Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica

Parra, Zuly E.; Baker, Michelle L.; Hathaway, Jennifer J.M.; Lopez, April M.; Trujillo, Jonathan; Sharp, Alana; Miller, Robert D.

doi:10.1186/1471-2164-9-111

Cited by 71 publications

(173 citation statements)

References 44 publications

(75 reference statements)

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“…Recently the opossum genome was determined [26]. An analysis of the genome for TCR variable gene segments confirmed the location of TRA, TRB, TRD, and TRG, and surprisingly a new locus TRM that seems to be a hybrid between a TCR and immunoglobulin locus [27]. This locus is similar to the shark NAR-TCR [28].…”

Section: Origins Of Tcr and Mhc Genesmentioning

confidence: 85%

TCR-MHC docking orientation: natural selection, or thymic selection?

Collins

Riddle

2008

Immunol Res

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T cell receptors (TCR) dock on their peptide-major histocompatibility complex (pMHC) targets in a conserved orientation. Since amino acid sidechains are the foundation of specific protein-protein interactions, a simple explanation for the conserved docking orientation is that key amino acids encoded by the TCR and MHC genes have been selected and maintained through evolution in order to preserve TCR/pMHC binding. Expectations that follow from the hypothesis that TCR and MHC evolved to interact are discussed in light of the data that both support and refute them. Finally, an alternative and equally simple explanation for the driving force behind the conserved docking orientation is described.

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Section: Origins Of Tcr and Mhc Genesmentioning

confidence: 85%

TCR-MHC docking orientation: natural selection, or thymic selection?

Collins

Riddle

2008

Immunol Res

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“…Although the structure of LRR-based antigen receptors in jawless vertebrates is quite distinct from that of Ig domain-based antigen receptors in jawed vertebrates, the overall genomic organization and the evolutionary dynamics of the VLRC locus have similarities to the genomic architecture and mode of evolution of Ig and TCR multigene families. From a genomic standpoint, the incomplete germ-line VLRC gene serves as an equivalent of the constant gene segment, whereas the clusters of different types of donor genomic cassettes represent the functional correlates of the clusters of V, D, and J gene segments of Ig or TCR loci in jawed vertebrates (20)(21)(22). Interestingly, the donor LRRencoding cassettes are not used equally for VLR assembly, in analogy with the preferential use of certain V, D, and J segments in Ig/TCR recombinations in jawed vertebrates (23)(24)(25)(26).…”

Section: Discussionmentioning

confidence: 99%

“…Despite their distinct sequence signatures, the different types of donor cassettes are interspersed in the VLRC-related scaffolds, a situation reminiscent of the interspersed arrangements of individual members of V gene families of Ig and TCR loci (20)(21)(22). We found evidence of multiple duplication events for the different types of donor cassettes in the VLRC locus; however, in the absence of a suitable outgroup, the number and the evolutionary timing of the apparent duplication events in the VLRC locus cannot be determined precisely.…”

Section: Discussionmentioning

confidence: 99%

Organization of lampreyvariable lymphocyte receptor Clocus and repertoire development

Das

Hirano

Aghaallaei

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Jawless vertebrates are pivotal representatives for studies of the evolution of adaptive immunity due to their unique position in chordate phylogeny. Lamprey and hagfish, the extant jawless vertebrates, have an alternative lymphocyte-based adaptive immune system that is based on somatically diversifying leucine-rich repeat (LRR)-based antigen receptors, termed variable lymphocyte receptors (VLRs). Lamprey T-like and B-like lymphocyte lineages have been shown to express VLRA and VLRB types of anticipatory receptors, respectively. An additional VLR type, termed VLRC, has recently been identified in arctic lamprey (Lethenteron camtschaticum), and our analysis indicates that VLRC sequences are well conserved in sea lamprey (Petromyzon marinus), L. camtschaticum, and European brook lamprey (Lampetra planeri). Genome sequences of P. marinus were analyzed to determine the organization of the VLRC-encoding locus. In addition to the incomplete germ-line VLRC gene, we have identified 182 flanking donor genomic sequences that could be used to complete the assembly of mature VLRC genes. Donor LRR cassettes were classifiable into five basic structural groups, the composition of which determines their order of use during VLRC assembly by virtue of sequence similarities to the incomplete germ-line gene and to one another. Bidirectional VLRC assembly was predicted by comparisons of mature VLRC genes with the sequences of donor LRR cassettes and verified by analysis of partially assembled intermediates. Biased and repetitive use of certain donor LRR cassettes was demonstrable in mature VLRCs. Our analysis provides insight into the unique molecular strategies used for VLRC gene assembly and repertoire diversification.

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“…It would have been from a V-J/C structure that modern Ig and TCR genes evolved. Although it has sometimes been suggested that the minimalist cartilaginous fish cluster represents the primordial segmental-rearranging organization, clusters could also have evolved independently, as had TCRμ genes in marsupial and monotreme mammals [23]. Additionally, cartilaginous fish TCR genes are in the translocon organization, showing that regulation and expression of genes arranged as in higher vertebrates was established by the time of chondrichthyan divergence [24, 25].…”

Section: Ig Organization In Cartilaginous Fishmentioning

confidence: 99%

Assembly and Expression of Shark Ig Genes

Hsu

2016

The Journal of Immunology

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Sharks are modern descendants of the earliest vertebrates possessing Ig superfamily receptor-based adaptive immunity. They respond to immunogen with antibodies which, upon boosting, appear more rapidly and show affinity maturation. Specific antibodies and immunological memory imply that antibody diversification and clonal selection exist in cartilaginous fish. Shark antigen receptors are generated through V(D)J recombination, and since it is a mechanism known to generate autoreactive receptors, this implies that shark lymphocytes undergo selection. In mouse, the ~2.8 Mb IgH and IgL loci require long-range, differential activation of component parts for V(D)J recombination, allelic exclusion, and receptor editing. These processes, including class switching, evolved with and appear inseparable from the complex locus organization. In contrast, shark Ig are encoded by 100–200 autonomously rearranging miniloci. This review describes how the shark primary antibody repertoire is generated in the absence of structural features considered essential in mammalian Ig gene assembly and expression.

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Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica

Cited by 71 publications

References 44 publications

TCR-MHC docking orientation: natural selection, or thymic selection?

TCR-MHC docking orientation: natural selection, or thymic selection?

Organization of lampreyvariable lymphocyte receptor Clocus and repertoire development

Assembly and Expression of Shark Ig Genes

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