Lambda Gene Research Articles

Functional and genetic analysis of regulatory regions of coliphage H-19B: location of shiga-like toxin and lysis genes suggest a role for phage functions in toxin release.

Analysis of the DNA sequence of a 17 kb region of the coli lambdoid phage H-19B genome located the genes encoding shiga-like toxin I (Stx-I) downstream of the gene encoding the analogue of the phage lambda Q transcription activator with its site of action, qut at the associated pR' late promoter, and upstream of the analogues of lambda genes encoding lysis functions. Functional studies, including measurement of the effect of H-19B Q action on levels of Stx expressed from an H-19B prophage, show that the H-19B Q acts as a transcription activator with its associated pR'(qut) by promoting readthrough of transcription terminators. Another toxin-producing phage, 933W, has the identical Q gene and pR'(qut) upstream of the stx-II genes. The H-19B Q also activates Stx-II expression from a 933W prophage. An ORF in H-19B corresponding to the holin lysis genes of other lambdoid phages differs by having only one instead of the usual two closely spaced translation initiation signals that are thought to contribute to the time of lysis. These observations suggest that stx-I expression can be enhanced by transcription from pR' as well as a model for toxin release through cell lysis mediated by action of phage-encoded lysis functions. Functional studies show that open reading frames (ORFs) and sites in H-19B that resemble components of the N transcription antitermination systems controlling early operons of other lambdoid phages similarly promote antitermination. However, this N-like system differs significantly from those of other lambdoid phages.

Molecular analyses of VH and VL genes used by 7 cases of Primary Effusion Lymphomas (PEL) disclose the presence of somatic mutations indicative of antigen selection.

99 Background: PELs are an uncommon subset of AIDS related lymphomas that grow mainly in the body cavities as lymphomatous effusions. Because of the presence of a clonal rearrangement of the Ig genes these lymphomas are classified of B lineage origin although they lack of surface B cell antigens. To date no data are available on the sequences of these rearranged genes. Methods: We have sequenced the VH and VL genes used by 4 cell lines (HBL6, BC1, BC2, and BC3) derived from PEL and from 4 biopsy samples. HBL6 and BC1 were derived from the same patient though at different times. Results: VH gene usage among the samples was the following: 3 cases used a VH3 family gene (two the 3-23 gene and one the 3-73 gene), 2 cases employed a VH4 gene (both 4-39), 1 case used a VH1 gene (1-03) and 1 a VH5 gene (5-51). The malignant cells expressed a JH5 (2 cases), JH6 (4 cases) segments, and quite strikingly JH4 (the most common JH) was expressed only by one case. The D segments were not clearly assignable except than in two cases in which stretches deriving from the D2-15/D and from the D5-18 genes were identified. Indeed in these two cases the CDR3 length was longer than in the others (16 and 20 aa respectively against a general average of 13 aa). A productive rearrangement of a Lambda light chain was found in 6 out of 7 samples. The only sample having a productive rearrangement was the cell line HBL6 (and BC1). Among the Lambda genes the VL3 family was used predominantly (4 out of six samples). In all instances but one (BC3 cell line), the comparison of the VH and VL sequences with a database discloses significant nucleotide differences with the presumptive germline. We analyzed the pattern of these mutations using the classical R:S ratio and using a statistical analysis proposed by Chang and Casali. Both these analyses disclosed that the mutations present in the antigen receptors were compatible with antigen selection either at VH or VL level in all the samples. Conclusions: The presence and the pattern of the point mutations at VH and VL level in the cases reported suggest that these were "experienced" cells that had undergone stimulation/selection by antigen(s). Overall these data suggest that (i) PEL frequently derives from memory cells possibly of GC- or post-GC B cell and (li) antigen induced stimulation and selection may be part of the pathogenic origin of these lymphomas.

Rearrangement of lambda light chain genes in mature B cells in vitro and in vivo. Function of reexpressed recombination-activating gene (RAG) products.

V(D)J (V, variable; D, diversity; J, joining) combination of immunoglobulin (Ig) genes established in premature B cells has been thought to be conserved throughout differentiation at mature stages. However, germinal center (GC) B cells have been shown to reexpress recombination-activating gene (RAG)-1 and RAG-2 proteins in immunized mice. Here, we present several lines of evidence indicating that RAG proteins thus induced are functional as the V(D)J recombinase. DNA excision product reflecting Vlambda1 to Jlambda1 rearrangement was generated in parallel with the expression of RAG genes in mature mouse B cells that were activated in vitro with LPS and IL-4. Similar lambda chain gene rearrangement was observed in the draining lymph node of immunized mice. Further, B cells that underwent lambda gene rearrangement were shown by in situ PCR to be localized within GCs. Thus, secondary rearrangement of Ig genes (receptor editing) can occur in mature B cells.

Kappa and lambda rearrangement occur simultaneously in transformed pre-B cells.

Murine B-lineage cells can express either kappa or lambda Ig light chains. However, most of these cells express kappa protein, a phenomenon that appears to be controlled in part at the level of gene rearrangement. This feature may reflect a preference for the kappa locus by the recombinase machinery, or it may indicate that kappa rearrangement begins before lambda rearrangement. These possibilities can be distinguished by measuring the kinetics with which light chain gene rearrangement at both loci actually occurs. To this end, we have used pre-B cells transformed by temperature-sensitive mutants of Abelson virus that undergo kappa and lambda gene rearrangement when shifted to the nonpermissive temperature. Competitive PCR analyses of rearrangement kinetics demonstrate that the kappa and lambda loci rearrange at about the same time in these cells. Consistent with this, some clones isolated from cells induced for a short period of time have rearranged only the lambda locus. However, the frequency with which lambda genes are rearranged is three- to sixfold lower than that with which kappa genes rearrange. These data indicate that the recombinase machinery targets both light chain loci at the same time, but acts preferentially at the kappa locus. The reduced ability of the recombinase machinery to target the lambda locus and selection pressures occurring during B cell development probably both contribute to the preferential usage of kappa genes in normal murine B lineage cells.

A 37-kb restriction map of the human immunoglobulin lambda variable locus, VB cluster, harboring four functional genes and two non-coding V<FONT FACE=Symbol>l</font> sequences

The human immunoglobulin lambda variable locus (IGLV) is mapped at chromosome 22 band q11.1-q11.2. The 30 functional germline v-lambda genes sequenced untill now have been subgrouped into 10 families (V<FONT FACE="Symbol">l</font>1 to V<FONT FACE="Symbol">l</font>10). The number of V<FONT FACE="Symbol">l</font> genes has been estimated at approximately 70. This locus is formed by three gene clusters (VA, VB and VC) that encompass the variable coding genes (V) responsible for the synthesis of lambda-type Ig light chains, and the J<FONT FACE="Symbol">l</font>-C<FONT FACE="Symbol">l</font> cluster with the joining segments and the constant genes. Recently the entire variable lambda gene locus was mapped by contig methodology and its one- megabase DNA totally sequenced. All the known functional V-lambda genes and pseudogenes were located. We screened a human genomic DNA cosmid library and isolated a clone with an insert of 37 kb (cosmid 8.3) encompassing four functional genes (IGLV7S1, IGLV1S1, IGLV1S2 and IGLV5a), a pseudogene (V<FONT FACE="Symbol">l</font>A) and a vestigial sequence (vg1) to study in detail the positions of the restriction sites surrounding the V<FONT FACE="Symbol">l</font> genes. We generated a high resolution restriction map, locating 31 restriction sites in 37 kb of the VB cluster, a region rich in functional V<FONT FACE="Symbol">l</font> genes. This mapping information opens the perspective for further RFLP studies and sequencing

Recombining sequence recombination in normal kappa-chain-expressing B cells.

Recombining sequence (RS) recombination is a DNA rearrangement that deletes one or two C kappa alleles in a large proportion of lambda-expressing B cells. Since its discovery, this recombination has been suggested to play a role in activating lambda gene rearrangements. A model involving a positive signal generated by RS recombination seems to be excluded, but another model that is still under consideration proposes that RS recombination removes DNA sequences within the kappa locus that would interfere with lambda gene assembly. Using PCR assays, we have found that kappa-expressing cells account for the majority of RS rearrangements in mouse spleen. RS rearrangements were also detected by Southern blot in kappa-secreting hybridomas. Quantification of rearrangements indicates that approximately 12% of kappa cells bear an RS recombination. From this finding, we infer that once a cell has performed an RS recombination on one kappa allele, it has a 3 times higher probability of rearranging functionally its other kappa allele rather than one of the lambda genes. These data call into question the role of RS recombination in the switch from kappa to lambda and suggest another function for this nonproductive rearrangement.

Generation of diversity in mammalian gut-associated lymphoid tissues: restricted V gene usage does not preclude complex V gene organization.

The sheep genome contains 60 to 90 V lambda genes distributed in least 6 different families, whereas 37 V lambda genes and 10 families exist in humans. Comparison with human V lamda sequences indicates that sheep V lambda genes display less overall sequence divergence, but are closer to the genes most frequently used in the human peripheral repertoire. In both species, 2 to 3 genes contribute half of the expressed sequences. Therefore, similar large combinatorial potential and restriction of the expressed repertoire can exist in two species whose strategy of diversification differs widely (ongoing rearrangement throughout life in human bone marrow vs postrearrangement diversification during early development in sheep ileal Peyer's patches).

The spatial distribution of human immunoglobulin genes within the nucleus: evidence for gene topography independent of cell type and transcriptional activity.

The three-dimensional positioning of immunoglobulin (Ig) genes within the nucleus of human cells was investigated using in situ hybridization and confocal microscopy. The visualization of heavy and light chain genes in B-lymphoid cells showed that the three Ig genes are differentially and nonrandomly distributed in different nuclear subvolumes: the kappa genes were found to be preferentially confined to an outer nuclear volume, whereas the gamma and lambda genes consistently occupied more central positions within the nucleus, the lambda genes being more interior when compared with the gamma genes. The data further show that these overall topographical distributions are independent of gene transcriptional activity and are conserved in different cell types. Although subtle gene movements within those defined topographical regions cannot be excluded by this study, the results indicate that tissue specificity of gene expression is not accompanied by drastic changes in gene nuclear topography, rather suggesting that gene organization within the nucleus may be primarily dependent on structural constraints imposed on the respective chromosomes.

Heterogeneity of antibodies reactive with the dominant antigen of Actinobacillus actinomycetemcomitans.

The serotype b-specific carbohydrate antigen (SbAg) of Actinobacillus actinomycetemcomitans Y4 is reported to be the O antigen of lipopolysaccharide, and the highest titers of serum antibody reactive with A. actinomycetemcomitans in early-onset periodontitis (EOP) patients bind SbAg. These high titers of serum antibody reactive with SbAg are associated with a lesser extent and severity of periodontal disease. The aim of this study was to determine if a limited number of genes code for anti-SbAg antibodies as has been shown for immunoglobulin G (IgG) reactive with the type b polysaccharide from Haemophilus influenzae. Serum IgG reactive with the SbAg was prepared from 20 high-titer EOP patients by affinity chromatography. The IgG subclass concentrations were determined, and heterogeneity was analyzed by isoelectric focusing (IEF). IgG2 was the dominant subclass (83% of total IgG) in the anti-SbAg IgG fraction and represented an average of 1.33% of total serum IgG2. The IgG2 reactive with SbAg was isolated from the affinity-purified IgG fraction by affinity chromatography with protein A and subclass-specific monoclonal antibodies. On IEF gels, only 4 to 20 bands were observed in the anti-SbAg IgG fractions, indicating limited heterogeneity. N-terminal amino acid sequence analysis of eight representative anti-SbAg IgG2 preparations indicated that variable heavy and light chains consisted largely of V(H)III and V(kappa)II, respectively. However, a significant fraction of anti-SbAg may use V(H) and V(lambda) genes with blocked N termini. In short, these findings indicate that IgG reactive with SbAg is very much like the antibody reactive with H. influenzae type b polysaccharide. Similarities include IgG2 dominance, limited bands on IEF gels, supporting an oligoclonal response, and use of genes from V(H)III and V(kappa)II regions.

Studies on the NusB protein of Escherichia coli--expression and determination of secondary-structure elements by multinuclear NMR spectroscopy.

The product of the nusB gene of Escherichia coli modulates the efficiency of transcription termination at nut (N utilization) sites of various bacterial and bacteriophage lambda genes. Similar control mechanisms operate in eukaryotic viruses (e.g. human immunodeficiency virus). A recombinant strain of E. coli producing relatively large amounts of NusB protein (about 10% of cell protein) was constructed. The protein could be purified with high yield by anion-exchange chromatography followed by gel-permeation chromatography. The protein is a monomer of 15.6 kDa as shown by analytical ultracentrifugation. Structural studies were performed using protein samples labelled with 15N, 13C and 2H in various combinations. Heteronuclear three-dimensional triple-resonance NMR experiments combined with a semi-automatic assignment procedure yielded the sequential assignment of the 1H, 13C and 15N backbone resonances. Based on experimentally derived scalar couplings, chemical-shift values, amide-exchange data, and a semiquantitative interpretation of NOE data, the secondary structure of NusB has classified as alpha helical, comprising seven alpha helices.

Shigella flexneri type-specific antigen V: cloning, sequencing and characterization of the glucosyl transferase gene of temperate bacteriophage SfV

With lysogeny by bacteriophage SfV, Shigella flexneri serotype Y is converted to serotype 5a. The glucosyl transferase gene ( gtr) from bacteriophage SfV of S. flexneri, involved in serotype-specific conversion, was cloned and characterized. The DNA sequence of a 3.7 kb EcoRI– BamHI fragment of bacteriophage SfV which includes the gtr gene was determined. This gene, encoding a polypeptide of 417 aa with 47.67 kDa molecular mass, caused partial serotype conversion of S. flexneri from serotype Y to type V antigen as demonstrated by Western blotting and the sensitivity of the hybrid strain to phage Sf6. The deduced protein of the partially sequenced open reading frame upstream of the gtr showed similarity to various glycosyl transferases of other bacteria. Orf3, separated from the gtr by a non-coding region and transcribed convergently, codes for a 167 aa (18.8 kDa) protein found to have homology with tail fibre genes of phage lambda and P2.

EcoRI Restriction Fragment-Length Polymorphism of the Human Immunoglobulin Variable Lambda 8 (IGLV8) Subgroup Reveals a Gene Family

The human immunoglobulin lambda locus (IGL) maps on chromosome 22q11.1–q11.2 and directs the synthesis of lambda-type Ig light chains. This locus is formed by three gene clusters (VA, VB and VC) that encompass the variable coding genes and the J-C cluster plus the joining segments and the constant genes. Recently the variable lambda gene clusters were mapped by the contig methodology which located all the known functional v-lambda genes and pseudogenes. The 30 functional v-lambda genes described so far were subgrouped into ten families (VλI to VλX), but RFLP studies have estimated that the germline repertoire contains about 70 genes. Based on sequence comparisons, we defined specific oligonucleotide primers for the unique IGLV8S1 genedescribed. The cloned 244 bp product obtained from genomic DNA with these primers was sequenced and used as probe in Southern hybridization EcoRI RFLP analysis of Brazilian people. We detected the IGLV8S1 gene in a 3.7 kb EcoRI restriction fragment present in all the individuals analyzed, in agreement with the physical map of the IGL locus. Moreover, we detected an 8.0 kb EcoRI monomorphic fragment and a 6.0 kb EcoRI polymorphic fragment. These data suggest that the IGLV8 subgroup is a gene family.

Functional expression and germline transmission of a human chromosome fragment in chimaeric mice.

Human chromosomes or chromosome fragments derived from normal fibroblasts were introduced into mouse embryonic stem (ES) cells via microcell-mediated chromosome transfer (MMCT) and viable chimaeric mice were produced from them. Transferred chromosomes were stably retained, and human genes, including immunoglobulin (Ig) kappa, heavy, lambda genes, were expressed in proper tissue-specific manner in adult chimaeric tissues. In the case of a human chromosome (hChr.) 2-derived fragment, it was found to be transmitted to the offspring through the germline. Our study demonstrates that MMCT allows for introduction of very large amounts of foreign genetic material into mice. This novel procedure will facilitate the functional analyses of human genomes in vivo.

Immunoglobulin lambda light chain orphons on human chromosome 8q11.2.

We have identified two V lambda genes outside the major lambda locus on chromosome 22q11.2, and shown that they reside on chromosome 8q11.2. One gene (Orphée1), hybridizing strongly to the V lambda probes, was sequenced and found to belong to the V lambda 8 family; the other gene (Orphée2) only hybridized weakly. Orphée1 was present in all individuals tested (140) from three different populations, and was also found in gorillas. We envisage that these genes were generated by duplication and translocation of the V lambda 8a gene (and a V lambda pseudogene) from the major locus, and that this event occurred before the evolutionary divergence of humans and gorillas. As there is no other evidence for V lambda genes outside the major locus, it appears that the human lambda locus has undergone considerably less evolutionary shuffling than either the human light chain kappa locus or the heavy chain locus.

One-megabase sequence analysis of the human immunoglobulin lambda gene locus.

A total of 1,025,415 bases of nucleotide sequence, including the entire human immunoglobulin lambda gene locus has been determined. This is the largest contiguous human DNA sequence ever published. The sequence data revealed the organization of 36 potentially active V lambda gene segments, 33 pseudogene segments, and seven J lambda-C lambda gene segments. Among these 69 functional or nonfunctional V lambda gene segments, 32 were newly discovered. These V lambda gene segments are located within five gene-rich clusters and are divided into five clans based on sequence identity. Five potentially active nonimmunoglobulin genes were also detected within the lambda gene locus, and two other genes were observed in the upstream region. Sequence organization suggests that large DNA duplications diversified the germ-line repertoire of the V lambda gene segments.

Cloning and characterization of bacteriophage-like DNA from Haemophilus somnus homologous to phages P2 and HP1.

In an attempt to identify and characterize components of a heme uptake system of Haemophilus somnus, an Escherichia coli cosmid library of H. somnus genomic DNA was screened for the ability to bind hemin (Hmb+). The Hmb+ phenotype was associated with a 7,814-bp HindIII fragment of H. somnus DNA that was subcloned and sequenced. Thirteen open reading frames (orfs) were identified, all transcribed in one direction, and transposon mutagenesis identified orf7 as the gene associated with the Hmb+ phenotype. Orf7 (178 amino acids) has extensive homology with the lysozymes of bacteriophages P-A2, P21, P22, PZA, phi-29, phi-vML3, T4, or HP1. The orf7 gene complemented the lytic function of the K gene of phage P2 and the R gene of phage lambda. A lysozyme assay using supernatants from whole-cell lysates of E. coli cultures harboring plasmid pRAP501 or pGCH2 (both of which express the orf7 gene product) exhibited significant levels of lysozyme activity. The orf6 gene upstream of orf7 has the dual start motif common to the holins encoded by lambdoid S genes, and the orf6 gene product has significant homology to the holins of phages HP1 and P21. When expressed from a tac promoter, the orf6 gene product caused immediate cell death without lysis, while cultures expressing the orf7 gene product grew at normal rates but lysed immediately after the addition of chloroform. Based on this data, we concluded that the Hmb+ phenotype was an artifact resulting from the expression of cloned lysis genes which were detrimental to the E. coli host. The DNA flanking the cloned lysis genes contains orfs that are similar to structural and DNA packaging genes of phage P2. Polyclonal antiserum against Orf2, which is homologous to the major capsid precursor protein (gpN) of phage P2, detected a 40,000-M(r) protein expressed from pRAP401 but did not detect Orf2 in H. somnus, lysates. The phage-like DNA was detected in the serum-susceptible preputial strains HS-124P and HS-127P but was absent from the serum-resistant preputial strains HS-20P and HS-22P. Elucidation of a potential role for this cryptic prophage in the H. somnus life cycle requires more study.

The production, binding characteristics and sequence analysis of four human IgG monoclonal antiphospholipid antibodies.

Antiphospholid antibodies (APL) have a notable association with recurrent miscarriages, arterial and venous thrombosis and thrombocytopenia. Analysis of the potential pathogenic effects of such human antibodies has been hampered by the considerable difficulty in producing IgG as opposed to IgM monoclonal immunoglobulins. We have developed four human monoclonal IgG APL (LJ1, AH2, DA3 and UK4) by fusing the peripheral blood lymphocytes of three patients with SLE with a mouse human heteromyeloma cell line, CB-F7. These antibodies bind to a variety of anionic phospholipids, two (LJ1 and AH2) bind total histones but none binds to ssDNA or dsDNA. Binding to beta 2 GPI is non-specific. UK4 alone demonstrates lupus anticoagulant activity. All four have lambda light chains, two are IgG1 (AH2 and UK4) and two are IgG3 (LJ1 and DA3). These APL utilize VH genes present in the fetally restricted repertoire and multiple somatic mutations in the CDR suggest an antigen-driven process. In contrast, there is no restriction in V lambda gene usage and only one lambda chain is extensively mutated. Two clonally related hybridomas were isolated from a single patients. This supports the theory that clonal expansion is the mechanism whereby antigen selects high affinity mutations.

FISH mapping of seven cDNA sequences in the pig.

Fluorescence in situ hybridization (FISH) technique was applied to localize seven clones derived from a porcine (SSC) intestinal directionally cloned cDNA library. The size of the clones ranged from 1.1 to 1.3 kb. Three of the clones corresponded to histidyl-tRNA synthetase (HARS), immunoglobulin alpha (IGA) and lysozyme (LYZ) and mapped to SSC2q28-q29, 7q2.6 and 5p11 respectively. The available human-pig comparative painting data and sequence homology comparisons assisted in a tentative identification of the other three clones as glutathione-S-transferase (GST), glutathione-S-transferase mu (GSTM1) and immunoglobulin lambda gene cluster (IGL@). These clones mapped to SSC14q21, 5q2.4 and 14q22-q23 respectively. The remaining clone representing an EST mapped to 1p24-p25. These localizations contribute to the transcript map in pig and are significant as comparative markers. Difficulties associated with the mapping of small sequences using FISH are discussed.

A third Ig light chain gene isotype in Xenopus laevis consists of six distinct VL families and is related to mammalian lambda genes.

Xenopus laevis is a unique model for studying the ontogenetic development of immune functions. A short primer PCR amplification method was employed to amplify fragments from Xenopus genomic DNA that are related to Ig light chains and TCR. One fragment was identified that appeared to represent a novel type of light chain and was used as a probe to recover the corresponding cDNA from a spleen cDNA library. We designate these light chains type III. Using an iterative screening procedure, six families of VL genes, two distinct JL and two distinct CL sequences, were identified. In a comparison of phylogenetically diverse light chains, the type III genes align with higher vertebrate lambda genes. Southern blot hybridization analyses with genomic DNA from different animals showed the VL and CL sequences to be both diverse and polymorphic. Intrafamily sequence comparisons of VL genes revealed additional diversity. Collectively, these studies confirm the existence of a third type of light chain gene in Xenopus, establish a high degree of genetic variation in the sequences encoding the light chain V regions, and provide the most significant evidence to date for the presence of a lambda-like light chain gene at the phylogenetic level of the amphibians.

The repertoire of human antibodies to the carbohydrate capsule of Streptococcus pneumoniae 6B.

Antibodies to Streptococcus pneumoniae 6B capsular polysaccharide (PS) induced with a 23-valent PS vaccine among 25 adults were examined. The magnitude of antibody responses among different subjects was highly correlated with the amount of anti-6B antibodies expressing IgG (r = 0.98) and lambda (r = 0.93) isotypes. Most individuals produced one or two dominant IgG antibody clones as identified by their isoelectric points. Two antibody clones with unique amino acid sequences could be readily purified, and the sequences of their light chains match those of A1/A17 V kappa and hslv2046 V lambda genes. Anti-6B antibodies isolated from different subjects used various VL genes and differed in their cross-reactivity with 6A PS. An isoelectric focusing study suggests that some IgG antibodies induced with 6B PS bind 6A PS with lower avidity.