Conserved V(D)J junctional sequence of cross-reactive cytotoxic T cell receptor idiotype and the effect of a single amino acid substitution

Escaping the cut by restriction enzymes through single-strand self-annealing of host-edited 12-bp and longer synthetic palindromes

Palindromati, the massive host-edited synthetic palindromic contamination found in GenBank, is illustrated and exemplified. Millions of contaminated sequences with portions or tandems of such portions derived from the ZAP adaptor or related linkers are shown (1) by the 12-bp sequence reported elsewhere, exon Xb, 5' CCCGAATTCGGG 3', (2) by a 22-bp related sequence 5' CTCGTGCCGAATTCGGCACGAG 3', and (3) by a longer 44-bp related sequence: 5' CTCGTGCCGAATTCGGCACGAGCTCGTGCCGAATTCGGCACGAG 3'. Possible reasons for why those long contaminating sequences continue in the databases are presented here: (1) the recognition site for the plus strand (+) is single-strand self-annealed; (2) the recognition site for the minus strand (-) is not only single-strand self-annealed but also located far away from the single-strand self-annealed plus strand, rendering impossible the formation of the active EcoRI enzyme dimer to cut on 5' G/AATTC 3', its target sequence. As a possible solution, it is suggested to rely on at least two or three independent results, such as sequences obtained by independent laboratories with the use, preferably, of independent sequencing methodologies. This information may help to develop tools for bioinformatics capable to detect/remove these contaminants and to infer why some damaged sequences which cause genetic diseases escape detection by the molecular quality control mechanism of cells and organisms, being undesirably transferred unchecked through the generations.

The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes

'The Mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes' 'IMGT Locus in Focus' report provides the first complete list of the mouse TRAV and TRDV genes which span 1550 kb on chromosome 14 at 19.7 cM. The total number of TRAV genes per haploid genome is 98 belonging to 23 subgroups. This includes 10 TRAV/DV genes which belong to seven subgroups. The functional TRAV genomic repertoire comprises 72-82 TRAV (including 9-10 TRAV/DV) belonging to 19 subgroups. The total number of TRDV genes per haploid genome is 16 (including the 10 TRAV/DV) belonging to 12 subgroups. The functional TRDV genomic repertoire comprises 14-15 genes (5 TRDV and 9-10 TRAV/DV) belonging to 11-12 subgroups. The eight tables and three figures of this report are available at the IMGT Marie-Paule page of IMGT. The international ImMunoGeneTics information system (http://imgt.cines.fr) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

Junctional biases in the naive TCR repertoire control the CTL response to an immunodominant determinant of HSV-1

The enormous diversity of the T cell pool makes it difficult to determine whether inherent biases in the naive TCR repertoire can influence T cell responsiveness. In C57BL/6 mice the cytotoxic T lymphocyte response to an immunodominant HSV-1 determinant (gB) is characterized by a prominent bias in Vbeta element usage, associated with a conserved and preferentially D element-encoded CDR3 sequence. Comparison of naive and gB-specific T cell populations revealed a similar enrichment of germline D element-encoded CDR3 sequences in the preimmune repertoire. Strikingly, eliminating the germline coding of the gB-specific CDR3 sequence caused an almost complete loss of the dominant subset of gB-specific T cells, illustrating that CDR3 biases can significantly alter both the composition and strength of an immune response.

Overlapping epitopes of friend murine leukemia virus gag-encoded leader sequence recognized by single cytotoxic T-lymphocyte clones

The leader signal sequence of the non-structural gag-encoded glycoprotein precursor, Pr75gag, of Friend murine leukemia virus (F-MuLV) contains overlapping epitopes, SIVLCCLCL (p71-79) and CCLCLTVFL (p75 83) that activate Friend virus (FV)-induced tumor (FBL-3)-specific cytotoxic T-lymphocytes (CTL) (Kondo et al., J. Virol., 69, 1995, 6735-6741; Chen et al., J. Virol., 70, 1996, 7773-7782). It was investigated whether these two peptides are recognized by a single CTL clone or by individual clones with different specificities. The results show that both hydrophobic and cysteine-containing peptides are bound to H-2Db class I major histocompatibility complex (MHC) molecules and cross-recognized by a single CTL clone as well as bulk-cultured CTL from the spleens of mice immunized with FBL-3. The peptide p71-79 was effective for sensitizing target cells to lysis by CTL in the concentration of common antigenic peptides. Moreover, peptide p75-83 was 1000-fold more potent than the peptide p71-79. Specific cytotoxicity assays with variant peptides with alanine- and serine-substitutions suggested a highly complex function of the disulfide bond-forming peptides potentially sensitive to small sequence differences. The dominance of CTL responses to the transmembrane region is discussed in light of the high affinity of a novel hydrophobic peptide to compete with other peptides for binding to MHC molecules.

Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones

Taking advantage of a potent MHC class I-restricted response that allows the identification of antigen-selected CD8 T cells directly ex vivo, we characterized the antigen-specific T cell repertoires that develop in individual mice by single-cell PCR analysis. Each of the immune mice displayed distinct yet structurally similar TCR repertoires. The overall repertoire size was estimated to be in the range of 15-20 for most mice. No major differences were observed between primary and secondary responses. Moreover, for a hyperimmunized mouse the antigen-specific TCR repertoire expressed 8 months after the initial immunization was very similar to that found at the peak of the primary response. Our results demonstrate that a high magnitude immune response may be composed of very few clones, and that at least in the system analyzed, the memory response largely reflects the repertoire selected by the peak of the primary response.

A single retroviral gag precursor signal peptide recognized by FBL-3 tumor-specific cytotoxic T lymphocytes

Several dominant T-cell receptors of cytotoxic T-lymphocyte (CTL) clones specific for FBL-3 tumor antigen were clonally amplified in mixed lymphocyte tumor cell cultures derived from an individual immune mouse. Every CTL clone analyzed had a common specificity for a single epitope in the precursor to cell membrane-associated nonstructural gag-encoded protein, Pr75gag, which can be minimally identified by nine amino acid residues, SIVLCCLCL. This epitope is located within the hydrophobic signal sequence motif that mediates translocation of the protein into the endoplasmic reticulum. These novel observations suggest that expression of Pr75gag in FBL-3 tumor cells led to the amplification of CTLs which recognize the signal sequence of the nonstructural gag-encoded glycoprotein precursor.

Mouse T-cell receptor variable gene segment families

All mouse T-cell receptor alpha/delta, beta, and gamma variable (Tcra/d-, b-, and g-V) gene segments were aligned to compare the sequences with one another, to group them into subfamilies, and to derive a name which complies with the standard nomenclature. It was necessary to change the names of some V gene segments because they conflicted with those of other segments. The traditional classification into subfamilies was re-evaluated using a much larger pool of sequences. In the mouse, most V gene segments can be grouped into subfamilies of closely related genes with significantly less similarity between different subfamilies.

Fine structure of a virus-encoded helper T-cell epitope expressed on FBL-3 tumor cells

Antigen peptide fn20 representing Friend murine leukemia virus env122-141 (DEPLTSLTPRCNTAWNRLKL) is recognized by two independent Friend virus-induced, FBL-3 tumor-specific helper T-cell (Th) clones. We isolated more Th clones from mice immunized with fn20 peptide. We examined the fine structure of the peptide required to activate a large group of fn20-specific Th clones. A systematic analysis of peptides of decreasing lengths eliciting Th proliferation defined the minimum core length as 13 amino acids (LTSLTPRCNTAWN). Functional proliferation and competition assays with variant peptides with alanine substitutions permitted the assignment of five peptide residues in two major histocompatibility complex-interacting and three T-cell-receptor-interacting sites. Th clones were different in their reactivities toward peptides of various lengths and the variant peptides.

Flexibility of the T cell receptor repertoire

Alternative T cell receptor (TcR) gene usage between mice of different Mls alleles has been demonstrated in a number of T cell responses. A clear illustration of a flexible TcR V beta usage in the same strain of mice remains to be established. Using a model system in which I-Ek-restricted T cells recognizing lambda repressor cI protein (cI) 12-26 and pigeon cytochrome c (pcc) 81-104 predominantly use V beta 3 in B10.A and B10.BR mice, and V beta 1 in Mls-2a-bearing A/J and C3H mice, we have first demonstrated that the hierarchy of TcR V beta usage can not be inferred from one strain of mice to the other. The presumed flexibility of V beta 3 to V beta 1 did not exist in B10.BR mice in the given responses. Instead, a switch of dominant TcR from V beta 1/V beta 3 to V beta 8 was identified in C3H and B10.BR mice. In contrast, there was an absolute rigidity in TcR repertoire usage in some mouse strains such as A/J. The lack of flexibility was not due to slow generating kinetics of replacing T cells; since A/J mice treated with staphylococcal enterotoxin A from birth on still responded poorly to cI 12-26 and pcc 81-104. Therefore, whether TcR V beta usage in a T cell response would be flexible or rigid is highly dependent on each strain of mice. However, even the plasticity seen in B10.BR mice is very limited and further tolerance of the V beta 8+ population results in non-responsiveness toward the given antigens.

Sequence restrictions in T cell receptor beta-chains that have specificity for a self-peptide/Ld complex

Cytotoxic T lymphocytes that react with a complex of Ld and a ubiquitous self-peptide derived from the enzyme alpha-ketoglutarate dehydrogenase (p2Ca, LSPFPFDL) can be readily elicited by the addition of synthetic peptide to cultures of BALB/c spleen cells. As with other Ld-restricted CTL, the p2Ca-specific cells use predominantly the V beta 8.3 region. In addition, the p2Ca-specific cells use almost exclusively one of three J beta gene segments. Selection for these J beta regions appears to be related to the presence of a glutamic acid residue that is encoded at the 5' end of the J beta and is present within the CDR3. As p2Ca does not contain a complementary charged residue, this finding may suggest that the beta-chain CDR3 from p2Ca-specific CTL contacts one of the five basic residues located on the Ld helices. Together, the results support the possibility that CDR1 and/or CDR2 (within V beta 8.3) and the CDR3 may each contact the Ld molecule. In contrast to the V beta and J beta regions, the V beta D beta J beta junctions and V alpha J alpha repertoires were diverse. The diversity could explain why p2Ca-specific CTL have relatively high precursor frequencies allowing them to be generated rapidly in primary cultures.

Conservation of sequence in recombination signal sequence spacers

The variable domains of immunoglobulins and T cell receptors are assembled through the somatic, site specific recombination of multiple germline segments (V, D, and J segments) or V(D)J rearrangement. The recombination signal sequence (RSS) is necessary and sufficient for cell type specific targeting of the V(D)J rearrangement machinery to these germline segments. Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif. The heptamer and nonamer motifs are separated by a 'spacer' that was not thought to possess significant sequence conservation, however the length of the spacer could be either 12 +/- 1 bp or 23 +/- 1 bp long. In this report we have assembled and analyzed an extensive data base of published RSS. We have derived, through extensive consensus comparison, a more detailed description of the RSS than has previously been reported. Our analysis indicates that RSS spacers possess significant conservation of sequence, and that the conserved sequence in 12 bp spacers is similar to the conserved sequence in the first half of 23 bp spacers.

T-cell receptors from virus-specific cytotoxic T lymphocytes recognizing a single immunodominant nine-amino-acid viral epitope show marked diversity

Following infection of the H-2d mouse by lymphocytic choriomeningitis virus, the newly generated cytotoxic T lymphocyte (CTL) response is focused to a single 9-amino-acid peptide sequence (epitope) of the virus. More than 96% of the primary, secondary, and clonal CTL respond to this lymphocytic choriomeningitis virus nucleoprotein epitope. This unique system affords the opportunity to evaluate the T-cell response to a single viral CTL epitope in a case in which the outcome of infection, either viral clearance or host death, is mediated by the CTLs. Specifically, the molecular structure of the T-cell receptors (TCRs) of CTLs responding to this epitope was analyzed. By using an anchored polymerase chain reaction, the TCR chains of three CTL clones cDNAs were amplified, sequenced, and found to have unique V alpha of V beta chains relative to each other as well as to lack restriction to any particular variable chain. These data indicate that the highly diverse antiviral CTL response is pleomorphic and probably provides an advantage to the host as it limits the emergence of viral variants that could more easily arise if the TCR response were homogeneous.

Multiplicity of virus-encoded helper T-cell epitopes expressed on FBL-3 tumor cells

To identify retroviral antigenic determinants recognized by CD4+ T helper cells during tumor rejection, we established four noncytolytic, helper-type, CD4+ T-cell clones by limiting dilution cultures of mixed lymphocyte-tumor cultures from mice immune to a Friend virus-induced tumor, FBL-3. Among these, three T helper cell clones were isolated from C57BL/6 mice and the fourth was isolated from a (BALB/c x C57BL/6)F1 mouse. All these clones proliferated in response to the immunizing FBL-3 tumor cells in a major histocompatibility complex class II-restricted manner. Each clone expressed a distinct T-cell receptor with a characteristic combination of alpha and beta chains. The localization of helper T-cell determinants on viral proteins was analyzed with recombinant vaccinia viruses expressing Friend murine leukemia virus (F-MuLV) gag or env genes or shorter fragments of the env gene. Epitopes recognized by these T-cell clones were mapped to at least two distinct portions in the env region of the F-MuLV genome. These epitopes were identified more precisely with synthetic peptides derived from the F-MuLV envelope protein sequence. One of these epitopes was common to Friend and Moloney MuLVs and was located in the N-terminal region of the gp70 glycoprotein at amino acids 122 to 141. The second epitope, which was recognized in the context of hybrid I-Eb/d major histocompatibility complex class II molecule, was located close to the C-terminal end of gp70 at amino acids 462 to 479. In addition, a possible third epitope was located in the N-terminal half of the gp70 sequence and differed from the first epitope in that it was not cross-reactive with the Moloney MuLV envelope protein.