Evolution of the recombination signal sequences in the Ig heavy-chain variable region locus of mammals

Characterization of the domestic goat γδ T cell receptor gene loci and gene usage

Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1⁺ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1⁺ γδ T cells. In contrast, caprine WC1⁺ and WC1^- γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle.

Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm

In jawed vertebrates, variable (V) genes code for antigen-binding regions of B and T lymphocyte receptors, which generate a specific response to foreign pathogens. Obtaining the detailed repertoire of these genes across the jawed vertebrate kingdom would help to understand their evolution and function. However, annotations of V-genes are known for only a few model species since their extraction is not amenable to standard gene finding algorithms. Also, the more distant evolution of a taxon is from such model species, and there is less homology between their V-gene sequences. Here, we present an iterative supervised machine learning algorithm that begins by training a small set of known and verified V-gene sequences. The algorithm successively discovers homologous unaligned V-exons from a larger set of whole genome shotgun (WGS) datasets from many taxa. Upon each iteration, newly uncovered V-genes are added to the training set for the next predictions. This iterative learning/discovery process terminates when the number of new sequences discovered is negligible. This process is akin to “online” or reinforcement learning and is proven to be useful for discovering homologous V-genes from successively more distant taxa from the original set. Results are demonstrated for 14 primate WGS datasets and validated against Ensembl annotations. This algorithm is implemented in the Python programming language and is freely available at http://vgenerepertoire.org.

Evolution of V genes from the TRV loci of mammals

Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionary origin of V genes that code for the α and β chains of the TCR loci of mammals. In particular, we demonstrate that most of the 35 TRAV and 25 TRBV conserved genes found in Primates are also found in other Eutheria, while in Marsupials, Monotremes, and Reptiles, these genes diversified in a different manner. We also show that in mammals, all TRAV genes are derived from five ancestral genes, while all TRBV genes originate from four such genes. In Reptiles, the five TRAV and three out of the four TRBV ancestral genes exist, as well as other V genes not found in mammals. We also studied the TRGV and TRDV loci from all mammals, and we show a relationship of the TRDV to the TRAV locus throughout evolutionary time.

V genes in primates from whole genome sequencing data

The adaptive immune system uses V genes for antigen recognition. However, the evolutionary diversification and selection processes within and across species and orders remain poorly understood. Here, we studied the amino acid (AA) sequences obtained from the translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose genomes have been sequenced. Multi-species comparative analysis supports the hypothesis that V genes in the IG loci undergo birth/death processes, thereby permitting rapid adaptability over evolutionary time. We also show that multiple cladistic groupings exist in the TRA (35 clades) and TRB (25 clades) V gene loci and that each primate species typically contributes at least one V gene to each of these clades. The results demonstrate that IG V genes and TR V genes have quite different evolutionary pathways; multiple duplications can explain the IG loci results, while coevolutionary pressures can explain the phylogenetic results of the TR V gene loci. Our results suggest that there exist evolutionary relationships between V gene clades in the TRA and TRB loci. Due to the long-standing preservation of these clades, such genes may have specific and necessary roles for the viability of a species.

Antigen receptor genes and the evolution of a recombinase

Antigen receptor genes exist in the germline in a "split" configuration and are assembled in developing B and T lymphocytes by V(D)J recombination. This site-specific recombination reaction is initiated by a complex containing the RAG1 and RAG2 proteins and completed by general DNA repair factors. RAG1 and RAG2, like the adaptive immune system itself, are found exclusively in jawed vertebrates, and are thought to have entered the vertebrate genome by horizontal transmission as components of a transposable element. This review discusses the structure of antigen receptor genes and the mechanisms by which they are assembled and diversified, and then goes on to consider the evolutionary implications of the arrival of the hypothetical "RAG transposon".

V(H) replacement in rearranged immunoglobulin genes

Examples suggesting that all or part of the V(H) segment of a rearranged V(H)DJ(H) may be replaced by all or part of another V(H) have been appearing since the 1980s. Evidence has been presented of two rather different types of replacement. One of these has gained acceptance and has now been clearly demonstrated to occur. The other, proposed more recently, has not yet gained general acceptance because the same effect can be produced by polymerase chain reaction artefact. We review both types of replacement including a critical examination of evidence for the latter. The first type involves RAG proteins and recombination signal sequences (RSS) and occurs in immature B cells. The second was also thought to be brought about by RAG proteins and RSS. However, it has been reported in hypermutating cells which are not thought to express RAG proteins but in which activation-induced cytidine deaminase (AID) has recently been shown to initiate homologous recombination. Re-examination of the published sequences reveals AID target sites in V(H)-V(H) junction regions and examples that resemble gene conversion.

Evolution of the variable gene segments and recombination signal sequences of the human T-cell receptor alpha/delta locus

The T-cell receptor (TCR) alpha and delta loci are particularly interesting because of their unique genomic structure, in that the gene segments for each locus are interspersed. The origin of this remarkable gene segment arrangement is obscure. In this report, we investigated the evolution of the TCRalpha and delta variable loci and their respective recombination signal sequences (RSSs). Our phylogenetic analyses divided the alpha and delta variable gene segments into two major groups each with distinguishing motifs in both the framework and complementarity determining regions (CDRs). Sequence analyses revealed that TCRdelta variable segments share similar CDR2 sequences with immunoglobulin light chain variable segments, possibly revealing similar evolutionary histories. Maximum likelihood analysis of the region on Chromosome 14q11.2 containing the loci revealed two possible ancestral TCR alpha/delta variable segments, TRDV2 and TRAV1-1/ 1-2, respectively. Maximum parsimony revealed different evolutionary patterns between the variable segment and RSS of the same variable gene arguing for dissimilar evolutionary origins. Two models could account for this difference: a V(D)J recombination activity involving embedded heptamer-like motifs in the germline genome, or, more plausibly, an unequal sister chromatid crossing-over. Either mechanism would have resulted in increased diversity for the adaptive immune system.

In vitro and in vivo studies on the generation of the primary T-cell receptor repertoire

The primary T-cell receptor repertoire is generated by somatic rearrangement of discontinuous gene segments. The shape of the combinatorial repertoire is stereotypical and, in part, evolutionarily conserved among mammals. Rearrangement is initiated by specific interactions between the recombinase and the recombination signals (RSs) that flank the gene segments. Conserved sequence variations in the RS, which modulate its interactions with the recombinase, appear to be a major factor in shaping the primary repertoire. In vitro, biochemical studies have revealed distinct steps in these complex recombinase-RS interactions that may determine the final frequency of gene segment rearrangement. These studies offer a plausible model to explain gene segment selection, but new, more physiological approaches will have to be developed to verify and refine the mechanism by which the recombinase targets the RS in its endogenous chromosomal context in vivo.

MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins

We evaluated the evolutionary conservation of glycine myristoylation within eukaryotic sequences. Our large-scale cross-genome analyses, available as MYRbase, show that the functional spectrum of myristoylated proteins is currently largely underestimated. We give experimental evidence for in vitro myristoylation of selected predictions. Furthermore, we classify five membrane-attachment factors that occur most frequently in combination with, or even replacing, myristoyl anchors, as some protein family examples show.

DNA shuffling: induced molecular breeding to produce new generation long-lasting vaccines

The paradigm for classic vaccines has been to mimic natural infection, and their success relies mostly on the induction of neutralizing antibodies followed by long-lasting immunity. The outcome of aggressive chronic infections such as HIV and HCV, the reappearance of fastidious diseases such as tuberculosis and the progression of cancer growth suggest that natural immune responses are definitely insufficient in many cases. A new paradigm is needed to design and develop a new high-efficiency generation of vaccines ideally able to surpass the capabilities of natural immune responses. In vitro evolution is a new, important laboratory method to evolve molecules with desired properties, which appears as an appealing alternative to achieve this goal. In its battle against disease, the vertebrate immune system triggers a series of well-known molecular events in order to produce protective neutralizing antibodies. This natural in vivo response shares remarkable similarities with the in vitro technique known as molecular breeding or "DNA shuffling." This method exploits the recombination between genes to dramatically accelerate the rate at which genes can be evolved under selection pressure in the laboratory, producing optimized high-efficiency mutant proteins. Since new generation vaccines are aimed to overcome natural selection and environmental pressures to fully inactivate rapidly developing pathogen variants, they could be engineered, developed and selected through the application of directed DNA shuffling procedures. This review highlights the potential of the procedure in the complex context of natural immune responses and the equilibrium and interaction existing in nature between hosts and pathogens.

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes

IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ((R)). IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.

DNA-Rag Protein Interactions in the Control of Selective D Gene Utilization in the TCRβ Locus

Ordered assembly of Ag receptor genes by VDJ recombination is a key determinant of successful lymphocyte differentiation and function. Control of gene rearrangement has been traditionally viewed as a result of complex reorganization of the nucleochromatin mediated by several nuclear factors. Selective recombination of the variable (V) genes to the diversity (D), but not joining (J), gene segments within the TCRbeta locus has been shown to be controlled by recombination signal (RS) sequences that flank the gene segments. Through ex vivo and in vitro recombination assays, we demonstrate that the Rag proteins can discriminate between the RS of the D and J genes and enforce selective D gene incorporation into the TCRbeta variable domain in the absence of other nuclear factors or chromatin structure. DNA binding studies indicate that discrimination is not simply caused by higher affinity binding of the Rag proteins to the isolated 12RS of the D as opposed to the J genes. Furthermore, we also demonstrate that the 12RS within the TCRbeta locus is functionally inferior to the consensus 12RS. We propose that selective gene segment usage is controlled at the level of differential assembly and/or stability of synaptic RS complexes, and that evolutionary "deterioration" of the RS motifs may have been important to allow the VDJ recombinase to exert autonomous control over gene segment use during gene rearrangement.

Evolutionarily conserved pattern of gene segment usage within the mammalian TCRbeta locus

Antigen receptor gene rearrangement is mediated by interactions between the VDJ recombinase and the recombination signal sequences that flank the antigen receptor gene segments. In this report I present phylogenetic analyses that suggest a remarkable evolutionary conservation of the recombination signal sequences flanking some of the orthologous T-cell receptor-beta locus gene segments between human and mouse. Comparison of published data on the usage of the same gene segments between human and mouse indicates similar conservation in the shape of the primary T-cell receptor-beta repertoire. I propose that interactions between the recombinase and its cognate recognition sequences play a hitherto underestimated role in the formation of the specific pattern of the primary, combinatorial antigen receptor repertoire and that this pattern appears to be conserved in diverse mammalian species. Generation of a conserved pattern of the primary T-cell receptor repertoire may be critical for efficient selection of immature T lymphocytes.

Spectrotype analysis and clonal characteristics of human anti-Gal alpha1-3Gal antibodies

Galalpha1-3Gal (anti-Gal), a polyclonal so-called natural antibody (Ab), is present in large amounts in human serum not only as IgG-, but also as IgM- and IgA-isotypes. It has gained a particular interest in the context of xenotransplantation, because the endothelial pig cells express the terminal Galalpha1-3Gal determinant on several adhesion molecules. Little is known of it's function and direct examination of the structure of the Ig genes responsible for coding anti-Gal is lacking. We used the technique of isoelectric focussing (IEF)/affinity immunoblotting for direct analysis of the clonal distribution and spectrotype analysis of IgM- and IgG anti-Gal. By single cell analysis of magnetic bead and fluorescent-activated cell sorter (FACS) isolated mature anti-Gal bearing human B cells from whole blood we analyzed the VH gene families involved in anti-Gal production. Oligoclonal and individually distinct IgG banding patterns were found with isoelectric points between 4 and 9. IgM spectrotypes revealed to be more uniform with a polyclonal banding pattern of more than 12 bands at a pH between 4.7 and 7. IgG- and IgM-banding patterns over a period of 6 months remained unchanged. Single cell polymerase chain reaction (PCR), with all family specific primers, revealed the use of the VH2f gene family for the IgG2 isoptype. The differences found in the spectrotype banding patterns of IgG and IgM could be explained by the suggestion that anti-Gal IgM were produced by the use of unmutated germline genes and the possibility of the absence of somatic mutations. The greater clonal heterogeneity in the IgG population could be explained by somatic hypermutations during the switch from IgM to IgG. The use of this VH2f gene family, which is also involved in the generation of Abs against bacterial pathogens, could mean that this is a predominant region used for the generation of such natural occurring antibodies.

The cleavage efficiency of the human immunoglobulin heavy chain VH elements by the RAG complex: implications for the immune repertoire

The human immunoglobulin heavy chain locus contains 39 functional human V(H) elements. All 39 V(H) elements (with their adjacent heptamer/nonamer signal) were tested for site-specific cleavage with purified human core RAG1 and RAG2, and HMG1 proteins in a 12/23-coupled cleavage reaction. Both nicking and hairpin formation were measured. The individual V(H) cleavage efficiencies vary over nearly a 30-fold range. These measurements will be useful in considering the factors affecting the generation of the immunoglobulin and T-cell receptor repertoires in the adult humans. Interestingly, when these cleavage efficiencies are summed for each of the V(H) families, the six V(H) family efficiencies correspond closely to the observed profile of unselected V(H) family usage in the peripheral B cells of normal adult humans. This correspondence raises the possibility that the dominant factor determining V(H) element utilization within the 1-megabase human genomic V(H) array is simply the individual RAG cleavage efficiencies.

Somatic generation of antigen-receptor diversity: a reprise

Thirty years ago, in his inaugural article entitled 'The somatic generation of immune recognition', Niels Jerne put forward the hypothesis that the primary antigen (Ag)-receptor repertoire must be restricted towards self-Ags before Ag-mediated selection. The subsequent discovery that Ag receptors are encoded by random rearrangements between discontinuous gene segments was, apparently, at odds with this hypothesis. However, recent findings have begun to reconcile these two concepts. The recombination process is, in fact, relatively precise, exhibiting marked preferences for some gene segments over others, even among members of the same gene family. The result is an intricately patterned primary repertoire that accommodates both sets of predictions, ensuring a balance between the efficiency of selection (requiring limited diversity) and the complexity of the repertoire (requiring maximum diversity).

The RAG proteins in V(D)J recombination: more than just a nuclease

V(D)J recombination is the process that generates the diversity among T cell receptors and is one of three mechanisms that contribute to the diversity of antibodies in the vertebrate immune system. The mechanism requires precise cutting of the DNA at segment boundaries followed by rejoining of particular pairs of the resulting termini. The imprecision of aspects of the joining reaction contributes significantly to increasing the variability of the resulting functional genes. Signal sequences target DNA recombination and must participate in a highly ordered protein-DNA complex in order to limit recombination to appropriate partners. Two proteins, RAG1 and RAG2, together form the nuclease that cleaves the DNA at the border of the signal sequences. Additional roles of these proteins in organizing the reaction complex for subsequent steps are explored.