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Falk K, Gratama JW, Rowe M, Zou JZ, Khanim F, Young LS, Oosterveer MA, Ernberg I. The role of repetitive DNA sequences in the size variation of Epstein-Barr virus (EBV) nuclear antigens, and the identification of different EBV isolates using RFLP and PCR analysis. J Gen Virol 1995; 76 ( Pt 4):779-90. [PMID: 9049323 DOI: 10.1099/0022-1317-76-4-779] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The six Epstein-Barr virus (EBV) nuclear antigen proteins (EBNA-1-6) show characteristic size variations between different virus isolates; this is a feature that has been used to identify the source of virus isolates in epidemiological studies (Ebnotyping). We have now studied the correlation between restriction fragment length polymorphisms (RFLPs) within exons coding for the EBNAs and the molecular masses of the respective proteins. The B95-8 EBV strain was used as the prototype virus. The variation in apparent molecular mass of EBNA-1, -3 and -6 correlated positively with the size of RFLP coding for repeat sequences in these polypeptides. For EBNA-2, no correlation between apparent molecular mass and length of the repetitive sequences was found. The EBNA-4 protein showed virtually no variation in apparent molecular mass and RFLP size across the repeat sequence. Based on the strong correlation between apparent molecular mass and RFLP size for EBNA-6, we developed an EBNA-6 PCR assay that discriminated between different isolates of EBV. This assay offers the advantage of EBV characterization using uncultured material (e.g. throat washings, blood or biopsies), thus avoiding the selection against poorly transforming strains that occurs during establishment of lymphoblastoid cell lines required for Ebnotyping at the protein level.
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Falk K, Rötzschke O, Takiguchi M, Gnau V, Stevanović S, Jung G, Rammensee HG. Peptide motifs of HLA-B51, -B52 and -B78 molecules, and implications for Behćet's disease. Int Immunol 1995; 7:223-8. [PMID: 7734418 DOI: 10.1093/intimm/7.2.223] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Here we report peptide motifs of five HLA-B molecules, B*5101, B*5102, B*5103 B*5201 and B*7801. Motifs were obtained by pool sequencing of natural ligands eluted from the respective molecules expressed in C1R cells upon transfection. A number of individual ligands that could be sequenced confirmed the motifs. All five HLA-B molecules belong to the HLA-B5, B35-cross-reactive group and are closely related as indicated by similar sequences. B51 and B52 are associated with Bw4, whereas B78 is associated with Bw6. One of the HLA-B molecules investigated here, HLA-B*5101, is associated with Behçet's disease, a multisystemic inflammatory disease affecting various organs. This disease is especially frequent among the Japanese population. The subtle differences between the peptide motifs of B*5101 as compared with the motifs of the four other closely related but not disease-associated molecules could shed light on the nature of the HLA-association of Behçet's disease.
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Falk K, Rötzschke O, Takiguchi M, Gnau V, Stevanović S, Jung G, Rammensee HG. Peptide motifs of HLA-B38 and B39 molecules. Immunogenetics 1995; 41:162-4. [PMID: 7806291 DOI: 10.1007/bf00182332] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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104
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Sidney J, del Guercio MF, Southwood S, Engelhard VH, Appella E, Rammensee HG, Falk K, Rötzschke O, Takiguchi M, Kubo RT. Several HLA alleles share overlapping peptide specificities. THE JOURNAL OF IMMUNOLOGY 1995. [DOI: 10.4049/jimmunol.154.1.247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Herein we describe the establishment of assays to measure peptide binding to purified HLA-B*0701, -B*0801, -B*2705, -B*3501-03, -B*5401, -Cw*0401, -Cw*0602, and -Cw*0702 molecules. The binding of known peptide epitopes or naturally processed peptides correlates well with HLA restriction or origin, underscoring the immunologic relevance of these assays. Analysis of the sequences of various HLA class I alleles suggested that alleles with peptide motifs characterized by proline in position 2 and aromatic or hydrophobic residues at their C-terminus shared key consensus residues at positions 9, 63, 66, 67, and 70 (B pocket) and residue 116 (F pocket). Prediction of the peptide-binding specificity of HLA-B*5401, on the basis of this consensus B and F pocket structure, verified this hypothesis and suggested that a relatively large family of HLA-B alleles (which we have defined as the HLA-B7-like supertype) may significantly overlap in peptide binding specificity. Availability of quantitative binding assays allowed verification that, indeed, many (25%) of the peptide ligands carrying proline in position 2 and hydrophobic/aromatic residues at the C-terminus (the B7-like supermotif) were capable of binding at least three of five HLA-B7-like supertype alleles. Identification of epitopes carrying the B7-like supermotif and binding to a family of alleles represented in over 40% of individuals from all major ethnic groups may be of considerable use in the design of peptide vaccines.
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105
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Steinle A, Falk K, Rötzschke O, Gnau V, Stevanović S, Jung G, Schendel DJ, Rammensee HG. Motif of HLA-B*3503 peptide ligands. Immunogenetics 1995; 43:105-7. [PMID: 8537112 DOI: 10.1007/bf00186615] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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106
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Falk K, Rötzschke O, Takiguchi M, Gnau V, Stevanović S, Jung G, Rammensee HG. Peptide motifs of HLA-B58, B60, B61, and B62 molecules. Immunogenetics 1995; 41:165-8. [PMID: 7806292 DOI: 10.1007/bf00182333] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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107
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Sidney J, del Guercio MF, Southwood S, Engelhard VH, Appella E, Rammensee HG, Falk K, Rötzschke O, Takiguchi M, Kubo RT. Several HLA alleles share overlapping peptide specificities. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 1995; 154:247-59. [PMID: 7527812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Herein we describe the establishment of assays to measure peptide binding to purified HLA-B*0701, -B*0801, -B*2705, -B*3501-03, -B*5401, -Cw*0401, -Cw*0602, and -Cw*0702 molecules. The binding of known peptide epitopes or naturally processed peptides correlates well with HLA restriction or origin, underscoring the immunologic relevance of these assays. Analysis of the sequences of various HLA class I alleles suggested that alleles with peptide motifs characterized by proline in position 2 and aromatic or hydrophobic residues at their C-terminus shared key consensus residues at positions 9, 63, 66, 67, and 70 (B pocket) and residue 116 (F pocket). Prediction of the peptide-binding specificity of HLA-B*5401, on the basis of this consensus B and F pocket structure, verified this hypothesis and suggested that a relatively large family of HLA-B alleles (which we have defined as the HLA-B7-like supertype) may significantly overlap in peptide binding specificity. Availability of quantitative binding assays allowed verification that, indeed, many (25%) of the peptide ligands carrying proline in position 2 and hydrophobic/aromatic residues at the C-terminus (the B7-like supermotif) were capable of binding at least three of five HLA-B7-like supertype alleles. Identification of epitopes carrying the B7-like supermotif and binding to a family of alleles represented in over 40% of individuals from all major ethnic groups may be of considerable use in the design of peptide vaccines.
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108
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Maier R, Falk K, Rötzschke O, Maier B, Gnau V, Stevanović S, Jung G, Rammensee HG, Meyerhans A. Peptide motifs of HLA-A3, -A24, and -B7 molecules as determined by pool sequencing. Immunogenetics 1994; 40:306-8. [PMID: 7521860 DOI: 10.1007/bf00189978] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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109
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Falk K, Rötzschke O, Stevanović S, Gnau V, Sparbier K, Jung G, Rammensee HG, Walden P. Analysis of a naturally occurring HLA class I-restricted viral epitope. Immunol Suppl 1994; 82:337-42. [PMID: 7525458 PMCID: PMC1414868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A previously described nonapeptide sequence motif for antigens recognized by T cells in the context of the human major histocompatibility complex (MHC) molecule HLA-A2.1 was used to identify the natural epitope of influenza A virus matrix protein. We show here that the peptide with the sequence GILGFVFTL is the synthetic analogue of the natural epitope by demonstrating the presence of the corresponding peptide on MHC molecules of virus-infected cells. The role of the hydrophobic anchor amino acids in positions 2 and 9, which constitute the epitope motif, was investigated with synthetic variants of the epitope and cytotoxic T lymphocytes as indicator cells. The crucial role of the side chains of amino acids in those positions was evidence by their influence on the efficiency of T-cell stimulation.
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Falk K, Rötzschke O, Takiguchi M, Grahovac B, Gnau V, Stevanović S, Jung G, Rammensee HG. Peptide motifs of HLA-A1, -A11, -A31, and -A33 molecules. Immunogenetics 1994; 40:238-41. [PMID: 8039832 DOI: 10.1007/bf00167086] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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111
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Wölfel T, Schneider J, Meyer Zum Büschenfelde KH, Rammensee HG, Rötzschke O, Falk K. Isolation of naturally processed peptides recognized by cytolytic T lymphocytes (CTL) on human melanoma cells in association with HLA-A2.1. Int J Cancer 1994; 57:413-8. [PMID: 8169004 DOI: 10.1002/ijc.2910570320] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cytolytic T lymphocyte (CTL) clones have previously been derived from peripheral blood of melanoma patient SK29(AV). They lyse autologous melanoma cells but not autologous Epstein-Barr virus (EBV)-transformed B lymphocytes. Immunoselection experiments indicate that these CTL clones recognize 4 different antigens (Aa, Ab, B, C) in association with a single HLA restriction element, HLA-A2.1. While the expression of antigens B and C appears to be confined to SK29-melanoma cells, antigens Aa and Ab are shared by a high proportion of allogeneic HLA-A2-positive melanoma lines. HLA-A2.1 and total HLA class I molecules have now been purified from SK29-melanoma cells using affinity chromatography and associated peptides have been eluted. Peptide pools eluted from HLA-A2.1 and total class I were separated by reversed phase high performance liquid chromatography (HPLC). Individual HPLC fractions were tested for their ability to sensitize target cells for recognition by SK29-CTL clones. The presence of antigens Aa, Ab, B and C was detected in distinct HPLC fractions that were identical for both peptide pools. As target for detection of peptide antigens in HPLC fractions, the use of the HLA-A2.1-positive antigen processing mutant cell line CEM x 721.174.T2 (T2), pre-incubated with anti-HLA-A2 monoclonal antibody (MAb) MA2.1, was shown to be essential. Single-peak target-sensitizing activity was found for antigens Ab and B, whereas multi-peak sensitizing activity was reproducibly detected for antigens Aa and C. We reason that at least some of these melanoma peptide antigens might occur in biochemically distinct isoforms.
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112
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Thoresen OF, Falk K, Evensen O. Comparison of immunohistochemistry, acid-fast staining, and cultivation for detection of Mycobacterium paratuberculosis in goats. J Vet Diagn Invest 1994; 6:195-9. [PMID: 8068751 DOI: 10.1177/104063879400600210] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Forty-seven paired specimens of ileum and mesenterial lymph nodes from goats originating from 2 herds with paratuberculosis were investigated. Culture of the specimens for Mycobacterium paratuberculosis was compared with Ziehl-Neelsen staining and with immunohistochemical tests on paraffin-embedded tissue sections, using a M. paratuberculosis immune serum and an avidin-biotin-alkaline phosphatase method. Immunohistochemical techniques detected most positive samples and produced more clearly visible reactions than did acid-fast staining. Eighteen of 47 samples were positive by immunohistochemical techniques may represent a valuable adjunct to standard techniques for diagnosis of paratuberculosis in goats.
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113
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Falk K, Rötzschke O, Stevanović S, Jung G, Rammensee HG. Pool sequencing of natural HLA-DR, DQ, and DP ligands reveals detailed peptide motifs, constraints of processing, and general rules. Immunogenetics 1994; 39:230-42. [PMID: 8119729 DOI: 10.1007/bf00188785] [Citation(s) in RCA: 176] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have approached the problem of MHC class II ligand motifs by pool sequencing natural peptides eluted from HLA-DR, DQ, and DP molecules. The results indicate surprisingly clear patterns, although not quite as clear as with natural class I ligands. The most striking feature is a highly dominant Proline at position 2. We interpret this to be a consequence of aminopeptidase N-like activity in processing. Another general aspect is the existence of three to four hydrophobic or aromatic anchors, whereby the first and the last are separated by five to eight residues. The peptide motifs for HLA-DR1, DR5, DQ7, and DPw4 are allele-specific and differ by spacing and occupancy of anchors. The anchors tend to be flanked by clusters of charged residues, and small residues, especially Ala, are frequent in the motif centers. These detailed motifs allow one to interpret most previous (DR-) motifs as fitting one or more of the anchors or conserved clusters. The relative motif symmetry suggests the possibility of bidirectional binding of peptides in the class II groove.
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Abstract
In the past few years a considerable number of naturally processed MHC class II ligands have been identified and sequenced. Most of them derive from endogenous sources, predominantly from plasma membrane proteins. Generally, they display variability in length but exhibit characteristic patterns of invariant amino acid positions, which reflect the allele-specific binding requirements. As a general feature, class II ligands also often contain a pattern of proline residues interpreted as a 'processing motif'.
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115
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Rötzschke O, Falk K, Stevanović S, Gnau V, Jung G, Rammensee HG. Dominant aromatic/aliphatic C-terminal anchor in HLA-B*2702 and B*2705 peptide motifs. Immunogenetics 1994; 39:74-7. [PMID: 8225441 DOI: 10.1007/bf00171803] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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116
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Falk K, Rötzschke O, Grahovac B, Schendel D, Stevanović S, Gnau V, Jung G, Strominger JL, Rammensee HG. Allele-specific peptide ligand motifs of HLA-C molecules. Proc Natl Acad Sci U S A 1993; 90:12005-9. [PMID: 8265661 PMCID: PMC48114 DOI: 10.1073/pnas.90.24.12005] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The consensus motifs of HLA-Cw3, -Cw4, -Cw6, and -Cw7 ligands were determined by pool sequencing. Together with information obtained by sequencing of some prominent individual peptides, the results indicate the following: (i) all four HLA-C molecules are associated with peptides. (ii) These peptides adhere to allele-specific motifs that are similar to those of to HLA-A or -B molecules; they have a preferred length of nine amino acids and an anchor residue at the C terminus. (iii) All four HLA-C molecules analyzed exhibit related peptide motifs, although each allelic product shows individual characteristics in fine specificity. (iv) Processing and origin of peptides appear not to be different from that of other class I molecules. (v) No obvious difference at C-terminal position 9 was present in the peptides isolated from the two dimorphic variants of HLA-C that determine dominant resistance to natural killer NK1-specific cells (HLA-Cw4, -Cw6) or to NK2-specific cells (HLA-Cw3, -Cw7) and that differ in two residues in or near the pocket at position 9.
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Malcherek G, Falk K, Rötzschke O, Rammensee HG, Stevanović S, Gnau V, Jung G, Melms A. Natural peptide ligand motifs of two HLA molecules associated with myasthenia gravis. Int Immunol 1993; 5:1229-37. [PMID: 8268130 DOI: 10.1093/intimm/5.10.1229] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The peptide motifs of two HLA molecules, B8 and DR3(17), which are associated with autoimmune diseases including myasthenia gravis, were determined from natural peptide pools using Edman degradation. The majority of HLA-B8 ligands are nonamers preferentially terminated by leucine. As a characteristic feature of the HLA-B8 motif, there is a high degree of conservation of positively charged amino acids at position 3 and 5, exclusively lysine at position 3, and lysine or arginine at position 5. Additional evidence for this allele-specific motif is the presence of these features in several viral peptides recognized by HLA-B8 restricted T cells. The DR3(17) motif is characterized by four conserved anchor-like positions ordered in an almost symmetrical arrangement, as has been found for DR1 and DR5 motifs. A first hydrophobic/aromatic anchor three to four residues apart from the N-terminus (at relative position 1) appears to be a common feature of DR ligands. The second anchor is an aspartate at relative position 4, which is likely to be the DR3(17)-specific contact site in the groove. Two additional conserved positions closer to the C-terminus are occupied by charged amino acids at relative position 6 and by hydrophobic/aromatic residues at positions 8, 9, or 10. Eight individual naturally processed DR17 ligands were sequenced and were found to be derived from exogenous proteins and cytoplasmic membrane receptors. These natural peptides conform well to the determined motif. A single exchange of the anchor-like positions in a model peptide abrogated binding to DR17+ cells.(ABSTRACT TRUNCATED AT 250 WORDS)
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Falk K, Rötzschke O, Faath S, Goth S, Graef I, Shastri N, Rammensee HG. Both human and mouse cells expressing H-2Kb and ovalbumin process the same peptide, SIINFEKL. Cell Immunol 1993; 150:447-52. [PMID: 8370082 DOI: 10.1006/cimm.1993.1212] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HeLa cells, derived from a human cervix carcinoma line, were transfected with a mouse MHC class I gene, H-2Kb, and chicken ovalbumin. H-2Kb-restricted cytotoxic mouse T cells specific for ovalbumin recognized the double-transfected human cells with similar efficiency as ovalbumin-transfected EL4 mouse thymoma cells (H-2b). The naturally processed ovalbumin T cell epitope was eluted from H-2Kb molecules from double-transfected HeLa cells and was biochemically compared to a synthetic peptide, SIINFEKL, known to be the natural Kb ligand of ovalbumin-transfected H-2b mouse cells. The results indicate that the ovalbumin-derived Kb-ligand of double-transfected HeLa cells is also SIINFEKL. Thus, both human cervix carcinoma cells and mouse thymoma cells expressing Kb and ovalbumin process the same octapeptide. Together with previous data, derived by comparing Kb ligands of unknown sequences from both human and mouse cells expressing Kb, it can be concluded that both mouse and human cells are capable of processing the same ligands for mouse MHC class I molecules. Hence, the general specificity of the peptide-generating mechanism for class I ligands is apparently conserved between evolutionary distant species.
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Falk K, Ernberg I. An origin of DNA replication (oriP) in highly methylated episomal Epstein-Barr virus DNA localizes to a 4.5-kb unmethylated region. Virology 1993; 195:608-15. [PMID: 8393238 DOI: 10.1006/viro.1993.1412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Epstein-Barr virus (EBV) reveals two types of interactions with human B lymphocytes. In immortalized lymphoblastoid cell lines (LCL), nine virus-coded proteins are expressed: six nuclear (EBNA1-6) and three membrane proteins (LMP1, TP 1,2). In Burkitt's lymphoma (BL) tumors and representative cell lines (type I) only EBNA-1 is expressed. The viral genomes are carried by the cells in an extrachromosal, episomal form. We have earlier described an overall difference in EBV DNA methylation between LCLs of normal B-cell origin and type I BL lines. EBV genomes are hypomethylated in the former, methylated in the latter. The origin of replication (oriP) for the episomal DNA is exempted from this overall methylation. This unmethylated region was analyzed in the BL derived type I cell line Rael. It starts just upstream of the coding exons for the small untranslated RNAs EBER I/II. It extends throughout oriP and includes several control elements between oriP and the first promoter for EBNA transcription (BCR2). The viral DNA was methylated around and downstream of that promoter, which is not used for EBNA-1 expression in Rael.
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Norda M, Falk K, Rötzschke O, Stevanović S, Jung G, Rammensee HG. Comparison of the H-2Kk- and H-2Kkm1-restricted peptide motifs. JOURNAL OF IMMUNOTHERAPY WITH EMPHASIS ON TUMOR IMMUNOLOGY : OFFICIAL JOURNAL OF THE SOCIETY FOR BIOLOGICAL THERAPY 1993; 14:144-9. [PMID: 8280703 DOI: 10.1097/00002371-199308000-00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Self-peptide pools eluted from purified H-2Kk or H-2Kkm1 molecules were sequenced. The majority of self-peptides associated with H-2Kk molecules were found to be octamers with two anchor positions. Position 2 is invariantly occupied with Glu, and the C-terminal residue at position 8 is almost always Ile. Comparison of this motif with synthetic peptides known to contain viral or parasite T-cell epitopes could be well aligned with this motif, except that the C-terminal Ile residue frequently appears to be at position 9 of the aligned sequences, instead of 8. Self-peptides eluted from mutant H-2Kkm1 molecules also appear to be mostly octamers with the same Ile residues at position 8 as with Kk. Position 2 is still dominantly occupied by Glu; in contrast to the Kk motif, however, Gln, Gly, and Pro are also allowed. Other differences between the two motifs indicate that a certain number of peptides presented by one of the molecules are not presented by the other.
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121
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Abstract
MHC class I molecules are peptide receptors of stringent specificity which however still allow millions of different ligands. This is achieved by the following specificity characteristics summarized as allele specific peptide motifs: Peptides are of defined length, depending on the class I allele (either 8 or 9 residues; exceptions have been observed). Typically, 2 of the 8 or 9 positions are anchors that can only be occupied by a single amino acid residue, or by residues with closely related side chains. Location and characteristics of anchors vary with class I alleles. The C terminus of the peptide ligands is frequently an aliphatic or charged residue. Such allele-specific class I peptide ligand motifs, known so far for H-2Kd, Kb, Kk, Kkm1, Db, HLA-A*0201, A*0205, and B*2705, are useful to predict natural T cell epitopes. The latter can be determined by extraction from cells recognized by the T cell of interest. It is not known how the class I ligands are produced in the cell, although speculative models exist. The peptide specificity of class I molecules and experimental evidence indicate that T cells are tolerant to only a small fraction of the expressed genomic sequences and are not tolerant to the remainder. The function of class I molecules is to present a collection of self-peptide samples at the cell surface for surveillance by T cells.
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Abstract
The introduction of a powerful peptide isolation method has paved the way for the characterization of the natural peptide-ligands of MHC class I molecules. More than 50 are already known by their amino acid sequence. As a striking feature, all these peptides display some common sequence characteristics: a distinct peptide length, normally 8 or 9 amino acids, and typically two invariant 'anchor' amino acids. These 'consensus-motifs' are different for each MHC-class-I allele and their usefulness for the precise prediction of peptide antigens has already been demonstrated. This review discusses the consensus motifs known at present and lists most of the sequences referring to natural MHC-ligands.
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Falk K, Rötzschke O, Grahovac B, Schendel D, Stevanović S, Jung G, Rammensee HG. Peptide motifs of HLA-B35 and -B37 molecules. Immunogenetics 1993; 38:161-2. [PMID: 8482580 DOI: 10.1007/bf00190906] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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124
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Harpur AG, Zimiecki A, Wilks AF, Falk K, Rötzschke O, Rammensee HG. A prominent natural H-2 Kd ligand is derived from protein tyrosine kinase JAK1. Immunol Lett 1993; 35:235-7. [PMID: 8514334 DOI: 10.1016/0165-2478(93)90188-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The first natural MHC ligand to be sequenced directly was the nonapeptide SYFPEITHI eluted from H-2 Kd molecules of a mouse tumour line, P815 [1]. A GenBank search indicated high homology to a nonapeptide contained within the human tyrosine kinase JAK1: SFFPEITHI, residues 355-363 [2]. This high homology prompted us to look at whether the mouse JAK1 protein has a Tyr residue at position 356 instead of Phe as in the human sequence. Cloning and sequencing of the mouse homologue gene confirmed that this is indeed the case. Thus, the physiological MHC ligand SYFPEITHI is derived from the protein tyrosine kinase, JAK1. The mouse tumor line P815 expresses the 5.4-kb JAK1 mRNA, and the 130,000 kDa JAK1 protein can be readily detected.
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Rötzschke O, Falk K, Stevanović S, Grahovac B, Soloski MJ, Jung G, Rammensee HG. Qa-2 molecules are peptide receptors of higher stringency than ordinary class I molecules. Nature 1993; 361:642-4. [PMID: 8437623 DOI: 10.1038/361642a0] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Class I molecules of the major histocompatibility complex (MHC) transport peptides to the cell surface for surveillance by T cells. Ligand specificity is stringent and differs from allele to allele. Here we report analysis of natural ligands of 'unconventional' glycophosphatidyl-anchored mouse class I molecules, Qa-2. The function of these molecules is unclear; they can serve as recognition structures for 'unrestricted' cytotoxic T cells but have not been found to present peptides to T cells, although the DNA sequence suggests a similar peptide binding groove to that of 'conventional' class I molecules, and other unconventional class I molecules can present antigens in a few cases. Pool sequencing of natural Qa-2 ligands shows that Qa-2 molecules are indeed peptide receptors, having ligand specificity similar to that of conventional class I molecules, that is, a predominant length of nine amino acids, anchor positions, and hydrophobic termination of peptides. But ligand specificity is much more stringent than with other class I molecules: of the nine positions, two are anchors and four have rather limited occupancy.
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