The XRCC4 gene encodes a novel protein involved in DNA double-strand break repair and V(D)J recombination

Interaction between DNA-dependent protein kinase and a novel protein, KIP

DNA-dependent protein kinase (DNA-PKcs) is the only eukaryotic kinase activated by DNA ends. Mutation of DNA-PKcs results in murine severe combined immune deficiency in mice and radiation sensitivity. Both the immune and the radiation defects are due to a failure in double-strand break repair. Biochemical studies indicate that DNA-PKcs kinase activity is stimulated by the presence of the DNA end binding protein. Ku. Autophosphorylation of DNA-PKcs results in its inactivation. Based on these studies, DNA-PKcs is presumed to play a direct and important role in the repair of double-strand breaks, but the details of its role are quite unclear. We have done two-hybrid analysis of this entire protein to identify other proteins with which it interacts. Thus far, extensive analysis has only revealed one strong interaction that satisfies both high genetic and biochemical stringency. The interaction is with a novel human protein that has 26% amino acid identity with the phosphatase component, calcineurin B. We discuss the interaction of DNA-PKcs with this novel calcium-binding protein family member in the context of possible kinase-phosphatase regulation of DNA end joining.

Ku70 is required for DNA repair but not for T cell antigen receptor gene recombination In vivo

Ku is a complex of two proteins, Ku70 and Ku80, and functions as a heterodimer to bind DNA double-strand breaks (DSB) and activate DNA-dependent protein kinase. The role of the Ku70 subunit in DNA DSB repair, hypersensitivity to ionizing radiation, and V(D)J recombination was examined in mice that lack Ku70 (Ku70(-/-)). Like Ku80(-/-) mice, Ku70(-/-) mice showed a profound deficiency in DNA DSB repair and were proportional dwarfs. Surprisingly, in contrast to Ku80(-/-) mice in which both T and B lymphocyte development were arrested at an early stage, lack of Ku70 was compatible with T cell receptor gene recombination and the development of mature CD4+CD8- and CD4-CD8+ T cells. Our data shows, for the first time, that Ku70 plays an essential role in DNA DSB repair, but is not required for TCR V(D)J recombination. These results suggest that distinct but overlapping repair pathways may mediate DNA DSB repair and V(D)J recombination.

Molecular processes and radiosensitivity

BACKGROUND

DNA double-strand breaks (DSB) are the most genotoxic lesions induced by ionizing radiation. At least 2 different pathways for DSB repair have been identified, homologous and non-homologous recombination.

METHODS

Studies on X-ray-sensitive mutants have led to the identification of several genes involved in processing of DSB in bacteria, yeast and mammalian cells.

RESULTS AND CONCLUSION

In mammalian cells non-homologous recombination is the main pathway for DSB repair, while the role of homologous recombination in DSB repair awaits clarification. It is known that, in addition to DNA repair, other safeguards control the human cellular response to ionizing radiation, such as cell cycle regulation and mechanisms involved in scavenging of free radicals produced by ionizing radiation.

The human XRCC9 gene corrects chromosomal instability and mutagen sensitivities in CHO UV40 cells

The Chinese hamster ovary (CHO) mutant UV40 cell line is hypersensitive to UV and ionizing radiation, simple alkylating agents, and DNA cross-linking agents. The mutant cells also have a high level of spontaneous chromosomal aberrations and 3-fold elevated sister chromatid exchange. We cloned and sequenced a human cDNA, designated XRCC9, that partially corrected the hypersensitivity of UV40 to mitomycin C, cisplatin, ethyl methanesulfonate, UV, and gamma-radiation. The spontaneous chromosomal aberrations in XRCC9 cDNA transformants were almost fully corrected whereas sister chromatid exchanges were unchanged. The XRCC9 genomic sequence was cloned and mapped to chromosome 9p13. The translated XRCC9 sequence of 622 amino acids has no similarity with known proteins. The 2.5-kb XRCC9 mRNA seen in the parental cells was undetectable in UV40 cells. The mRNA levels in testis were up to 10-fold higher compared with other human tissues and up to 100-fold higher compared with other baboon tissues. XRCC9 is a candidate tumor suppressor gene that might operate in a postreplication repair or a cell cycle checkpoint function.

RAGged repair: what's new in V(D)J recombination

Antigen-specific immunity is due to the generation of a multitude of both immunoglobulins and T-cell receptors through a process designated V(D)J recombination. In vitro reconstitution of this system has taught us a great deal about the molecular mechanism underlying this site-specific recombination process. Hence, it became obvious that the initial steps of the reaction are carried out by the lymphocyte-specific proteins RAG1 and RAG2 (recombination-activating genes), with the help of members of the high mobility group protein family of DNA-binding proteins, HMG1 or HMG2. Structural resemblance between RAG1 and a prokaryotic recombinase, the Salmonella Hin Recombinase, together with mechanistic similarities between V(D)J recombination and bacterial transposition reactions, make it likely that these different processes have evolved from a common ancestral recombination system. The second step in V(D)J recombination is catalysed by the ubiquitous DNA double-strand break repair machinery. The link between V(D)J recombination and double-strand break repair was established through some mutational complementation groups, including the murine SCID mutation (severe combined immunodeficiency), which were shown to be defective in both V(D)J recombination and double-strand break repair. The multisubunit DNA-dependent protein kinase appears to be a key player in these processes. Thus, from an evolutionary point of view, antigen-specific immunity in mammals, e.g., humans and mice, appears to be the result of an evolutionary combination of two unrelated systems involved in DNA metabolism.

Coding joint formation in a cell-free V(D)J recombination system

V(D)J recombination assembles the variable portion of antigen receptor genes in developing lymphocytes and is the only site-specific recombination reaction known in vertebrates. A cell-free system has been established that performs DNA cleavage, end processing, and joining to yield V(D)J coding joints that exhibit structural features similar to those formed in vivo. The reaction has the expected substrate, metal ion, and RAG protein requirements. The efficiency of coding joint formation is reduced dramatically by uncoupling the cleavage and joining portions of the reaction, indicating that a postcleavage coding end complex facilitates joining. By varying the reaction conditions, nucleotide loss from coding ends and heterogeneity of coding joints can be regulated. This cell-free system provides a novel tool for detailed mechanistic analyses of the end processing and joining steps of V(D)J recombination.

Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV

BACKGROUND

Mammalian cells deficient in the XRCC4 DNA repair protein are impaired in DNA double-strand break repair and are consequently hypersensitive to ionising radiation. These cells are also defective in site-specific V(D)J recombination, a process that generates the diversity of antigen receptor genes in the developing immune system. These features are shared by cells lacking components of the DNA-dependent protein kinase (DNA-PK). Although the XRCC4 gene has been cloned, the function(s) of XRCC4 in DNA end-joining has remained elusive.

RESULTS

We found that XRCC4 is a nuclear phosphoprotein and was an effective substrate in vitro for DNA-PK. Human XRCC4 associated extremely tightly with another protein(s) even in the presence of 1 M NaCl. Co-immunoprecipitation and adenylylation assays demonstrated that this associated factor was the recently identified human DNA ligase IV. Consistent with this, XRCC4 and DNA ligase IV copurified exclusively and virtually quantitatively over a variety of chromatographic steps. Protein mapping studies revealed that XRCC4 interacted with ligase IV via the unique carboxy-terminal ligase IV extension that comprises two tandem BRCT (BRCA1 carboxyl terminus) homology motifs, which are also found in other DNA repair-associated factors and in the breast cancer susceptibility protein BRCA1.

CONCLUSIONS

Our findings provide a function for the carboxy-terminal region of ligase IV and suggest that BRCT domains of other proteins may mediate contacts between DNA repair components. In addition, our data implicate mammalian ligase IV in V(D)J recombination and the repair of radiation-induced DNA damage, and provide a model for the potentiation of these processes by XRCC4.

Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells

Mutation of the XRCC4 gene in mammalian cells prevents the formation of the signal and coding joints in the V(D)J recombination reaction, which is necessary for production of a functional immunoglobulin gene, and renders the cells highly sensitive to ionizing radiation. However, XRCC4 shares no sequence homology with other proteins, nor does it have a biochemical activity to indicate what its function might be. Here we show that DNA ligase IV co-immunoprecipitates with XRCC4 and that these two proteins specifically interact with one another in a yeast two-hybrid system. Ligation of DNA double-strand breaks in a cell-free system by DNA ligase IV is increased fivefold by purified XRCC4 and seven- to eightfold when XRCC4 is co-expressed with DNA ligase IV. We conclude that the biological consequences of mutating XRCC4 are primarily due to the loss of its stimulatory effect on DNA ligase IV: the function of the XRCC4-DNA ligase IV complex may be to carry out the final steps of V(D)J recombination and joining of DNA ends.

Ku70-deficient embryonic stem cells have increased ionizing radiosensitivity, defective DNA end-binding activity, and inability to support V(D)J recombination

V(D)J recombination requires both lymphoid-specific and generally expressed enzymatic activities. All three known generally expressed activities involved in V(D)J recombination are also involved in DNA double-strand break repair (DSBR). Two of these are components of the DNA-dependent protein kinase (DNA-PK) and include Ku80 and DNA-PK catalytic subunit (DNA-PKcs); the third, XRCC4, is a protein of unknown function. The Ku70 protein is an additional component of DNA-PK; Ku70 forms a heterodimer with Ku80 to generate the DNA end-binding component of the enzyme. To test putative functions for Ku70, we have used gene-targeted mutation to generate a murine embryonic stem cell line which lacks Ku70 expression. We find that the Ku70(-/-) cells produce no detectable Ku70 and very little Ku80, suggesting a direct interrelationship between their levels. Correspondingly, these cells lack the nonspecific DNA end-binding activity associated with Ku. Significantly, the Ku70(-/-) embryonic stem cells have markedly increased sensitivity to gamma-irradiation relative to Ku70(+/-) or wild-type embryonic stem cells. Furthermore, the Ku70(-/-) cells lack the ability to effectively rejoin signal and coding ends liberated in transiently introduced V(D)J recombination substrates by enforced RAG-1 and RAG-2 expression. We conclude that the Ku70 gene product is involved in DSBR and V(D)J recombination and confirm that the Ku70 gene can be classified as a member of the x-ray cross-complementation group 6 (XRCC6). Potential differences between the Ku70(-/-) and Ku80(-/-) V(D)J recombination defects are discussed.

V(D)J recombination in Ku86-deficient mice: distinct effects on coding, signal, and hybrid joint formation

Ku, a heterodimer of 70 and 86 kDa subunits, plays a critical but poorly understood role in V(D)J recombination. Although Ku86-deficient mice are defective in coding and signal joint formation, rare recombination products have been detected by PCR. Here, we report nucleotide sequences of 99 junctions from Ku86-deficient mice. Over 90% of the coding joints, but not signal or hybrid joints, exhibit short sequence homologies, indicating that homology is required to join coding ends in the absence of Ku86. Our results suggest that Ku86 may normally have distinct functions in the formation of these different types of junctions. Furthermore, Ku86(-/-) joints are unexpectedly devoid of N-region diversity, suggesting a novel role for Ku in the addition of N nucleotides by terminal deoxynucleotidyl transferase.

RAB22 and RAB163/mouse BRCA2: proteins that specifically interact with the RAD51 protein

The human RAD51 protein is a homologue of the bacteria RecA and yeast RAD51 proteins that are involved in homologous recombination and DNA repair. RAD51 interacts with proteins involved in recombination and also with tumor suppressor proteins p53 and breast cancer susceptibility gene 1 (BRCA1). We have used the yeast two-hybrid system to clone murine cDNA sequences that encode two RAD51-associated molecules, RAB22 and RAB163. RAB163 encodes the C-terminal portion of mouse BRCA2, the homologue of the second breast cancer susceptibility gene protein in humans, demonstrating an in vitro association between RAD51 and BRCA2. RAB22 is a novel gene product that also interacts with RAD51 in vitro. To detect RAD51 interactions in vivo, we developed a transient nuclear focus assay that was used to demonstrate a complete colocalization of RAB22 with RAD51 in large nuclear foci.

V(D)J recombination: modulation of RAG1 and RAG2 cleavage activity on 12/23 substrates by whole cell extract and DNA-bending proteins

Antigen receptor gene rearrangement is directed by DNA motifs consisting of a conserved heptamer and nonamer separated by a nonconserved spacer of either 12 or 23 base pairs (12 or 23 recombination signal sequences [RSS]). V(D)J recombination requires that the rearranging DNA segments be flanked by RSSs of different spacer lengths, a phenomenon known as the 12/23 rule. Recent studies have shown that this restriction operates at the level of DNA cleavage, which is mediated by the products of the recombination activating genes RAG1 and RAG2. Here, we show that RAG1 and RAG2 are not sufficient for 12/23 dependent cleavage, whereas RAG1 and RAG2 complemented with whole cell extract faithfully recapitulates the 12/23 rule. In addition, HMG box containing proteins HMG1 and HMG2 enhance RAG1- and RAG2-mediated cleavage of substrates containing 23 RSS but not of substrates containing only 12 RSS. These results suggest the existence of a nucleoprotein complex at the cleavage site, consisting of architectural, catalytic, and regulatory components.

RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination

During V(D)J recombination, RAG1 and RAG2 cleave DNA adjacent to highly conserved recombination signals, but nothing is known about the protein-DNA complexes that exist after cleavage. Using a properly regulated in vitro V(D)J cleavage system, together with nuclease sensitivity, mobility shift, and immunoprecipitation experiments, we provide evidence that a stable complex is formed postcleavage between synapsed recombination signals. This complex includes the proteins RAG1, RAG2, HMG-1 or the closely related HMG-2 protein, and the components of the DNA-dependent protein kinase. The existence of such a stable complex explains a number of in vivo observations and suggests that remodeling of postcleavage synaptic complexes is an important step in the resolution of signal ends in V(D)J recombination.

A complex of RAG-1 and RAG-2 proteins persists on DNA after single-strand cleavage at V(D)J recombination signal sequences

The recombination activating gene (RAG) 1 and 2 proteins are required for initiation of V(D)J recombination in vivo and have been shown to be sufficient to introduce DNA double-strand breaks at recombination signal sequences (RSSs) in a cell-free assay in vitro. RSSs consist of a highly conserved palindromic heptamer that is separated from a slightly less conserved A/T-rich nonamer by either a 12 or 23 bp spacer of random sequence. Despite the high sequence specificity of RAG-mediated cleavage at RSSs, direct binding of the RAG proteins to these sequences has been difficult to demonstrate by standard methods. Even when this can be demonstrated, questions about the order of events for an individual RAG-RSS complex will require methods that monitor aspects of the complex during transitions from one step of the reaction to the next. Here we have used template-independent DNA polymerase terminal deoxynucleotidyl transferase (TdT) in order to assess occupancy of the reaction intermediates by the RAG complex during the reaction. In addition, this approach allows analysis of the accessibility of end products of a RAG-catalyzed cleavage reaction for N nucleotide addition. The results indicate that RAG proteins form a long-lived complex with the RSS once the initial nick is generated, because the 3'-OH group at the nick remains obstructed for TdT-catalyzed N nucleotide addition. In contrast, the 3'-OH group generated at the signal end after completion of the cleavage reaction can be efficiently tailed by TdT, suggesting that the RAG proteins disassemble from the signal end after DNA double-strand cleavage has been completed. Therefore, a single RAG complex maintains occupancy from the first step (nick formation) to the second step (cleavage). In addition, the results suggest that N region diversity at V(D)J junctions within rearranged immunoglobulin and T cell receptor gene loci can only be introduced after the generation of RAG-catalyzed DNA double-strand breaks, i.e. during the DNA end joining phase of the V(D)J recombination reaction.

Control of immunoglobulin gene rearrangements in developing B cells

The antigen receptor on B lymphocytes is the product of a series of gene rearrangements which ends when a functional receptor gene is assembled. Recent work has shown that the receptor-associated molecules Ig alpha and Ig beta provide the signals that lead to inhibition of further recombination. Furthermore, Ig beta has been implicated in initiating the last step of the recombination reaction.

Molecular and biochemical characterization of xrs mutants defective in Ku80

The gene product defective in radiosensitive CHO mutants belonging to ionizing radiation complementation group 5, which includes the extensively studied xrs mutants, has recently been identified as Ku80, a subunit of the Ku protein and a component of DNA-dependent protein kinase (DNA-PK). Several group 5 mutants, including xrs-5 and -6, lack double-stranded DNA end-binding and DNA-PK activities. In this study, we examined additional xrs mutants at the molecular and biochemical levels. All mutants examined have low or undetectable levels of Ku70 and Ku80 protein, end-binding, and DNA-PK activities. Only one mutant, xrs-6, has Ku80 transcript levels detectable by Northern hybridization, but Ku80 mRNA was detectable by reverse transcription-PCR in most other mutants. Two mutants, xrs-4 and -6, have altered Ku80 transcripts resulting from mutational changes in the genomic Ku80 sequence affecting RNA splicing, indicating that the defects in these mutants lie in the Ku80 gene rather than a gene controlling its expression. Neither of these two mutants has detectable wild-type Ku80 transcript. Since the mutation in both xrs-4 and xrs-6 cells results in severely truncated Ku80 protein, both are likely candidates to be null mutants. Azacytidine-induced revertants of xrs-4 and -6 carried both wild-type and mutant transcripts. The results with these revertants strongly support our model proposed earlier, that CHO-K1 cells carry a copy of the Ku80 gene (XRCC5) silenced by hypermethylation. Site-directed mutagenesis studies indicate that previously proposed ATP-binding and phosphorylation sites are not required for Ku80 activity, whereas N-terminal deletions of more than the first seven amino acids result in severe loss of activities.

The role of DNA repair in development

Several pathways of DNA repair are essential for maintaining genomic integrity in mammalian cells. Mismatch repair is the final line of defense against polymerase errors during normal cellular replication. Base excision repair removes endogenous DNA damage resulting from normal cellular metabolism. Nucleotide excision repair removes bulky, transcription blocking, lesions resulting from endogenous and environmental insults to the DNA. The role of DNA repair in mammalian development is not well understood. Nevertheless, clues to the essential nature of these processes are evident in the human DNA repair syndromes, in the nature of the interactions between DNA repair and other proteins, and in the phenotypes of genetically engineered, knockout mice lacking functional repair genes. Questions remain: what is the relative importance of endogenous vs. environmental DNA damage and is repair itself critical for normal development or are transcription-repair interactions more crucial?

On the role of DNA double-strand breaks in toxicity and carcinogenesis

DNA double-strand breaks are associated with various endogenous processes, such as transcription, recombination, replication, and with the process of active cell death, which aims to eliminate cells. In addition, DNA double-strand breaks can be induced by irradiation, exposure to chemicals, increased formation of reactive oxygen species, and, indirectly, during repair of other types of DNA damage or as a consequence of extranuclear lesions. In addition to the neutral filter elution of DNA, the recently introduced pulsed-field gel electrophoresis is capable of determining DNA double-strand breaks with higher accuracy and sensitivity and is expected to increase our knowledge on the frequency and the role of DNA breakage. Parallel determination of parameters for cytotoxicity is necessary to elucidate the causal primary lesion. Although the repair of DNA double-strand breaks is a complex task, cells are capable of repairing--with or without errors and up to a certain extent--and surviving this DNA lesion. Gene translocations, rearrangements, amplifications, and deletions arising during repair and misrepair of double-strand breaks may contribute to cell transformation and tumor development.

Specificity in V(D)J recombination: new lessons from biochemistry and genetics

Recent in vitro work on V(D)J recombination has helped to clarify its mechanism. The first stage of the reaction, which can be reproduced with the purified RAG1 and RAG2 proteins, is a site-specific cleavage that generates the same broken DNA species found in vivo. The cleavage reaction is closely related to known types of transpositional recombination, such as that of HIV integrase. All the site specificity of V(D)J recombination, including the 12/23 rule, is determined by the RAG proteins. The later steps largely overlap with the repair of radiation-induced DNA double-strand breaks, as indicated by the identity of several newly characterized factors involved in repair. These developments open the way for a thorough biochemical study of V(D)J recombination.

Potential molecular targets for manipulating the radiation response

Recent advances in our understanding of the molecular events that occur following ionizing radiation leading to DNA damage and repair, apoptosis, and cell-cycle arrests suggest new ways in which the radiation response might be manipulated. Specific targets which, if inactivated, might increase radiosensitivity include Ras, which has been implicated in the radioresistant phenotype, and components of DNA-dependent protein kinase or other molecules involved in the recognition or repair of DNA damage. In some tumors, apoptosis is an important mode of cell death following radiation, so agents that promote this may prove useful therapeutically. Conversely, side effects may result from radiation-induced apoptosis of normal tissues: for example, pneumonitis following the destruction of endothelial cells in the pulmonary vasculature. Therefore, decreasing apoptosis in these tissues may reduce late effects. It may also be possible to prevent late effects such as fibrosis by blocking the induction of certain genes such as transforming growth factor beta. Cell-cycle regulation is another area that could be manipulated to increase radiosensitivity. There is evidence that the G2 delay following radiation is important in protecting cells from death. Abolition of this delay may increase radiosensitivity, especially in cells with mutant p53 that have lost the G1 checkpoint.

Tying loose ends: roles of Ku and DNA-dependent protein kinase in the repair of double-strand breaks

A convergence of information from biochemistry, yeast and mammalian genetics, immunology, and radiation biology has permitted identification of some of the protein participants - Ku, DNA-PK, XRCC4 - and the reaction intermediates in DNA end joining, suggesting how broken chromosomal ends may be recognized and repaired in eukaryotic cells. Some components may be defective in inherited disorders.

Assessing the pathogenic potential of the V(D)J recombinase by interlocus immunoglobulin light-chain gene rearrangement

Chromosomal translocations involving antigen receptor genes and oncogenes have been observed in several forms of lymphoid malignancy. Observations of their lymphocyte-restricted occurrence and a molecular analysis of some translocation breakpoints have suggested that some of these rearrangements are generated by V(D)J recombinase activity. However, a direct correlation between this activity and the generation of such rearrangements has never been established. In addition, because these aberrant rearrangements are usually detected only after a tumor has been formed, the frequency with which the recombinase machinery generates translocations has never been assessed directly. To approach these issues, immunoglobulin light-chain gene rearrangements were induced in pre-B cells transformed by temperature-sensitive mutants of Abelson murine leukemia virus and PCR was used to identify interlocus recombinants. Vlambda Jkappa and Vkappa Jlambda rearrangements as well as signal joints resulting from the recombination of Vlambda and Jkappa coding elements were recovered and were found to be similar in structure to conventional intrachromosomal joints. Because these products were detected only when the cells were undergoing active intralocus rearrangement, they provide direct evidence that translocations can be generated by the V(D)J recombinase machinery. Dilution analyses revealed that interlocus rearrangements occur about 1,000 times less frequently than conventional intralocus rearrangements. Considering the large numbers of lymphocytes generated throughout life, aberrant rearrangements generated by the V(D)J recombinase may be relatively common.

A role for molecular radiobiology in radiotherapy?

As we learn more about the cellular response to radiation and its genetic control, new avenues are opened up that have the potential to have a significant impact on radiotherapy practice. The recognition of the importance of the control of DNA damage induction and repair, cell cycle arrest and apoptosis gives us the primary areas to investigate, and the improvements in molecular technology make the application of our new knowledge more feasible. It can only be hoped that specific means can be found to assist in the prediction of normal tissue and tumour radiosensitivity and to manipulate sensitivity when that is desirable.

Naturally occurring primary deficiencies of the immune system

Naturally occurring genetic disorders of the immune system provide many models for the study of its development and function. In a way, their analysis complements the information provided by the generation of genetic defects in mice created using homologous recombination techniques. In this review, the recent findings made in three areas are focused upon deficiencies in T cell differentiation and in T lymphocyte activation, and on the control process of peripheral immune response.

In vitro V(D)J recombination: signal joint formation

The first step of V(D)J recombination, specific cleavage at the recombination signal sequence (RSS), can be carried out by the recombination activating proteins RAG1 and RAG2. In vivo, the cleaved coding and signal ends must be rejoined to generate functional antigen receptors and maintain chromosomal integrity. We have investigated signal joint formation using deletion and inversion substrates in a cell free system. RAG1 and RAG2 alone or in combination were unable to generate signal joints. However, RAG1 and RAG2 complemented with nuclear extracts were able to recombine an extrachromosomal substrate and form precise signal joints. The in vitro reaction resembled authentic V(D)J recombination in being Ku-antigen-dependent.

Mouse RAD50 has limited epitopic homology to p53 and is expressed in the adult myocardium

Previous studies have identified a 180-kDa mouse cardiomyocyte phosphoprotein with limited epitopic homology to p53. In this study, the protein was purified and partially sequenced. Oligonucleotide probes based on the available amino acid sequence data were used to isolate cDNA clones. Sequence analyses revealed that the clones encoded a protein with regional homology to the yeast RAD50 gene product. Expression of the mouse cDNA rescued the methyl methanesulfonate-sensitive phenotype in rad50 mutant yeast, indicating that the cardiomyocyte phosphoprotein is the mammalian homologue of the yeast RAD50 gene product. Fluorescence in situ hybridization analyses localized the mouse RAD50 gene to the A5-B1 region of chromosome 11. Northern blot analyses demonstrated a complex pattern of RAD50 expression during mouse development which was further complicated by the presence of several alternatively spliced transcripts. High levels of RAD50 expression was evident in the adult myocardium, a somewhat surprising observation given the absence of DNA synthesis in adult cardiomyocytes.

Developmental regulation of V(D)J recombination and lymphocyte differentiation

Recent insights into the mechanism of V(D)J recombination have clarified the direct role of the products of the recombination-activating genes Rag-1 and Rag-2 in site-specific DNA cleavage at recombination signal sequences and have identified components of the general DNA double-strand break repair pathway that participate in the rejoining of the Rag-1 and Rag-2-cut receptor gene segments. The V(D)J reaction is restricted to particular antigen receptor loci in a lineage-specific and stage-specific manner. This specificity appears to involve cis-regulatory elements, some of which also regulate transcription of the germline antigen receptor loci. Early developmental steps in the T and B lineages - including phenotypic differentiation, expansion of precursors, and selection processes - are effected in a stepwise fashion by signals generated, at least in part, by the products of the functionally rearranged antigen receptor genes themselves.

Rad51 expression and localization in B cells carrying out class switch recombination

Rad51 is a highly conserved eukaryotic homolog of the prokaryotic recombination protein RecA, which has been shown to function in both recombinational repair of DNA damage and meiotic recombination in yeast. In primary murine B cells cultured with lipopolysaccharide (LPS) to stimulate heavy chain class switch recombination, Rad51 protein levels are dramatically induced. Immunofluorescent microscopy shows that anti-Rad51 antibodies stain foci that are localized within the nuclei of switching B cells. Immunohistochemical analysis of splenic sections shows that clusters of cells that stain brightly with anti-Rad51 antibodies are evident within several days after primary immunization and that Rad51 staining in vivo is confined to B cells that are switching from expression of IgM to IgG antibodies. Following switch recombination, B cells populate splenic germinal centers, where somatic hypermutation and clonal proliferation occur. Germinal center B cells are not stained by anti-Rad51 antibodies. Rad51 expression is therefore not coincident with somatic hypermutation, nor does Rad51 expression correlate simply with cell proliferation. These data suggest that Rad51, or a highly related member of the conserved RecA family, may function in class switch recombination.

The recombination activating gene 2 (RAG2) of the rainbow trout Oncorhynchus mykiss

We have previously described the isolation and expression of RAG1 in trout to provide an initial understanding regarding the tissues involved in V(D)J recombination of antigen receptors in this teleost. Here we report that the recombination activating gene 2 (RAG2) of rainbow trout has now been cloned and characterized. The rainbow trout genomic RAG2 gene (1602 base pairs) displays an average of 60% and 75% similarity at the nucleotide and amino acid level when compared with clones from other species and was found to contain an acidic region in the carboxyl terminal end, which is typical of RAG2 sequences. The proximity of RAG1 and -2 within this teleost is similar to that found in other vertebrates. The genes are convergently transcribed and share a 3' untranslated (UT) region [2. 8 kilobases (kb)] which is much shorter than that found in higher vertebrates (6 - 8 kb). The entire 3' UT region was also sequenced and used in conjunction with cDNA clones to identify the polyadenylation sites for both RAG genes. Northern blot analysis of one-year-old trout demonstrated strong expression of RAG2 in the thymus, with a much weaker signal being detected in the pronephros. Using reverse transcriptase-polymerase chain reaction, we detected the highest expression of both RAG1 and -2 in the thymus followed by the pronephros, with much fainter signals being observed in the spleen, mesonephros, and liver. Finally, both genes are expressed in embryos beginning at approximately day 10 post-fertilization. Taken together, these findings indicate that the thymus and pronephros most likely serve as the primary lymphoid tissues in trout, based upon RAG expression. In addition, the trout sequences may provide further insight into the evolution and origins of the RAG genes as well as that of the immune system itself.

Lack of detectable defect in DNA double-strand break repair and DNA-dependent protein kinase activity in radiosensitive human severe combined immunodeficiency fibroblasts

The initial step of the V(D)J recombination occurs through the generation of a DNA double-strand break (dsb). Defects in the DNA-dependent protein kinase complex (DNA-PK) result in an inability to perform either V(D)J recombination or any dsb repair effectively. The human autosomal T-B-severe combined immunodeficiency (SCID) condition is characterized by an absence of both B and T lymphocytes and is accompanied in some patients by an increase in gamma-ray sensitivity (T-B-RS SCID) comparable to that found in mouse SCID cells. We show here that cells from six patients with T-B-RS SCID had normal DNA-dsb repair kinetics. Furthermore, DNA-PK activity was present in extracts from these human T-B-RS SCID fibroblasts. We therefore conclude that some human T-B-RS SCID disorders are not caused by a defect in an essential DNA-PK component.

Cutting apart V(D)J recombination

The past year has seen major advances in our understanding of the recombination mechanism by which antibody and T cell receptor genes are assembled during lymphoid development. The initial cleavage events can be carried out in vitro by purified RAG1 and RAG/ protein. In addition, a number of genes involved in later steps of the reaction have been cloned, opening the way for an in-depth biochemical analysis of this critical developmental process.

Mechanism of V(D)J recombination

V(D)J recombination can be separated into two basic operations: DNA cleavage and joining of broken ends. Our understanding of both reactions has increased substantially in the past year. Major advances include the development of a cell-free system capable of cleavage and the identification of several proteins involved in both V(D)J recombination and double-strand break repair.

Cellular and molecular analysis of lymphoid development using Rag-deficient mice

The establishment of a functional immune system with diverse antigen receptors is dependent on the V(D)J recombination activating gene products Rag-1 and Rag-2. These two proteins constitute the key lymphoid components required for the activation of antigen receptor rearrangement. Both Rag-1 and Rag-2 are required for the catalysis of the initial stages of V(D)J recombination. Thus, functional disruption of either the Rag-1 or Rag-2 genes by homologous recombination, leads to immunodeficiency due to lymphoid arrest at a stage prior to the recombination of the antigen receptor loci. In Rag-deficient mice, both B- and T-cell differentiation is eliminated due to the absence of antigen receptors. Lymphoid development can be restored by the introduction of rearranged antigen receptor transgenes that give rise to monoclonal populations of fully mature B- or T-cells. The absence of the major conventional populations of B- and T-cells from the Rag-deficient mice provided an excellent background for studying the molecular and cellular mechanisms of lymphoid differentiation. The Rag-deficient background has been used as a system for: the functional analysis of Rag-1 and Rag-2; studying the developmental functions of antigen receptors and other molecules of the immune system; the molecular analysis of the early stages of the B- and T-cell lineages; the co-development of lymphocytes with stroma cells; the identification of minor subpopulations of the developing immune system; the involvement of lymphoid populations in the onset of pathogenesis. In addition, the development of the "blastocyst complementation assay" methodology, based on the phenotype of the Rag-/- mice, allowed the functional analysis of numerous lymphoid specific components.