The LE1 bacteriophage replicates as a plasmid within Leptospira biflexa: construction of an L. biflexa-Escherichia coli shuttle vector.

We have discovered that LE1, one of the plaque-forming phages previously described as lytic for the Leptospira biflexa saprophytic spirochete (I. Saint Girons, D. Margarita, P. Amouriaux, and G. Baranton, Res. Microbiol. 141:1131-1138, 1990), was indeed temperate. LE1 was found to be unusual, as Southern blot analysis indicated that it is one of the few phages to replicate in the prophage state as a circular plasmid. The unavailability of such small endogenous replicons has hindered genetic experimentation in Leptospira. We have developed a shuttle vector with DNA derived from LE1. Random LE1 DNA fragments were cloned into a pGEM 7Zf(+) derivative devoid of most of the bla gene but carrying a kanamycin resistance marker from the gram-positive bacterium Enterococcus (Streptococcus) faecalis. These constructs were transformed into L. biflexa strain Patoc 1 by electroporation, giving rise to kanamycin-resistant transformants. A 2.2-kb fragment from LE1 was responsible for replication of the vector in L. biflexa. However, a larger region including an intact parA gene homologue was necessary for the stability of the shuttle vector. Direct repeats and AT-rich regions characterized the LE1 origin of replication. Our data indicate that the replicon derived from the LE1 leptophage, together with the kanamycin resistance gene, is a promising tool with which to develop the genetics of Leptospira species.

Analysis of BR96 binding sites for antigen and anti-idiotype by codon-based scanning mutagenesis.

We performed a scanning mutagenesis study of heavy chain complementarity-determining region (CDR) residues to identify how mutations affected binding of the anti-carcinoma mAb BR96 to Ag, Lewis Y, and to an anti-Id Ab (anti-Id). By ELISA, we demonstrated that the anti-Id bound close to the Ag binding site of BR96, but the anti-Id and Ag sites were not identical. Immunoblot analysis and screening of light and heavy chain CDR libraries with multiple mutations in each CDR suggested that the heavy chain had greater involvement in anti-Id binding. We then analyzed contributions of individual residues in the heavy chain CDRs to binding of Ag and anti-Id. In a filamentous phage vector containing BR96 V region sequences, mutations were introduced by codon-based mutagenesis at single positions within the three heavy chain CDRs. The resulting libraries of Fab fragments had all amino acids represented at a CDR position. We evaluated the expressed Fabs for binding to Ag and anti-Id by plaque lift assay. We identified the positions with mutations that had the greatest negative effect on binding to the anti-Id and to Ag and analyzed them on the basis of the BR96 x-ray structure. The residues most important for binding to the anti-Id were located in heavy chain CDR1 and CDR2 and were peripheral to the residues within the Lewis Y binding pocket.

A combinatorial library strategy for the rapid humanization of anticarcinoma BR96 Fab.

We have used a combinatorial mutagenesis strategy to humanize BR96, a monoclonal antibody that binds to the Lewis Y class of tumor antigens. This approach allows simultaneous assessment of hundreds of humanized variable regions to identify the molecules that best preserve affinity, thus overcoming the major drawback of current humanization procedures, the requirement to construct and analyze each humanized antibody separately. Murine residues of BR96 were mutated to human if they were solvent-exposed residues that did not participate in the formation of the antigen binding site and were not at the interface of the light and heavy chain. At positions that might be involved in binding to antigen, the choice between the murine and human residue was more difficult. Murine and human alternatives were incorporated into a combinatorial library at positions representing buried residues that might affect the structural integrity of the antigen binding site. By encoding this library of humanized BR96 Fabs in an M13 phage vector, we rapidly identified several candidates with nearly identical antigen binding, within 2-fold, of the chimeric Fab. Additional mutagenesis directed at sites suggested in the literature as potentially important for antigen binding in a similar anti-Lewis Y antibody yielded no further improvements.

Modifying the specificity and activity of the Enterobacter cloacae P99 beta-lactamase by mutagenesis within an M13 phage vector.

A library of Enterobacter cloacae P99 beta-lactamase mutants was produced to investigate the importance of residues 286-290 for substrate binding and catalysis and to characterize mutants with altered specificities and activities for various 3'-substituted cephalosporins. This region of the enzyme is a component of the active site that has not been implicated as participating in the catalytic mechanism but, based on molecular modeling, should contact the 3' substituents of cephalosporins. Random mutagenesis was carried out within an M13 phage vector by hybridization mutagenesis, and the phage library could be highly enriched for active beta-lactamase genes by incubation of infected bacteria with beta-lactam antibiotics. The mutants were characterized by Michaelis-Menten kinetic analyses with several cephalosporin substrates and spanned a 25-fold range of k(cat), 24-fold range of K(m), and 6-fold range of k(cat)/K(m) values. All five amino acid positions were found to be permissive to substitution, but the active mutant proteins carried substitutions that likely maintained the structure of the region. Serine 287 was the least permissive to change, requiring small, uncharged residues for retention of catalytic activity. The variation of Michaelis-Menten kinetic parameters observed in these enzymes was shown to be significant in the context of in vitro cytotoxicity assays with the cephalosporin-doxorubicin prodrug C-Dox and is suitable for experiments to probe the relationship between enzyme kinetics and efficacy in enzyme-prodrug approaches to targeted therapy.

FliH and fliI of Borrelia burgdorferi are similar to flagellar and virulence factor export proteins of other bacteria.

Two motility genes (fliH and fliI) of the Lyme disease spirochete Borrelia burgdorferi were cloned, physically mapped and sequenced, FliH and FliI showed extensive homology to the proteins involved in the export of flagellar components and to virulence factors found in both animal and plant bacterial pathogens. The results suggest that the flagellar apparatus and associated protein export pathway are well conserved in evolution.

Rapid and reliable cloning of antibody variable regions and generation of recombinant single chain antibody fragments.

Single chain antibody variable region fragments (sFv), by virtue of their size and method of construction are potentially useful as therapeutic reagents and as tools for exploring cell surface receptor function. sFv offer several advantages over the intact immunoglobulin molecule. For instance, they are expressed from a single transcript and can be molecularly linked to other proteins to generate bispecific sFv molecules or single-chain immunotoxins. The relatively small size of sFv is an advantage in allowing for easier penetrance into tissue spaces, and their clearance rate is exceedingly rapid. sFv are useful for gene therapy since they can be directed to a specific cellular localization and can be fused to retroviral env genes to control viral host range. To prepare sFv to murine and human leukocyte CD antigens, we devised a method for rapid cloning and expression that can yield functional protein within 2-3 weeks of RNA isolation from hybridoma cells. The variable regions were cloned by poly-G tailing the first strand cDNA followed by anchor PCR with a forward poly-C anchor primer and a reverse primer specific for constant region sequence. Both primers contain flanking restriction sites for insertion into PUC19. Sets of PCR primers for isolation of murine, hamster and rat VL and VH genes were generated. Following determination of consensus sequences for a specific VL and VH pair, the VL and VH genes were linked by DNA encoding an intervening peptide linker [usually (Gly4Ser)3] and the VL-link-VH gene cassettes were transferred into the pCDM8 mammalian expression vector. The constructs were transfected into COS cells and sFvs were recovered from spent culture supernatant. We have used this method to generate functional sFv to human CD2, CD3, CD4, CD8, CD28, CD40, CD45 and to murine CD3 and gp39, from hybridomas producing murine, rat, or hamster antibodies. Initially, the sFvs were expressed as fusion proteins with the hinge-CH2-CH3 domains of human IgG1 to facilitate rapid characterization and purification using goat anti-human IgG reagents or protein A. We also found that active sFv could be expressed with a small peptide > or = tag > or = or in a tail-less form. Expression of CD3 (G19-4) sFv tail-less or Ig tailed forms demonstrated increased cellular signalling activity and suggested that sFv have potential for activating receptors.

Affinity maturation of the BR96 anti-carcinoma antibody by codon-based mutagenesis.

We have increased up to 65-fold the avidity of BR96, a mAb recognizing Lewis Y (Le(y))-related Ags expressed on the surface of many human carcinomas. Libraries of mutations in the complementarity-determining regions (CDRs) of BR96 were constructed in an M13 phage Fab expression vector by codon-based mutagenesis, a method that efficiently introduces large numbers and potentially all combinations of amino acid substitutions. Two mutants that improved the affinity of BR96 to tumor Ag were identified by screening the libraries on carcinoma cell lines. One mutant, M1, at position 97 (Asp to Ala) in CDR3 of the heavy chain, resulted in an 8- to 10-fold improvement in Ag binding, as assessed by ELISA. A second mutant, M2, at position 53 (Gly to Asp) in CDR2 of VH increased binding three- to fivefold. When these mutations were combined, the resulting Fab M3 was improved approximately 30-fold. An additional library was constructed in CDR1 of M1. M4, a mutation with three amino acid substitutions in CDR1, was isolated by screening the library with an enzyme conjugate of synthetic Le(y) tetrasaccharide (sLe(y)). This mutant improved BR96 Fab affinity to sLe(y) an estimated 15- to 20-fold by ELISA, and 14-fold as measured by surface plasmon resonance. The M4 IgG had 65-fold improved avidity to sLe(y) relative to the BR96 IgG. The mutants will be useful for comparison of the efficacy of Abs with different affinities for delivery of cytotoxic agents to tumor cells.

The x-ray structure of an anti-tumour antibody in complex with antigen.

The crystal structures of the murine BR96 Fab and its human chimera have been determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey) at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a large pocket which is formed by residues of all CDR loops except L2. The binding of the carbohydrate is mediated predominantly by aromatic residues in BR96. Analysis of the structure suggests that BR96 is capable of recognizing a structure larger than the Le(y) tetrasaccharide, providing a possible explanation for its high tumour selectivity. The structure provides a rationale for mutagenesis experiments that have resulted in BR96 CDR loop mutants with increased affinity for nLey and/or tumour cells.

Identification of residues in the monoclonal antitumor antibody L6 important for binding to its tumor antigen.

L6 is a monoclonal antitumor antibody which recognizes an epitope located in a 42-residue extracellular domain of a tumor-associated approximately 22 kDa glycoprotein antigen. The L6 mAb localizes to solid tumors in vivo and triggers complement activation and antibody-dependent cellular cytotoxicity. It has been the subject of phase I clinical trials. Previously, we had reported the derivation and analysis of a three-dimensional model of the L6 Fv. The model suggests that L6 displays a generally aromatic CDR surface. We aim at improving the affinity for tumor antigen of L6 by in vitro mutagenesis. As the first step toward this end, we have attempted to identify residues critical for the binding of L6 to tumor antigen. On the basis of the model, seven residues were selected which we thought may be critical for L6 antigen binding. Criteria for the selection of these residues were their accessibility and central position on the CDR surface and the residue character. Large polar or charged residues such as arginine, asparagine, and tyrosine were preferred. Nine site-specific single and double mutants were generated using oligonucleotide-directed mutagenesis in an M13 expression vector encoding the L6 Fab. The binding of these mutant Fabs to the L6 tumor antigen and a set of three anti-idiotypic antibodies was quantified in an ELISA. In eight out of nine mutants, binding to L6 tumor antigen was either abolished or substantially reduced. In contrast, the binding of the mutants to the anti-idiotypic antibodies was largely unaffected, suggesting that no significant structural perturbations were introduced as a consequence of these mutations.

Cloning and analysis of the leuB gene of Leptospira interrogans serovar pomona.

The leuB gene of Leptospira interrogans serovar pomona strain kenniwicki has been cloned on a 9.5 kb plasmid, pWVL1, by complementation of Escherichia coli leuB mutants. Subcloning and Tn5 mutagenesis showed that the region required for complementation was approximately 1.2 kb in length. Enzyme assays showed that the product of the cloned gene was a beta-isopropylmalate dehydrogenase. Defects in the leuA, leuC and leuD genes of E. coli were not complemented by pWVL1. The nucleotide sequence of the leuB-complementing region and surrounding DNA has been determined. Three open reading frames were found which encode proteins of 40.9, 38.8 and 15 kDa. Analysis of subclones containing nucleotide deletions of varying sizes showed that only the 38.8 kDa protein was necessary to obtain complementation of E. coli leuB mutations. The PIR data base was searched and the enzyme 3-isopropylmalate dehydrogenase from six different micro-organisms was found to share significant amino acid sequence similarity (43-57%) with the 38.8 kDa L. interrogans leuB gene product. The organization of the leucine biosynthetic genes in L. interrogans differs from that found in E. coli, Salmonella typhimurium and Bacillus subtilis.

Phase I trial of chimeric (human-mouse) monoclonal antibody L6 in patients with non-small-cell lung, colon, and breast cancer.

We report a single institution phase I trial of chimeric (mouse-human) monoclonal antibody (chL6) directed against a tumor-associated cell surface antigen expressed in non-small cell lung, colon, and breast cancer. The results of the study were contrasted with a previous trial of murine L6. ChL6 was administered intravenously to 18 patients with advanced cancer as a single, 4-16 infusion in doses ranging from 350 mg/m2 to 700 mg/m2. One patient received four weekly doses of 350 mg/m2. Patients were followed for side effects, localization of antibody to tumor cells, pharmacokinetics and the development of antibodies against chL6. Side effects associated with treatment were chills, fever, and nausea, which lasted 24-48 hours. Platelet count and absolute leukocyte count fell immediately after treatment, but returned to pretreatment levels by day 7. Localization of chL6 to tumor cells in vivo was seen at 350 mg/m2 and "saturation" at 700 mg/m2 and 350 mg/m2 per week x 4. The pharmacokinetics of this antibody appeared similar to its murine analogue. Human antibodies against chL6 were detected in only 4 of 18 patients. These antibodies were directed against murine variable regent and their titers were lower than those occurring in most patients who received murine L6 in an earlier trial. No tumor reductions were seen. Chimeric L6 appears to be a suitable antibody for delivering anti-tumor agents because of its low immunogenicity and favorable in vivo tumor binding characteristics.

Antibody engineering by codon-based mutagenesis in a filamentous phage vector system.

A novel codon-based mutagenesis procedure is described that allows rapid and efficient modification of antibody amino acid sequences expressed as F(ab) fragments in M13. The procedure succeeded in generating a library of mutations in the complementarity-determining regions of chimeric L6, an antibody against a tumor-associated Ag. A set of anti-Id antibodies (anti-Id 1, 3, and 7) that bind near the L6 Ag-binding site served as model Ag. The goal was to select mutant antibody sequences that altered the L6 reactivity with the anti-Id in subtle ways, i.e., to eliminate the binding to one anti-Id while preserving other reactivities or to identify mutants with increased binding. A high frequency of variant M13 phage clones exhibiting altered specificity for the anti-Id were identified. Codon-based mutagenesis in conjunction with the M13 antibody expression and screening system should provide an efficient and general approach for redirecting the specificity and potentially improving the affinity of antibodies in vitro.

Application of a filamentous phage pVIII fusion protein system suitable for efficient production, screening, and mutagenesis of F(ab) antibody fragments.

We describe the application of a novel filamentous phage vector system suitable for efficient screening and production of F(ab) antibody fragments. The vector system can concurrently produce free F(ab) fragments and F(ab) displayed on the surface of M13 bacteriophage via a VHCH1-pVIII fusion protein. When expressed in a supO (nonsuppressor) strain of Escherichia coli free F(ab) can be produced. Antibody F(ab) fragments are secreted into culture medium at concentrations up to 0.3 mg/liter and conveniently subjected to detailed analysis with little or no purification. Higher concentrations of F(ab) (approximately 10 mg/liter) were found to accumulate in the periplasmic space. In this report the vector system is shown to produce correctly folded and assembled F(ab) fragments of chimeric L6, a mAb against a tumor-associated Ag expressed by many human carcinomas.

Molecular genetic analysis of a class B periplasmic-flagellum gene of Treponema phagedenis.

Treponema phagedenis is a host-associated spirochete with multiple polypeptides making up its periplasmic flagella (PFs). Each PF has a 39-kDa polypeptide making up the sheath (class A PF polypeptide) and two to four antigenically similar 33- to 34-kDa polypeptide species making up the core (class B PF polypeptides). A genetic analysis of the PF-deficient mutants T-40 and T-55 has shown that the PFs are involved in motility. To better understand the synthesis and assembly of these complex organelles and to compare the PF genes with those of other spirochetes, we cloned and characterized the T. phagedenis flaB2 gene, which encodes one class B polypeptide. The flaB2 gene consists of an open reading frame of 858 nucleotides capable of encoding a protein of 31.5 kDa. The predicted amino acid sequence of the FlaB2 polypeptide was 92% identical to that of T. pallidum FlaB2, with a 76% identity at the nucleotide level. These results confirm previous immunological and N-terminal-sequence analyses which suggested that the PF genes are well conserved in the spirochetes. Primer extension analysis of T. phagedenis flaB2 indicated that the start site of transcription was 127 nucleotides upstream from the ATG initiation codon. Preceding the start site is a DNA sequence similar to the sigma 28 consensus promoter sequence commonly found associated with motility genes. Northern (RNA) blots probed with a segment of flaB2 DNA revealed a 1,000-nucleotide monocistronic transcript in the wild type and in PF-deficient mutants T-40 and T-55. DNA sequencing of most of the flaB2 gene of the mutants revealed no differences from the wild-type gene. Because the mutants fail to synthesize detectable class B PF polypeptides yet synthesize extensive amounts of flaB2 mRNA, PF synthesis in T. phagedenis is likely to involve regulation at the translational level.

Chimeric L6 anti-tumor antibody. Genomic construction, expression, and characterization of the antigen binding site.

We report the cloning of the genomic variable region genes of the human carcinoma reactive murine monoclonal antibody L6 and their genetic linkage to human constant region exons to encode a human IgG1/kappa chimeric antibody. The chimeric protein was produced at levels greater than 20 micrograms/ml (enabling the initiation of clinical trials) and was found to have binding properties identical with that of the murine parent. The nucleic acid sequence of the variable regions was determined and found to be different than that previously reported (1). The deduced amino acid sequence was then used to generate a structural homology based three-dimensional model of the antibody binding site, which was found to share features with antibodies known to interact with a protein surface, but distinct from those that bind to carbohydrate epitopes. Biochemical analysis of binding between antibody and the in vitro-translated product of a cDNA clone that confers L6 immunoreactivity demonstrates that the antibody recognizes a protein epitope encoded by this transcript which requires the presence of membranes, but is unaffected by the removal of carbohydrate side chains.

Genetic approaches to cell biology and metabolism of spirochetes.

Genetic analysis and methodology have only comparatively recently been applied to the study of spirochetes. Although genetic transfer procedures for spirochetes are not widely available, there are several examples of progress in genetic analysis of spirochetes by other approaches. Some examples of these approaches are the following. 1) Genes for synthetic pathways in Treponema and Leptospira have been cloned by complementation of Escherichia coli serving as plasmid hosts. 2) The OspA protein of Borrelia burgdorferi has been overexpressed in E. coli without the signal peptide; the recombinant product has been suitable for circular dichroism as well as other biochemical analyses. 3) The heat shock proteins of B. burgdorferi are homologous to heat shock proteins of E. coli. 4) Enzyme activity profiles of B. burgdorferi and other spirochetes show strain heterogeneity and also indicate which biosynthetic and enzymatic activities are conserved within different spirochetes. 5) The gene organization of rRNA genes have revealed differences between spirochetes and other types of bacteria.

Treponema phagedenis encodes and expresses homologs of the Treponema pallidum TmpA and TmpB proteins.

We cloned and sequenced the genes from Treponema phagedenis Kazan 5 encoding proteins homologous to the TmpA and TmpB proteins of Treponema pallidum subsp. pallidum Nichols (hereafter referred to as T. pallidum). Although previous reports suggested that the TmpA and TmpB proteins were specific for T. pallidum, we found that homologs for both were expressed in T. phagedenis Kazan 5 and Reiter. The TmpA protein from T. phagedenis contained the consensus sequence that bacterial lipoproteins require for posttranslational modification and subsequent proteolytic cleavage by signal peptidase II and showed 42% amino acid sequence identity with the TmpA protein from T. pallidum. The TmpB proteins of T. phagedenis and T. pallidum had similar amino acid sequences at their amino- and carboxy-terminal ends. The central portions of both of these proteins contained four repeats of the amino acid sequence EAARKAAE. The TmpB protein from T. phagedenis had an additional amino acid sequence repeat (consensus sequence KAAKE/D) that was not found in the TmpB protein from T. pallidum; this repeat was most remarkable, as it occurred 17 times in succession. These repeated amino acid sequences probably created an extensive alpha-helix region within the TmpB proteins. As with T. pallidum, the stop codon of the T. phagedenis tmpA gene overlapped the start codon of its tmpB gene. Northern blot analysis showed that the T. phagedenis tmpA and tmpB genes were probably transcribed into a single 2.5-kb mRNA molecule. Western blot (immunoblot) analysis demonstrated that both proteins were expressed by T. phagedenis. The high degree of amino acid sequence conservation seen with the TmpA and TmpB proteins from two different Treponema species suggests that they may play crucial roles in the biology of these organisms.

Epitope mapping and use of anti-idiotypic antibodies to the L6 monoclonal anticarcinoma antibody.

Mouse monoclonal anti-idiotypic antibodies (anti-ids) were raised against L6, a murine IgG2a monoclonal antibody specific for a cell surface antigen expressed by many human carcinomas. Ten distinct anti-ids were generated. Eight anti-ids were shown to inhibit the binding of L6 to its target antigen and were characterized in detail. The heavy and light chain variable region gene segments of the monoclonal antibody L6 linked to human constant regions (chimeric L6) were expressed separately or together, to map the epitopes recognized by the anti-ids. Individual anti-ids were shown to recognize heavy chain, light chain, or combinatorial variable region determinants. Defining these specificities enabled us to select particular anti-ids for assays to monitor the pharmacokinetics of either murine or chimeric L6 antibodies in the circulation of human patients. A quantitative enzyme-linked immunosorbent assay developed with two anti-ids accurately detects less than 5 ng/ml. Anti-ids specific for light chain variable region-encoded determinants were capable of recognizing L6 antigen-binding fragments bound to the surface of human carcinoma cells. These anti-ids can be used to study the binding of chimeric L6 antibody at the surface of tumor cells in histological sections of tumor biopsies.

Identification and nucleotide sequence of the Leptospira biflexa serovar patoc trpE and trpG genes.

Leptospira biflexa is a representative of an evolutionarily distinct group of eubacteria. In order to better understand the genetic organization and gene regulatory mechanisms of this species, we have chosen to study the genes required for tryptophan biosynthesis in this bacterium. The nucleotide sequence of the region of the L. biflexa serovar patoc chromosome encoding the trpE and trpG genes has been determined. Four open reading frames (ORFs) were identified in this region, but only three ORFs were translated into proteins when the cloned genes were introduced into Escherichia coli. Analysis of the predicted amino acid sequences of the proteins encoded by the ORFs allowed us to identify the trpE and trpG genes of L. biflexa. Enzyme assays confirmed the identity of these two ORFs. Anthranilate synthase from L. biflexa was found to be subject to feedback inhibition by tryptophan. Codon usage analysis showed that there was a bias in L. biflexa towards the use of codons rich in A and T, as would be expected from its G + C content of 37%. Comparison of the amino acid sequences of the trpE gene product and the trpG gene product with corresponding gene products from other bacteria showed regions of highly conserved sequence.