satta Y. Evolutionary Relationships of Major Histocompatibility Complex Class I Genes in Simian Primates. Genetics 2004. [DOI: 10.1093/genetics/166.4.1897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
New World monkeys (NWMs) occupy a critical phylogenetic position in elucidating the evolutionary process of major histocompatibility complex (MHC) class I genes in primates. From three subfamilies of Aotinae, Cebinae, and Atelinae, the 5′-flanking regions of 18 class I genes are obtained and phylogenetically examined in terms of Alu/LINE insertion elements as well as the nucleotide substitutions. Two pairs of genes from Aotinae and Atelinae are clearly orthologous to human leukocyte antigen (HLA) -E and -F genes. Of the remaining 14 genes, 8 belong to the distinct group B, together with HLA-B and -C, to the exclusion of all other HLA class I genes. These NWM genes are classified into four groups, designated as NWM-B1, -B2, -B3, and -B4. Of these, NWM-B2 is orthologous to HLA-B/C. Also, orthologous relationships of NWM-B1, -B2, and -B3 exist among different families of Cebidae and Atelidae, which is in sharp contrast to the genus-specific gene organization within the subfamily Callitrichinae. The other six genes belong to the distinct group G. However, a clade of these NWM genes is almost equally related to HLA-A, -J, -G, and -K, and there is no evidence for their orthologous relationships to HLA-G. It is argued that class I genes in simian primates duplicated extensively in their common ancestral lineage and that subsequent evolution in descendant species has been facilitated mainly by independent loss of genes.
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Affiliation(s)
- Hiromi Sawai
- Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
| | - Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Naoyuki Takahata
- Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
| | - Yoko Satta
- Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
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27
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Doyle CK, Cook RG, Rich RR, Rodgers JR. Cotton rat Sihi-M3 is a minimally oligomorphic Mhc I-b molecule that binds the chemotactic peptide fMLF under stringent conditions. Evidence that positive selection drives inter-species diversity of residues interacting with the termini of short peptides. Immunogenetics 2003; 55:389-94. [PMID: 12942207 DOI: 10.1007/s00251-003-0593-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Revised: 06/18/2003] [Indexed: 11/27/2022]
Abstract
The leading model for class I-b evolution suggests non-polymorphic I-b genes evolve by gene duplication from polymorphic I-a genes. We recently found N-formyl peptide-specific orthologs of the class I-b gene H2-M3 in the rodent subfamily Sigmodontinae. To test if sigmodont M3 is a I-b gene, we sequenced M3 from wild cotton rats ( Sigmodon hispidus) diverse at the class II locus, Sihi-DQA. These haplotypes carry a single allele of M3 that closely resembles H2-M3. However, peptide-binding assays showed that cotton rat M3 bound the chemotactic N-formylpeptide fMLF better than did rat or mouse M3. The Ala116-->Lys substitution in cotton rat M3 might enhance binding of fMLF and is one of eight residues of M3 that interact with ligand residues P3 and P4 and that are positively selected, with a d(N) /d(S) ratio of 1.8. Thus, M3 is a class I-b gene in both sigmodontine and murine murids, but positive selection operates on a small subset of residues in the traditionally defined antigen recognition site.
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Affiliation(s)
- C Kuyler Doyle
- Department of Immunology, Baylor College of Medicine, TX 77030, Houston, USA
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28
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Abstract
The Human Genome Project transformed the quest of more than 50 years to understand the major histocompatibility complex (Mhc). The sequence of the Mhc from human and mouse, together with a large amount of sequence and mapping information from several other species, allows us to draw general conclusions about the organization and origin of this crucial part of the immune system. The Mhc is a mosaic of stretches formed by conserved and nonconserved genes. Surprisingly, of the approximately 3.6-Mb Mhc, the stretches that encode the class I and class II genes, which epitomize the Mhc, are the least conserved part, whereas the approximately 1.7-Mb stretches that encode at least 115 other genes are highly conserved. We summarize the available data to answer the questions (a) What is the Mhc? and (b) How can we define it in a general, not species-specific, way? Knowing what is essential and what is incidental helps us understand the fundamentals of the Mhc, and defining the species differences makes the model organisms more useful.
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Affiliation(s)
- Attila Kumánovics
- Center for Immunology University of Texas Southwestern Medical Center, Dallas 75390-9050, USA.
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29
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Suárez CF, Cárdenas PP, Llanos-Ballestas EJ, Martínez P, Obregón M, Patarroyo ME, Patarroyo MA. Alpha1 and alpha2 domains of Aotus MHC class I and Catarrhini MHC class Ia share similar characteristics. TISSUE ANTIGENS 2003; 61:362-73. [PMID: 12753655 DOI: 10.1034/j.1399-0039.2003.00045.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Functional and structural analyses of major histocompatibility complex (MHC) class I molecules of the Aotus genus are necessary to validate it as a solid animal model for biomedical research. We thus isolated, cloned and sequenced exons 2 and 3 from three Aotus species (A. nancymaae, A. nigriceps and A. vociferans). We found 24 sequences, which divided into two different groups (Ao-g1 and Ao-g2). A further sequence was identified as a processed pseudogene (Aona-PS2). Both sequence evolution and variability analyses showed that Ao-g1 and Ao-g2 display similar characteristics to Catarrhini's classical loci, such as positive selection pressure at the peptide binding region (PBR) high variability and a trans-specific evolution pattern.
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Affiliation(s)
- C F Suárez
- Fundación Instituto de Inmunología de Colombia, FIDIC, Bogotá, Colombia.
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30
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Carosella ED, Moreau P, Le Maoult J, Le Discorde M, Dausset J, Rouas-Freiss N. HLA-G Molecules: from Maternal–Fetal Tolerance to Tissue Acceptance. Adv Immunol 2003; 81:199-252. [PMID: 14711057 DOI: 10.1016/s0065-2776(03)81006-4] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past few years, HLA-G, the non-classical HLA class I molecule, has been the center of investigations that have led to the description of its specific structural and functional properties. Although located in the HLA class I region of chromosome six, the HLA-G gene may be distinguished from other HLA class I genes by its low polymorphism and alternative splicing that generates seven HLA-G proteins, whose tissue-distribution is restricted to normal fetal and adult tissues that display a tolerogeneic function toward both innate and acquired immune cells. We review these points, with special emphasis on the role of HLA-G in human pathologies, such as cancer, viral infection, and inflammatory diseases, as well as in organ transplantation.
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Affiliation(s)
- Edgardo D Carosella
- Service de Recherches en Hémato-Immunologie, Direction des Sciences du Vivant, Département de Recherche Médicale, CEA Commissariat à l'Energie Atomique, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, 75010 Paris, France.
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31
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Langat DK, Hunt JS. Do nonhuman primates comprise appropriate experimental models for studying the function of human leukocyte antigen-G? Biol Reprod 2002; 67:1367-74. [PMID: 12390864 DOI: 10.1095/biolreprod.102.005587] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The expression and function of the human major histocompatibility complex (MHC) class Ia genes, human leukocyte antigen (HLA)-A, -B, and -C, is well-established; they are expressed in most nucleated cells and present endogenous peptides to CD8+ T cells. However, MHC class Ib genes are poorly characterized and have unknown functions. In humans, the best-characterized class Ib gene is HLA-G. This gene has a restricted tissue expression of the mRNA and a unique pattern of protein expression; it is expressed mainly in the extravillous cytotrophoblast cells in the placenta. The function of HLA-G is not clear, but its presence at the maternal-fetal interface suggests a role in protection of the semiallogeneic fetus. Whereas functional studies using in vitro models and transgenic mice provide useful insights regarding the potential function of this molecule, in vivo studies cannot be performed in humans. Nonhuman primates that are closely related to humans phylogenetically contain homologues of HLA-G. The MHC-G loci in nonhuman primates appear to have diverged from the human HLA-G. However, in the rhesus monkey (Macaca mulatta) and olive baboon (Papio anubis), a novel class Ia-related locus has been described. This gene encodes glycoproteins with characteristics that resemble those of HLA-G, including restricted tissue distribution, alternative splicing of mRNA, truncated cytoplasmic domain, and limited polymorphism. Thus, this molecule may be the functional homologue of HLA-G, and these two species may comprise appropriate models for elucidating the function of HLA-G.
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32
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de Groot NG, Otting N, Doxiadis GGM, Balla-Jhagjhoorsingh SS, Heeney JL, van Rood JJ, Gagneux P, Bontrop RE. Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc Natl Acad Sci U S A 2002; 99:11748-53. [PMID: 12186979 PMCID: PMC129340 DOI: 10.1073/pnas.182420799] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2002] [Indexed: 11/18/2022] Open
Abstract
MHC class I molecules play an essential role in the immune defense against intracellular infections. The hallmark of the MHC is its extensive degree of polymorphism at the population level. However, the present comparison of MHC class I gene intron variation revealed that chimpanzees have experienced a severe repertoire reduction at the orthologues of the HLA-A, -B, and -C loci. The loss of variability predates the (sub)speciation of chimpanzees and did not effect other known gene systems. Therefore the selective sweep in the MHC class I gene may have resulted from a widespread viral infection. Based on the present results and the fact that chimpanzees have a natural resistance to the development of AIDS, we hypothesize that the selective sweep was caused by the chimpanzee-derived simian immunodeficiency virus (SIVcpz), the closest relative of HIV-1, or a closely related retrovirus. Hence, the contemporary chimpanzee populations represent the offspring of AIDS-resistant animals, the survivors of a HIV-like pandemic that took place in the distant past.
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Affiliation(s)
- Natasja G de Groot
- Department of Immunobiology, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands
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33
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Münz C, Bickham KL, Subklewe M, Tsang ML, Chahroudi A, Kurilla MG, Zhang D, O'Donnell M, Steinman RM. Human CD4(+) T lymphocytes consistently respond to the latent Epstein-Barr virus nuclear antigen EBNA1. J Exp Med 2000; 191:1649-60. [PMID: 10811859 PMCID: PMC2193162 DOI: 10.1084/jem.191.10.1649] [Citation(s) in RCA: 258] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Epstein-Barr virus (EBV)-encoded nuclear antigen EBNA1 is critical for the persistence of the viral episome in replicating EBV-transformed human B cells. Therefore, all EBV-induced tumors express this foreign antigen. However, EBNA1 is invisible to CD8(+) cytotoxic T lymphocytes because its Gly/Ala repeat domain prevents proteasome-dependent processing for presentation on major histocompatibility complex (MHC) class I. We now describe that CD4(+) T cells from healthy adults are primed to EBNA1. In fact, among latent EBV antigens that stimulate CD4(+) T cells, EBNA1 is preferentially recognized. We present evidence that the CD4(+) response may provide a protective role, including interferon gamma secretion and direct cytolysis after encounter of transformed B lymphocyte cell lines (B-LCLs). Dendritic cells (DCs) process EBNA1 from purified protein and from MHC class II-mismatched, EBNA1-expressing cells including B-LCLs. In contrast, B-LCLs and Burkitt's lymphoma lines likely present EBNA1 after endogenous processing, as their capacity to cross-present from exogenous sources is weak or undetectable. By limiting dilution, there is a tight correlation between the capacity of CD4(+) T cell lines to recognize autologous B-LCL-expressing EBNA1 and DCs that have captured EBNA1. Therefore, CD4(+) T cells can respond to the EBNA1 protein that is crucial for EBV persistence. We suggest that this immune response is initiated in vivo by DCs that present EBV-infected B cells, and that EBNA1-specific CD4(+) T cell immunity be enhanced to prevent and treat EBV-associated malignancies.
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Affiliation(s)
- Christian Münz
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
| | - Kara L. Bickham
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
| | - Marion Subklewe
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
| | - Ming L. Tsang
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
| | - Ann Chahroudi
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
| | - Michael G. Kurilla
- Department of Pathology and Microbiology, University of Virginia, Charlottesville, Virginia 22908
| | - Dan Zhang
- Laboratory of DNA Replication and Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021-6399
| | - Michael O'Donnell
- Laboratory of DNA Replication and Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021-6399
| | - Ralph M. Steinman
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021-6399
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Urvater JA, Otting N, Loehrke JH, Rudersdorf R, Slukvin II, Piekarczyk MS, Golos TG, Hughes AL, Bontrop RE, Watkins DI. Mamu-I: a novel primate MHC class I B-related locus with unusually low variability. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:1386-98. [PMID: 10640754 DOI: 10.4049/jimmunol.164.3.1386] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The rhesus macaque is an important animal model for several human diseases and organ transplantation. Therefore, definition of the MHC of this species is crucial to the development of these models. Unfortunately, unlike humans, lymphocytes from a single rhesus macaque express up to 12 different MHC class I cDNAs. From which locus these various alleles are derived is unclear. In our attempts to define the MHC class I loci of the rhesus macaque, we have identified an unusual MHC class I locus, Mamu-I. We isolated 26 I locus alleles from three different macaque species but not from three other Cercopithecine genera, suggesting that the I locus is the result of a recent duplication of the B locus occurring after the divergence of macaques from the ancestor of the other extant Cercopithecine genera. Mamu-I mRNA transcripts were detected in all tissues examined and Mamu-I protein was produced in rhesus B lymphoblastoid cell lines. Furthermore, Mamu-I protein was detected by flow cytometry on the surface of human 721.221 cells transfected with Mamu-I. In contrast to the polymorphism present at this locus, there is unusually low sequence variability, with the mean number of nucleotide differences between alleles being only 3.6 nt. Therefore, Mamu-I is less variable than any other polymorphic MHC class I locus described to date. Additionally, no evidence for positive selection on the peptide binding region was observed. Together, these results suggest that Mamu-I is an MHC class I locus in primates that has features of both classical and nonclassical loci.
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Affiliation(s)
- J A Urvater
- Wisconsin Regional Primate Research Center, Department of Genetics, University of Wisconsin, Madison, WI 53715, USA
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35
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Arnaiz-Villena A, Morales P, Gomez-Casado E, Castro MJ, Varela P, Rojo-Amigo R, Martinez-Laso J. Evolution of MHC-G in primates: a different kind of molecule for each group of species. J Reprod Immunol 1999; 43:111-25. [PMID: 10479048 DOI: 10.1016/s0165-0378(99)00026-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When MHC-G molecules in primates (New World and Old World monkeys, Anthropoids and humans) were compared phylogenetically, very different evolutionary patterns within each species were found; their molecules did not have a straight forward and linear development throughout the postulated evolutionary pathway of primates. The earlier New World monkeys (South America) had relatively more alleles and the polymorphism was placed in the T-cell receptor (TcR), NK receptors and antigen binding sites; MHC-G probably works as a classical class I presenting molecule in these monkeys. MHC-G intron 2 from New World monkeys does not show the typical 23 bp deletion found in all other more recent primate species. Thus, it is possible that MHC-G molecules in New World monkeys belong to a different lineage than the MHC from higher primates. Another early lineage, Eurasian Old World monkeys, shows stop codons at exon 3: MHC-G proteins lacking the alpha2 domain may functionally suffice or otherwise reading-through stop-codon translational mechanisms may exist, as shown for other genes. Orangutans show lower (but significant) polymorphism than New World monkeys at NK, TcR and antigen binding regions; gorilla and chimpanzee show very low polymorphism. Humans only show three different HLA-G proteins with changes not affecting NK, TcR or antigen binding sites. It is observed that the more exposed the mother to allogeneic fetuses (polygamy), the less polymorphic HLA-G is observed within a given species. The data are concordant with the postulated immune inhibitory function for MHC-G in Old World monkeys, anthropoids and humans both at placental and inflammatory level.
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Affiliation(s)
- A Arnaiz-Villena
- Department of Immunology, Hospital 12 de Octubre, Universidad Complutense, Madrid, Spain.
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36
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Evans DT, Knapp LA, Jing P, Piekarczyk MS, Hinshaw VS, Watkins DI. Three Different MHC Class I Molecules Bind the Same CTL Epitope of the Influenza Virus in a Primate Species with Limited MHC Class I Diversity. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.7.3970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
One of the most remarkable features of the MHC class I loci of most outbred mammalian populations is their exceptional diversity, yet the functional importance of this diversity remains to be fully understood. The cotton-top tamarin (Saguinus oedipus) is unusual in having MHC class I loci that exhibit both limited polymorphism and sequence variation. To investigate the functional implications of limited MHC class I diversity in this outbred primate species, we infected five tamarins with influenza virus and defined the CTL epitopes recognized by each individual. In addition to an immunodominant epitope of the viral nucleoprotein (NP) that was recognized by all individuals, two tamarins also made a response to the same epitope of the matrix (M1) protein. Surprisingly, these two tamarins used different MHC class I molecules, Saoe-G*02 and -G*04, to present the M1 epitope. In addition, CTLs from one of the tamarins recognized target cells that expressed neither Saoe-G*02 nor -G*04, but, rather, a third MHC class I molecule, Saoe-G*12. Sequence analysis revealed that Saoe-G*12 differs from both Saoe-G*02 and -G*04 by only two nucleotides and was probably generated by recombination between these two alleles. These results demonstrate that at least three of the tamarin’s MHC class I molecules can present the same epitope to virus-specific CTLs. Thus, four of the tamarin’s 12 MHC class I molecules bound only two influenza virus CTL epitopes. Therefore, the functional diversity of cotton-top tamarin’s MHC class I loci may be even more limited than their genetic diversity suggests.
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Affiliation(s)
| | | | | | | | - Virginia S. Hinshaw
- ‡Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706
| | - David I. Watkins
- *Wisconsin Regional Primate Research Center and
- †Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53715; and
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Vogel TU, Evans DT, Urvater JA, O'Connor DH, Hughes AL, Watkins DI. Major histocompatibility complex class I genes in primates: co-evolution with pathogens. Immunol Rev 1999; 167:327-37. [PMID: 10319271 DOI: 10.1111/j.1600-065x.1999.tb01402.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The major histocompatibility complex (MHC) is the most polymorphic genetic system known, playing a central role in the cellular immune response to pathogens. The relationship between the MHC of humans and non-human primates has increased our understanding of MHC evolution and how polymorphism of this gene family may have been generated. We will review MHC class I evolution in great apes and Old World and New World primates and discuss new data from the simian immunodeficiency virus/rhesus monkey animal model that demonstrate the role of MHC class I alleles in selecting for new populations of viruses. This suggests that certain pathogens co-evolve with the MHC class I molecules they encounter in a population.
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Affiliation(s)
- T U Vogel
- Wisconsin Regional Primate Research Center, University of Wisconsin, Madison 53715-1299, USA
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38
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Hashimoto K, Okamura K, Yamaguchi H, Ototake M, Nakanishi T, Kurosawa Y. Conservation and diversification of MHC class I and its related molecules in vertebrates. Immunol Rev 1999; 167:81-100. [PMID: 10319253 DOI: 10.1111/j.1600-065x.1999.tb01384.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The elucidation of the complete peptide-binding domains of the highly polymorphic shark MHC class I genes offered us an opportunity to examine the characteristics of their predicted protein products in the light of the latest advance in the structural studies of the MHC class I molecules. The results suggest that the fundamental characteristics in the T-cell recognition of the MHC class I molecule/peptide complex are expected to have been established at the early stage of the vertebrate evolution. The elucidation of the typical classical class I molecules from fishes and also of some MHC class I-related molecules may help us-to explore the common denominator of the ancient class I molecules.
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Affiliation(s)
- K Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Aichi, Japan.
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39
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Yeager M, Hughes AL. Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunol Rev 1999; 167:45-58. [PMID: 10319250 DOI: 10.1111/j.1600-065x.1999.tb01381.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genes that encode molecules involved in antigen presentation within the class I and class II regions of the mammalian major histocompatibility complex (MHC) include several that are highly polymorphic. There is evidence that this polymorphism is maintained by positive selection, most likely overdominant selection, relating to their role in presenting foreign peptides to T cells. This selection can maintain allelic lineages for much longer periods of time than neutral polymorphisms are expected to last, but sharing of polymorphic amino acid motifs among species of different mammalian orders is due to independent (or convergent) evolution rather than common ancestry. It has been suggested that interallelic recombination (gene conversion) plays a role in enhancing polymorphism, but there is evidence of striking differences among loci with respect to the rate at which such recombination has contributed to current polymorphism. Recent attempts to interpret linkage relationships in the MHC region as evidence of ancient genomic duplications are not supported by phylogenetic analysis. Rather, natural selection may have played a role in the linkage of other genes to those of the MHC.
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Affiliation(s)
- M Yeager
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri, USA
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40
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Abstract
To set an accurate chronological framework to the evolution of primate class I and II genes in the major histocompatibility complex (Mhc), the rate of silent nucleotide substitutions in exons and introns is examined for various cDNA and genome sequences currently available. The rate is sensitive to the GC content and correlates negatively with increased GC biases at the third codon positions of Mhc genes. The intergenic recombination rate in the HLA region is estimated from the synonymous nucleotide differences at 37 linked loci. Any HLA subregion is recombined more or less at the ordinary rate of 1 cM per 1 Mb, although the rate may be reduced in some subregions. This information is used to discuss HLA haplotypes when they are applied to studies of human demography. The unusual polymorphism in the alpha-helix of HLA-DRB1 is also revisited in relation to intragenic recombination, but the molecular mechanism and the evolutionary cause both remain enigmatic.
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Affiliation(s)
- Y Satta
- Department of Biosystems Science, Graduate University for Advanced Studies, Kanagawa, Japan
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41
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Abstract
Because major histocompatibility complex (MHC) genes play a major role in the development of acquired immune responses, it is essential to obtain comparative information on their organisation, expression and possible functional dichotomies in different species. In human, three classical, polymorphic class I genes (HLA-A, B- and -C) and four expressed A/B class II gene pairs (HLA-DM, -DP, -DQ and -DR) are each present on all haplotypes. With the exception of the HLA-DRB loci, it has been assumed that a similar rigid organisational situation exists in other mammalian species. However, extensive analysis of the bovine MHC (BoLA) at both the genomic and transcriptional levels has revealed a degree of genetic fluidity not described in other species. None of the four (or more) classical class I genes identified is consistently expressed, and haplotypes differ from one another in both the number and composition of expressed class I genes. Similarly, in the class II region, the number of DQ genes varies between haplotypes in both number and composition. These variations in both class I and II (which appear to reflect differences at the genomic level) are likely to play an important role in cattle immune responses. The observed phenotypic differences in cattle demonstrate very clearly the dynamic nature of the MHC region. This review addresses the functional impact of such variation in different breeds and populations, and its significance in terms of MHC evolution.
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Affiliation(s)
- S A Ellis
- Institute for Animal Health, Compton, UK.
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42
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Hughes AL, Yeager M, Ten Elshof AE, Chorney MJ. A new taxonomy of mammalian MHC class I molecules. IMMUNOLOGY TODAY 1999; 20:22-6. [PMID: 10081226 DOI: 10.1016/s0167-5699(98)01377-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- A L Hughes
- Dept of Biology, Pennsylvania State University, University Park 16802, USA.
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Antunes SG, de Groot NG, Brok H, Doxiadis G, Menezes AA, Otting N, Bontrop RE. The common marmoset: a new world primate species with limited Mhc class II variability. Proc Natl Acad Sci U S A 1998; 95:11745-50. [PMID: 9751736 PMCID: PMC21711 DOI: 10.1073/pnas.95.20.11745] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The common marmoset (Callithrix jacchus) is a New World primate species that is highly susceptible to fatal infections caused by various strains of bacteria. We present here a first step in the molecular characterization of the common marmoset's Mhc class II genes by nucleotide sequence analysis of the polymorphic exon 2 segments. For this study, genetic material was obtained from animals bred in captivity as well as in the wild. The results demonstrate that the common marmoset has, like other primates, apparently functional Mhc-DR and -DQ regions, but the Mhc-DP region has been inactivated. At the -DR and -DQ loci, only a limited number of lineages were detected. On the basis of the number of alleles found, the -DQA and -B loci appear to be oligomorphic, whereas only a moderate degree of polymorphism was observed for two of three Mhc-DRB loci. The contact residues in the peptide-binding site of the Caja-DRB1*03 lineage members are highly conserved, whereas the -DRB*W16 lineage members show more divergence in that respect. The latter locus encodes five oligomorphic lineages whose members are not observed in any other primate species studied, suggesting rapid evolution, as illustrated by frequent exchange of polymorphic motifs. All common marmosets tested were found to share one monomorphic type of Caja-DRB*W12 allele probably encoded by a separate locus. Common marmosets apparently lack haplotype polymorphism because the number of Caja-DRB loci present per haplotype appears to be constant. Despite this, however, an unexpectedly high number of allelic combinations are observed at the haplotypic level, suggesting that Caja-DRB alleles are exchanged frequently between chromosomes by recombination, promoting an optimal distribution of limited Mhc polymorphisms among individuals of a given population. This peculiar genetic make up, in combination with the limited variability of the major histocompatability complex class II repertoire, may contribute to the common marmoset's susceptibility to particular bacterial infections.
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Affiliation(s)
- S G Antunes
- Department of Immunobiology, Biomedical Primate Research Centre, Lange Kleiweg 151, 2288 GJ Rijswijk, The Netherlands
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44
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Velten F, Rogel-Gaillard C, Renard C, Pontarotti P, Tazi-Ahnini R, Vaiman M, Chardon P. A first map of the porcine major histocompatibility complex class I region. TISSUE ANTIGENS 1998; 51:183-94. [PMID: 9510374 DOI: 10.1111/j.1399-0039.1998.tb02963.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A map of the SLA complex, or swine major histocompatibility complex (MHC), class I region was constructed by alignment of yeast artificial chromosomes (YACs) harboring MHC class I genes as well as anchor genes already mapped within the human MHC complex (HLA). Five YACs containing 9 anchor genes built a contig of about 1.0-1.2 Mb between the SLA class III BAT1 locus and the olfactory receptor-like genes OLF42. Ten different SLA class I sequences, including putative allelic forms of published classical and non-classical SLA class I genes, were assigned to the 400-kb enclosing centromeric part of the contig. Three additional YACs comprising the OLF89 genes and two YACs containing the butyrophilin gene were located telomeric to the contig. Comparison between the human and porcine MHC complexes showed a perfect conserved order of anchor genes, whereas no orthologous relationships were found for the class I loci.
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Affiliation(s)
- F Velten
- Laboratoire mixte INRA-CEA de Radiobiologie appliquée, Domaine de Vilvert, Jouy-en-Josas, France
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45
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Knapp LA, Cadavid LF, Watkins DI. The MHC-E Locus Is the Most Well Conserved of All Known Primate Class I Histocompatibility Genes. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.160.1.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The HLA-E locus is characterized by limited polymorphism and low levels of cell surface expression. However, the function of the products of this nonclassical MHC class I gene remains unknown. To evaluate the conservation of the MHC-E locus throughout anthropoid primate evolution, we identified the homologue of the HLA-E locus in six different New World monkey species. Full-length sequencing of MHC-E cDNAs in four unrelated cotton-top tamarins (Saguinus oedipus) revealed no evidence for polymorphism. Using the PCR, denaturing gradient gel electrophoresis, and direct sequencing, we also identified MHC-E alleles in five other New World monkey species, representing all extant platyrrhine families. In contrast to all other classical and nonclassical MHC class I genes in primates, the rate of synonymous nucleotide substitution is much greater than the rate of nonsynonymous nucleotide substitution within exons 2 and 3 encoding the peptide binding region (PBR) in MHC-E genes. The PBR of the MHC-E molecule, therefore, has evolved under purifying selective pressures, and the very unusual evolutionary history of this ancient gene provides further evidence that the products of the HLA-E locus serve a critical immunological function. Given the remarkable conservation of the PBR during primate evolution, this critical immunological function is probably related to the peptide binding ability of the MHC-E protein.
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Affiliation(s)
- Leslie A. Knapp
- *Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Luis F. Cadavid
- *Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - David I. Watkins
- *Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, WI 53715
- †HLA/Molecular Diagnostics Laboratory, Department of Pathology, University of Wisconsin, Madison, WI 53792
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46
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Cadavid LF, Shufflebotham C, Ruiz FJ, Yeager M, Hughes AL, Watkins DI. Evolutionary instability of the major histocompatibility complex class I loci in New World primates. Proc Natl Acad Sci U S A 1997; 94:14536-41. [PMID: 9405648 PMCID: PMC25046 DOI: 10.1073/pnas.94.26.14536] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Homologues of the human major histocompatibility complex (MHC) HLA-A, -B, -E, -F, and -G loci are present in all the Catarrhini (Old World primates, apes, and humans), and some of their allelic lineages have survived several speciation events. Analysis of 26 MHC class I cDNAs from seven different genera of New World primates revealed that the Callitrichinae (tamarins and marmosets) are an exception to these rules of MHC stability. In gene trees of primate MHC class I genes, sequences from the Callitrichinae cluster in a genus-specific fashion, whereas in the other genera of New World primates, as in the Catarrhini, they cluster in a transgeneric way. The genus-specific clustering of the Callitrichinae cDNAs indicates that there is no orthology between MHC class I loci in genera of this phyletic group. Additionally, the Callitrichinae genera exhibit limited variability of their MHC class I genes, in contrast to the high variability displayed by all other primates. Each Callitrichinae genus, therefore, expresses its own set of MHC class I genes, suggesting that an unusually high rate of turnover of loci occurs in this subfamily. The limited variability of MHC class I genes in the Callitrichinae is likely the result of the recent origin of these loci.
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Affiliation(s)
- L F Cadavid
- Wisconsin Regional Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53715, USA.
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Cadavid LF, Watkins DI. Heirs of the jaguar and the anaconda: HLA, conquest and disease in the indigenous populations of the Americas. TISSUE ANTIGENS 1997; 50:702-11. [PMID: 9458134 DOI: 10.1111/j.1399-0039.1997.tb02940.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- L F Cadavid
- Wisconsin Regional Primate Research Center, University of Wisconsin, Madison 53715, USA
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Cadavid LF, Watkins DI. Heirs of the jaguar and the anaconda: HLA, conquest and disease in the indigenous populations of the Americas. TISSUE ANTIGENS 1997; 50:209-18. [PMID: 9331944 DOI: 10.1111/j.1399-0039.1997.tb02865.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- L F Cadavid
- Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, USA
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49
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Martinez-Naves E, Barber LD, Madrigal JA, Vullo CM, Clayberger C, Lyu SC, Williams RC, Gorodezky C, Markow T, Petzl-Erler ML, Parham P. Interactions of HLA-B*4801 with peptide and CD8. TISSUE ANTIGENS 1997; 50:258-64. [PMID: 9331948 DOI: 10.1111/j.1399-0039.1997.tb02869.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Functional properties of the B*4801 allotype were investigated using HLA class I-deficient 221 cells transfected with B*4801 cDNA. From pool sequence analysis of endogenously bound peptides, B*4801 was shown to select for nonamer peptides having glutamine or lysine at position 2 and leucine at the carboxyl-terminus. In an in vitro cell-cell binding assay, B*4801 binds CD8 alpha homodimers weakly due to the presence of a threonine residue at position 245 in the alpha 3 domain. A mutant B*4801 molecule in which alanine replaces threonine 245, binds CD8 alpha homodimers at levels comparable to those of other HLA class I allotypes. Despite the low affinity of B*4801 for CD8 alpha, alloreactive T-cells that recognize B*4801 molecules expressed by the 221 transfectant are inhibited by anti-CD8 monoclonal antibodies. Analysis of 25 B*48-expressing individuals from various populations showed threonine 245 was encoded by every B*48 allele.
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Affiliation(s)
- E Martinez-Naves
- Department of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, California, USA
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