Helicobacter pylori physiology predicted from genomic comparison of two strains.

Helicobacter pylori is a gram-negative bacteria which colonizes the gastric mucosa of humans and is implicated in a wide range of gastroduodenal diseases. This paper reviews the physiology of this bacterium as predicted from the sequenced genomes of two unrelated strains and reconciles these predictions with the literature. In general, the predicted capabilities are in good agreement with reported experimental observations. H. pylori is limited in carbohydrate utilization and will use amino acids, for which it has transporter systems, as sources of carbon. Energy can be generated by fermentation, and the bacterium possesses components necessary for both aerobic and anaerobic respiration. Sulfur metabolism is limited, whereas nitrogen metabolism is extensive. There is active uptake of DNA via transformation and ample restriction-modification activities. The cell contains numerous outer membrane proteins, some of which are porins or involved in iron uptake. Some of these outer membrane proteins and the lipopolysaccharide may be regulated by a slipped-strand repair mechanism which probably results in phase variation and plays a role in colonization. In contrast to a commonly held belief that H. pylori is a very diverse species, few differences were predicted in the physiology of these two unrelated strains, indicating that host and environmental factors probably play a significant role in the outcome of H. pylori-related disease.

Genetics of multidrug resistance: relationship of a cloned gene to the complete multidrug resistant phenotype.

Resistance to multiple chemotherapeutic agents remains the major cause of failure in cancer chemotherapy. Multidrug resistant cell lines developed in vitro have provided a useful model for analyzing this phenomenon. We describe a complementary DNA, lambda DR11, which is present in normal cells and overexpressed in multidrug resistant cell lines. We have placed this complementary DNA in an expression vector which uses the beta-actin promoter to drive transcription and introduced this vector via transfection into drug sensitive cells. Cells expressing increased levels of lambda DR11 are resistant to the same broad spectrum of chemotherapeutic agents which characterize the multidrug resistant phenotype. The expression of this complementary DNA in transfected clones is dependent upon the number of copies of lambda DR11 integrated in the genome as well as the amount of selective pressure placed on the clone during selection of the clone. Furthermore, the number of copies of lambda DR11 in the genome and the expression of lambda DR11 can be modulated by releasing an individual clone from selective pressure or by increasing the selective pressure on the clone. The endogenous sequences encoding the multidrug resistance gene are not amplified in transfected drug resistant clones. Finally, the drug resistant phenotype is reversed in the transfected clones by verapamil just as drug resistance is reversed in multidrug resistant cell lines.

Identification and cloning of EI24, a gene induced by p53 in etoposide-treated cells.

To search for candidate genes involved in p53-mediated apoptosis, the differential display technique was used to identify RNA species whose expression was altered in murine NIH3T3 cells treated with the cytotoxic drug etoposide. We report here the isolation and characterization of EI24, a novel gene whose 2.4 kb mRNA is induced following etoposide treatment. Induction of EI24 mRNA by etoposide required expression of wild-type p53 in murine embryonic fibroblasts which had been transformed with the oncogenes E1A and T24 H-ras; and overexpression of functional p53 in these cells was sufficient to induce expression of the EI24 mRNA. The EI24 mRNA was also induced in a p53-dependent manner by ionizing irradiation of primary murine thymocytes. Isolation of a full-length EI24 cDNA revealed that its protein product bears homology to CELF37C12.2, a Caenorhabditis elegans protein of unknown function.

Comparison of surface accessible residues in human and murine immunoglobulin Fv domains. Implication for humanization of murine antibodies.

Statistical analysis of a database of unique human and murine immunoglobulin heavy chain and light chain variable regions reveals that the precise patterns of exposed residues are different in human and murine antibodies, while most individual surface positions have strong preferences for a small number of residue types. Consideration of these surface patterns alone generates almost identical family groupings for light and heavy chain variable domain sequences to those produced by methods such as those of Kabat et al., where N-terminal framework sequences only are compared, or Tomlinson et al., in which entire variable region nucleotide sequences are used. This unexpected result suggests that the surfaces of V-regions are at least as well conserved as the core framework sequences. Furthermore, using these patterns of human and murine surface residues a novel method for the "humanization" of murine antibodies has been developed and tested.

Human and murine class I MHC antigens share conserved serine 335, the site of HLA phosphorylation in vivo.

The site of phosphorylation of the HLA-B7 antigen in vivo is serine 335, which is located in the intracellular region. Pseudomonas fragi protease was used in limited proteolysis experiments of HLA antigens to identify the position of the phosphoserine residue. The intracellular region is composed of 30 amino acids at the carboxyl terminus of the heavy chain; up to nine serine residues are located in this region. Four of the serines are found at the distal end, and are encoded by exon 7 in both human and murine class I MHC antigens. Alignment of the protein and DNA sequences of the intracellular regions of human and murine class I antigens demonstrates conservation of the serine positions located within this exon. Realignment of exon 7, by introducing a gap in the murine sequences, increases homology across species, and reveals two conserved serines at 332 and 335 within the conserved sequence Ser-Asp/Glu-X-Ser(P)-Leu. The preservation of this sequence and the site of phosphorylation suggests that this modification of the intracellular region of histocompatibility antigens is functionally significant.

HLA-A2 antigen phosphorylation in vitro by cyclic AMP-dependent protein kinase. Sites of phosphorylation and segmentation in class i major histocompatibility complex gene structure.

The heavy chain of the HLA-A2 antigen is phosphorylated by cyclic AMP-dependent protein kinase at two serine residues of the intracellular region. Limited proteolysis was performed on purified [32P]HLA-A2 antigens in order to define the sites of phosphorylation. Both of the phosphorylated serine residues are located in the carboxyl terminus of the heavy chain; one is encoded by exon 5, while the other is encoded by exon 6. The phosphoserine encoded by exon 5 is part of the conserved sequence Arg-Arg-Lys-Ser-Ser. This protein sequence contains the proper arrangement of amino acids for recognition and phosphorylation by the catalytic subunit of cyclic AMP-dependent protein kinase. In the murine class I antigens (H-2), exon 5 encodes a similar sequence of basic residues followed by one intervening residue and a threonine rather than a serine residue in the last amino acid position. A composite figure is presented that compares the carboxyl-terminal sequences of human and murine class I antigens and illustrates the known sites of phosphorylation recognized by various kinases. Each site of phosphorylation in the carboxyl terminus is contained within a conserved protein sequence encoded by one of the three exons. A separation and preservation of unique sites of phosphorylation could explain why there is segmentation in the genomic arrangement of class I molecules.

Phosphorylation in vivo and in vitro of human histocompatibility antigens (HLA-A and HLA-B) in the carboxy-terminal intracellular domain.

HLA-A and -B antigens are phosphorylated in transformed lymphoblastoid cells and peripheral blood lymphocytes, both incubated with 32Pi. The phosphate group is attached to HLA-A and -B heavy chain (p44) as identified by immunoprecipitation with anti-beta2-microglobulin IgG, sodium dodecyl sulfate/polyacrylamide gel electrophoresis, isoelectric focusing, and susceptibility to limited proteolysis by papain and trypsin. The site(s) of phosphorylation is identified as a serine residue(s) located in the hydrophilic carboxy terminus of the p44 chain. HLA antigens are also phosphorylated in isolated membranes from transformed lymphoblastoid cells that are incubated with [gamma32P]ATP. The phosphorylation of the carboxy terminus of HLA-A and -B antigens in vivo is good evidence that this portion of the molecule is intracellular. Furthermore, this modification suggests a general way in which interactions between membrane proteins and cytoskeletal elements may be regulated.

HLA-A2 and HLA-B7 antigens are phosphorylated in vitro by rous sarcoma virus kinase (pp60v-src) at a tyrosine residue encoded in a highly conserved exon of the intracellular domain.

HLA-A2 and -B7 antigens are phosphorylated by Rous sarcoma kinase (pp60v-src) in vitro. The phosphate group is attached to the heavy chains as determined by NaDodSO4/polyacrylamide gel electrophoresis. The site of phosphorylation was localized to the COOH-terminal intracellular domain by its susceptibility to limited trypsin proteolysis. Furthermore, the 32P-labeled amino acid is a single tyrosine residue located in the COOH terminus of the heavy chain. The protein sequences of known class I human and murine intracellular domains contain a highly conserved sequence -K-G-G-X-Y- located NH2-terminally to the single tyrosine residue of this domain. The DNA sequences that encode class I antigen intracellular domains were compared by computer with a homology matrix program. Exon 6 which encodes the conserved tyrosine-containing protein sequence in both human and mouse is 75% homologous across species and 90-100% homologous within species. The significance of the high degree of conservation within exon 6 is discussed.

Development of retrovirus vectors useful for expressing genes in cultured murine embryonal cells and hematopoietic cells in vivo.

A series of retrovirus vectors were constructed in which cellular promoter elements derived from the chicken beta-actin and human histone H4 genes were introduced within the proviral transcriptional unit of Moloney murine leukemia virus in order to promote expression of inserted sequences. Each of these vectors gave rise to high titer of virus capable of transferring the expected proviral structure to cells. Inclusion of normal 5' splice sequences or a portion of viral gag sequences in these constructions resulted in significant increases in virus titer. Each construction was transcriptionally active in NIH 3T3 cells and in undifferentiated F9 cells. One of the vectors, HSG-neo, which contained the human histone H4 promoter, was shown to be transcriptionally active in hematopoietic cells derived from long-term reconstituted bone marrow transplant recipients engrafted with transduced stem cells. These vectors should be of general use for obtaining efficient gene expression in embryonal and hematopoietic cells.

Retroviral transfer of a murine cDNA for multidrug resistance confers pleiotropic drug resistance to cells without prior drug selection.

We have constructed a retrovirus expression vector that carries the murine mdr cDNA transcribed under the control of the human H4 histone promoter to examine the feasibility of efficiently transferring a multidrug resistance phenotype to cells without requiring drug selection. This approach will facilitate the transfer of mdr cDNA to hematopoietic progenitor cells for the study of multidrug resistance in vivo. The retrovirus vector pHmdr has been used for transmission and expression of the mdr cDNA in initially drug-sensitive NIH 3T3 fibroblasts. Selection of pHmdr infectants in the cytotoxic agents colchicine or doxorubicin gave rise to highly multidrug-resistant colonies containing a single gene copy of the vector. Moreover, in the analysis of 12 cloned unselected NIH 3T3 cell infectants, a multidrug resistance phenotype was conferred by as few as two copies of the pHmdr vector. Overexpression of the mdr cDNA in drug-selected and unselected pHmdr infectants was directly related to cell survival in three cytotoxic agents tested. These results hold significant implications for the study of multidrug resistance in vivo.

Reconstitution of purified detergent-soluble HLA-A and HLA-B antigens into phospholipid vesicles.

Purified detergent-soluble human histocmpatibility antigens (HLA-A and HLA-B) were reconstituted into phospholipid vesicles by mixing the protein and lipid together in the presence of either octylglucoside (octyl-beta-D-glucopyranoside) or deoxycholate and removing the detergent by dialysis. The resulting preparation consisted of lipid vesicles containing all or most of the added protein. The protein in the vesicles was antigenically active, as demonstrated by specific binding to anti-beta2-microglobulin IgG-Sepharose beads and by specific inhibition of alloantibody and complement-mediated cytotoxicity. Protein incorporated into vesicles at a protein/phospholipid ratio of 1:10 showed an asymmetric distribution of the HLA-A and HLA-B molecules, with virtually all of the antigens oriented facing the external medium. Cleavage experiments with proteases showed that the molecule was attached to the vesicle membrane via the COOH terminus, consistent with its proposed structure in intact cellular plasma membranes. Electron micrographs of the vesicles showed 50-60 A knobs on the outer surface similar to structures observed for other membrane proteins. HLA-A and HLA-B could also be incoporated into vesicles together with Semliki Forest virus membrane proteins. The resulting preparations should be useful in defining the molecular interactions involving HLA-A and HLA-B antigens in the immune response.

Phage display of ricin B chain and its single binding domains: system for screening galactose-binding mutants.

We demonstrate that the B chain of ricin toxin preserves its lectin activity when expressed as a fusion protein on the surface of fd phage. Moreover, B chain, which folds into two topologically similar globular domains, can be dissected into amino-terminal and carboxyl-terminal domains to form single binding domains (SBDs) of B chain, each of which displays specificity for complex galactosides. The specific binding exhibited by the fusion protein of these SBDs was eliminated when amino acid substitutions Gly-46 in SBD1 or Gly-255 in SBD2 for native asparagine were introduced to alter key residues implicated in hydrogen bonding with substrate. These data demonstrate that it is possible to use a prokaryotic expression system to stably express and screen ricin B chain and its SBDs for sugar-binding mutants. Expression of ricin B chain on the surface of fd phage provides a method that can be used to efficiently select mutants with altered binding activities from a randomly generated library.

Expression and secretion of a recombinant ricin immunotoxin from murine myeloma cells.

Expression plasmids carrying a humanized N901 immunoglobulin heavy chain gene (hN901HC) fused to a gene encoding the native B chain of ricin toxin (RTB), hN901HC-RTB, or a sugar binding mutant of RTB, hN901HC-RTB delta gly, were constructed. In each case, the fused gene constructions were co-expressed in murine myeloma cells (Sp2/0) with the gene for humanized N901 immunoglobulin light chain to produce the secreted recombinant products hN901-RTB and hN901-RTB delta gly, respectively. When purified by affinity chromatography, both the hN901-RTB and hN901-RTB delta gly products were found to have an apparent molecular mass of M(r) = 210,000 and to be composed of two hN901 antibody heavy chains each fused to a full-length copy of RTB and two hN901 antibody light chains. In each of the recombinant fusions the hN901 antibody moiety retained the full binding affinity and specificity for its cognate antigen, CD56. Moreover, when mixtures of hN901-RTB and native ricin A chain were incubated in the presence of the antigen-positive target cell line SW-2, antigen-specific potentiation of ricin A chain cytotoxicity was observed. It has been demonstrated previously that lectin activity of the B chain is essential for A chain cytotoxicity, and we conclude that the fused wild-type B chain was properly folded and maintained lectin activity. These data demonstrate that feasibility of using recombinant ricin B chain in an immunotoxin and of using mammalian cell culture for its expression. The use of recombinant hN901-RTB fusion protein to evaluate the contribution of the lectin activity of ricin B chain in the penetration of cell membranes by ricin A chain is proposed.

Mutational and structural analysis of the lectin activity in binding domain 2 of ricin B chain.

The study of the lectin binding sites of ricin B chain and of other homologous members of the small gene family that make up ricin-like molecules has revealed a number of key contact residues involved in sugar binding. In particular, on the basis of data generated by the X-ray crystallographic structure of ricin, comparisons of sequence homologies to other ricin-like molecules and substrate binding studies with these molecules, it has been proposed that His248 of Ricinus communis agglutinin (RCA) B chain may interfere with galactose binding in the second binding domain of that lectin. To test that hypothesis, single binding domain 2 (SBD2) of ricin B chain was expressed as a gene 3 fusion protein on the surface of fd phage to measure directly the effect of mutational changes on this binding site. Replacement of tyrosine with histidine at amino acid position 248 of SBD2 of ricin B chain was shown to reduce lectin activity. The sequences of RCA and ricin B chains were aligned and compared with the tertiary structure of ricin B chain to select various mutations that were introduced as controls in the study. One of these controls, Leu247 to Val247, displayed increased affinity for galactosides. The role of sequence changes is discussed in relation to the structural and functional divergence in these molecules.

Induction of apoptosis by the Bcl-2 homologue Bak.

Cells are eliminated in a variety of physiological settings by apoptosis, a genetically encoded process of cellular suicide. Apoptosis comprises an intrinsic cellular defence against tumorigenesis, which, when suppressed, may contribute to the development of malignancies. The bcl-2 oncogene, which is activated in follicular lymphomas, functions as a potent suppressor of apoptosis under diverse conditions. Here we describe the complementary DNA cloning and functional analysis of a new Bcl-2 homologue, Bak, which promotes cell death and counteracts the protection from apoptosis provided by Bcl-2. Moreover, enforced expression of Bak induces rapid and extensive apoptosis of serum-deprived fibroblasts. This raises the possibility that Bak is directly involved in activating the cell death machinery.

A comparison of two murine monoclonal antibodies humanized by CDR-grafting and variable domain resurfacing.

The variable domain resurfacing and CDR-grafting approaches to antibody humanization were compared directly on the two murine monoclonal antibodies N901 (anti-CD56) and anti-B4 (anti-CD19). Resurfacing replaces the set of surface residues of a rodent variable region with a human set of surface residues. The method of CDR-grafting conceptually consists of transferring the CDRs from a rodent antibody onto the Fv framework of a human antibody. Computer-aided molecular modeling was used to design the initial CDR-grafted and resurfaced versions of these two antibodies. The initial versions of resurfaced N901 and resurfaced anti-B4 maintained the full binding affinity of the original murine parent antibodies and further refinements to these versions described herein generated five new resurfaced antibodies that contain fewer murine residues at surface positions, four of which also have the full parental binding affinity. A mutational study of three surface positions within 5 A of the CDRs of resurfaced anti-B4 revealed a remarkable ability of the resurfaced antibodies to maintain binding affinity despite dramatic changes of charges near their antigen recognition surfaces, suggesting that the resurfacing approach can be used with a high degree of confidence to design humanized antibodies that maintain the full parental binding affinity. By comparison CDR-grafted anti-B4 antibodies with parental affinity were produced only after seventeen versions were attempted using two different strategies for selecting the human acceptor frameworks. For both the CDR-grafted anti-B4 and N901 antibodies, full restoration of antigen binding affinity was achieved when the most identical human acceptor frameworks were selected. The CDR-grafted anti-B4 antibodies that maintained high affinity binding for CD19 had more murine residues at surface positions than any of the three versions of the resurfaced anti-B4 antibody. This observation suggests that the resurfacing approach can be used to produce humanized antibodies with reduced antigenic potential relative to their corresponding CDR-grafted versions.

Anti-B4-blocked ricin synergizes with doxorubicin and etoposide on multidrug-resistant and drug-sensitive tumors.

Anti-B4-blocked ricin (anti-B4-bR) is an immunotoxin directed against CD19-positive cells that is currently being tested in several B-cell leukemia/lymphoma clinical trials. To explore the possibility of using anti-B4-bR in combination with chemotherapy protocols, we investigated the in vitro and in vivo cytotoxic effects of combining it with doxorubicin or etoposide using the lymphoma cell line Namalwa and a P-glycoprotein-expressing cell line, Namalwa/mdr-1, obtained by retroviral infection of Namalwa cells with the mdr-1 gene. Namalwa/mdr-1 cells were slightly more sensitive to anti-B4-bR than Namalwa cells; IC37 values were approximately 4 pmol/L and 8 pmol/L, respectively. When anti-B4-bR was combined simultaneously with doxorubicin or etoposide, additive to supra-additive killing of Namalwa and Namalwa/mdr-1 cells was observed. In xenografts of Namalwa/mdr-1 cells in severe combined immunodeficiency (SCID) mice, doxorubicin and etoposide at their maximum tolerated doses (3 mg/kg x 3 or 15 mg/kg x 3) showed no therapeutic effect. However, treatment with 5 daily bolus injections of anti-B4-bR (50 micrograms/kg) followed by treatment with doxorubicin or etoposide significantly increased the life span of the mice by 129% and 115%, respectively. After treatment with anti-B4-bR, the Namalwa/mdr-1 population expressed lower levels of P-glycoprotein, and this decrease may account for the synergistic action of the drug combinations. These results suggest that anti-B4-bR could be used to good effect in combination with current treatment regimens and further hint at a promising role for this immunotoxin in treatment of disease at the minimal residual disease stage, where cells may be resistant to chemotherapy.

Humanization of murine monoclonal antibodies through variable domain resurfacing.

Two murine monoclonal antibodies, N901 (anti-CD56) and anti-B4 (anti-CD19), were humanized by a process we call "resurfacing." A systematic analysis of known antibody structures has been used to determine the relative solvent accessibility distributions of amino acid residues in murine and human antibody variable (Fv) regions and has shown that the sequence alignment positions of surface amino acids for human and murine variable region heavy (VH) and light (VL) chains are conserved with 98% fidelity across species. While the amino acid usage at these surface positions creates surface residue patterns that are conserved within species, there are no identical patterns across species. However, surprisingly few amino acid changes need to be made to convert a murine Fv surface pattern to that characteristic of a human surface. Resurfacing was used to change the patterns of surface accessible residues in the Fv regions of the N901 and anti-B4 antibodies to resemble those found on the Fv regions of human antibody sequences. Two different procedures for selecting a human sequence were compared. For anti-B4, a data base of clonally derived human VL-VH sequence pairs was used, while for N901, sequences for VL and VH were independently selected from the Kabat et al. data base [Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M. & Gottesman, K. S. (1991) Sequences of Proteins of Immunological Interest (DHHS, Washington, DC), 5th Ed.]. Resurfaced N901 and anti-B4 antibodies had apparent affinities for their cell surface ligands that were identical to those of their respective parent murine antibodies. These data provide evidence that, despite the differences in the surfaces of mouse and human Fv regions, it is possible to substitute one for the other while retaining full antigen binding affinity.

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.

Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the gastric mucosa, where it appears to persist throughout the host's life unless the patient is treated. Colonization induces chronic gastric inflammation which can progress to a variety of diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer and mucosal-associated lymphoma. Strain-specific genetic diversity has been proposed to be involved in the organism's ability to cause different diseases or even be beneficial to the infected host and to participate in the lifelong chronicity of infection. Here we compare the complete genomic sequences of two unrelated H. pylori isolates. This is, to our knowledge, the first such genomic comparison. H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but we find that the overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar. Between 6 to 7% of the genes are specific to each strain, with almost half of these genes being clustered in a single hypervariable region.