The bacterial lipocalins.

The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.

Transfer of palmitate from phospholipids to lipid A in outer membranes of gram-negative bacteria.

Regulated covalent modifications of lipid A are implicated in virulence of pathogenic Gram-negative bacteria. The Salmonella typhimurium PhoP/PhoQ-activated gene pagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic anti-microbial peptides. Palmitoylated lipid A can also function as an endotoxin antagonist. We now show that pagP and its Escherichia coli homolog (crcA) encode an unusual enzyme of lipid A biosynthesis localized in the outer membrane. PagP transfers a palmitate residue from the sn-1 position of a phospholipid to the N-linked hydroxymyristate on the proximal unit of lipid A (or its precursors). PagP bearing a C-terminal His(6)-tag accumulated in outer membranes during overproduction, was purified with full activity and was shown by cross-linking to behave as a homodimer. PagP is the first example of an outer membrane enzyme involved in lipid A biosynthesis. Additional pagP homologs are encoded in the genomes of Yersinia and Bordetella species. PagP may provide an adaptive response toward both Mg(2+) limitation and host innate immune defenses.

The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death.

Antidote/toxin gene pairs known as "addiction modules" can maintain plasmids in bacterial populations by means of post-segregational killing. However, several chromosome-encoded addiction modules may provide an entirely distinct function in the programmed cell death of moribund subpopulations under starvation conditions. We now report a novel chromosomal bacteriolytic module of Escherichia coli called the entericidin locus, which is activated in stationary phase under high osmolarity conditions by sigmaS and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins. An attenuator precedes ecnA and an ompR-sensitive sigmaS promoter governs expression of ecnB. The entericidin A lipoprotein is an antidote to the bacteriolytic lipoprotein entericidin B. The entericidins are predicted to adopt amphipathic alpha-helical structures and to reciprocally modulate membrane stability. The entericidin locus is not present on any known plasmids, but is conserved in the homologous region of the Citrobacter freundii chromosome. Although the cloned C. freundii entericidin locus is expressed in E. coli independently of ompR, it carries an additional ompR-like gene called ecnR. The organization of the entericidin locus as a chromosomal antidote/toxin gene pair, which is regulated by both positive and negative osmotic signals during starvation, is consistent with an emerging paradigm of programmed bacterial cell death.

Vitamin B6 and cancer: synthesis and occurrence of adenosine-N6-diethylthioether-N-pyridoximine-5'-phosphate, a circulating human tumor marker.

In the course of studies aimed at deciphering the metabolic transformations of [3,4-14C] and [3H]C6-pyridoxine hydrochloride by tumor-bearing rats and tumor cells in culture, biosynthesis of a novel labeled product was observed. Its production began with the onset of tumor growth and increased as cell proliferation increased. Chemical, enzymatic, precursor labeling, and analytical tests on the isolated product indicated this product as adenosine-N6-diethylthioether-N-pyridoximine-5'-phosphate (compound 1). In confirmation, the chemical synthesis and characterization of compound 1 are presented in this study. In addition, blood samples from 28 normal subjects, 28 cancer patients with different malignancies, and 39 patients with a variety of other than cancer ailments were screened for compound 1 on a blind basis using reverse phase ion-paired high-performance liquid chromatography. The results show that the level of the vitamin B6 conjugate in the circulation of control subjects, cancer patients in remission, and patients with other diseases was only minimal. Cancer patients with active disease had 3-4-fold higher levels (P < 0.00001). Our results also confirm previous findings regarding the structure of compound 1 and show its potential value as a circulating human tumor marker that could be successfully used for cancer detection.

O6-ethylguanine and O6-benzylguanine incorporated site-specifically in codon 12 of the rat H-ras gene induce semi-targeted as well as targeted mutations in Rat4 cells.

To examine the miscoding properties of modified guanine residues bearing increasingly bulky O6-substituents, Rat4 cells, grown in the presence of O6-benzylguanine to deplete the DNA repair protein O6-alkylguanine-DNA alkyltransferase, were transfected with plasmids carrying H-ras genes in which O6-methyl, O6-ethyl- and O6-benzylguanine were substituted for the first, second or both the first and second guanine residues of codon 12 (GGA). DNA from isolated transformed colonies was amplified by PCR and directly sequenced by high-temperature manual and automated methods. The results show that O6-ethylguanine and O6-benzylguanine induced semi-targeted as well as targeted mutations, in contrast to O6-methylguanine, which induced only targeted mutations. When incorporated in place of the first guanine of H-ras codon 12, the targeted mutations induced by all these modified guanines were exclusively G-->A transitions. When incorporated at the second position of codon 12, O6-benzylguanine induced G-->A, G-->T and G-->C mutations. O6-Ethylguanine at the second position induced chiefly G-->A transitions, and O6-methylguanine induced G-->A transitions exclusively. Semi-targeted mutations were strictly G-->A at the base 3' to a position 1 adduct or 5' to a position 2 adduct. The mechanism for induction of targeted mutations probably involves decreasing preference to thymidine incorporation opposite an O6-modified guanine as the size of the O6-substituent increases, while the mechanism for non-targeted mutations may be related to abasic site formation or to translesion synthesis which might be made error-prone by obstructive DNA lesions in this context.

Stationary phase expression of a novel Escherichia coli outer membrane lipoprotein and its relationship with mammalian apolipoprotein D. Implications for the origin of lipocalins.

We report a novel outer membrane lipoprotein of Escherichia coli. DNA sequencing between ampC and sugE at the 94.5 min region of the E. coli chromosome revealed an open reading frame specifying 177 amino acid residues. Primer extension analysis demonstrated that the promoter is activated at the transition between exponential and stationary growth phases under control of the rpoS sigma factor gene, and this was confirmed in vivo by monitoring expression of beta-galactosidase activity from a lacZ translational fusion. The amino acid sequence exhibited 31% identity with human apolipoprotein D (apoD), which is a component of plasma high density lipoprotein and belongs to the eukaryotic family of lipocalins. The bacterial lipocalin (Blc) contained a short deletion of 7 amino acid residues corresponding to a hydrophobic surface loop that is thought to facilitate the physical interaction between apoD and high density lipoprotein. However, Blc exhibited a typical prokaryotic lipoprotein signal peptide at its amino terminus. Overexpression, membrane fractionation, and metabolic labeling with [3H]palmitate demonstrated that Blc is indeed a globomycin-sensitive outer membrane lipoprotein. Blc represents the first bacterial member of the family of lipocalins and may serve a starvation response function in E. coli.

Vitamin B6 and cancer: adenosine-N6-diethylthioether N1-pyridoximine 5'-PO4, a circulating human tumor marker.

Studies in my laboratory on the metabolism and utilization of labeled vitamin B6 by tumor-bearing animals and tumor cells in culture have shown the production and presence in the circulation of a novel pyridoxal 5'-phosphate conjugate metabolite (1-5). Using specific radiolabeling and analytical tests, its structure was tentatively identified (now confirmed) as adenosine-N6-diethylthioether-N1-pyridoximine 5'-phosphate (4-6). The novel vitamin conjugate was isolated from the plasma of patients and control subjects following extraction with perchloric acid and separation by pair-ion HPLC. This communication reports the chromatographic separation of the novel compound and its plasma levels in control subjects, cancer patients and patients with other ailments. The results show that the novel metabolite is a circulating human tumor marker with levels of up to 4x or greater seen in cancer patients compared to controls and to subjects with other ailments. The results indicate strongly that the novel circulating vitamin B6 conjugate compound can be successfully used for the detection of different malignancies in humans by evaluating its level in circulation.

Analysis of sequence contexts flanking T.G mismatches leads to predictions about reactivity of the mismatched T to osmium tetroxide.

Osmium tetroxide and hydroxylamine are used to detect mutations in DNA and RNA after hybridization of mutant and wild-type DNA. Mismatched T and C bases, respectively, are modified by these reagents and the DNA strand cleaved at the mismatched bases by subsequent treatment with piperidine. This allows detection and location of the mutation. Although most T.G mismatches have been reported to be reactive to osmium tetroxide, some have been reported to be unreactive. The aim of this study was to collect and analyze the reactive and unreactive T.G mismatches. We have collected sequence contexts of all reactive and unreactive T.G mismatches for analysis. This involves 10 unreactive T.G mismatches (plus one T.C) and 19 reactive T.G mismatches. Sequence effects of bases surrounding these mismatches must influence this reactivity. There must be many types of such sequence effects. We postulate that because of the dominance of 5' G bases near the T of unreactive T.G mismatches and the absence of 5' G bases in reactive T.G mismatches that the stacking of the 5' G on the mismatched T is the reason for this lack of reactivity in the majority of the cases studied here.

Complementation of growth defect in an ampC deletion mutant of Escherichia coli.

beta-Lactamase genes of class-A (Rtem) and class-C (ampC) were placed under control of an inducible tac-promoter and expressed in Escherichia coli. Expression of RTEM had no observable effect on the growth properties of E. coli strains HB101 (ampC+) or MI1443 (delta ampC). E. coli MI1443 exhibited a decline in growth rate at mid-exponential phase which could be delayed by expression of AmpC at early-exponential phase. AmpC expression otherwise inhibited growth, particularly during the transition into exponential phase where growth was prevented altogether. We suggest that the AmpC beta-lactamase, but not RTEM, may have an additional cellular function as a peptidoglycan hydrolase.

The role of O6-alkylguanine-DNA alkyltransferase in protecting Rat4 cells against the mutagenic effects of O6-substituted guanine residues incorporated in codon 12 of the H-ras gene.

The role of rat O6-alkylguanine-DNA alkyltransferase (AGT) in modulating mutagenesis by O6-substituted guanines in the rat H-ras gene was examined. Rat4 cells were transfected with vectors carrying O6-methyl-, O6-ethyl- or O6-benzylguanine residues in place of the normal guanines at either the first, second, or both the first and second positions in codon 12 (GGA) of the H-ras coding sequence. The percentage of transformed colonies was determined for cells grown in normal medium or in medium containing O6-benzylguanine to completely deplete AGT. In parallel experiments with O6-methylguanine-containing vectors, the percentage of cellular DNA harboring codon 12 mutations was determined for normal cells and cells lacking AGT. A reasonable correspondence was observed between the percentage of mutated DNA and the percentage of transformed colonies produced in both types of cells. The results indicate that the contribution of AGT to the repair of O6-substituted guanine damage decreases as the O6 substituent is changed from methyl > ethyl > benzyl. Additionally, cellular AGT appears to repair an O6-methylguanine more readily at the first position of codon 12 than the second position. However, other repair mechanisms in these mammalian cells appear to play a major role in correcting low levels of O6-substituted guanine damage including O6-methylguanine damage.

Overproduction, solubilization, purification and DNA-binding properties of AmpR from Citrobacter freundii.

AmpR belongs to the LysR family of prokaryotic DNA-binding transcriptional regulators and controls induction of the enterobacterial ampC beta-lactamase gene. The ampR gene of Citrobacter freundii was deregulated by employing the polymerase chain reaction to introduce an efficient ribosome-binding sequence and suitable restriction enzyme sites for cloning into a chemically inducible tac-promoter expression vector. When induced in Escherichia coli, the modified ampR gene rapidly overproduced the AmpR protein as an insoluble aggregate. The AmpR protein could be solubilized with 1.32 M guanidine/HCl and remained soluble when dialyzed against 0.5 M NaCl. The solubility properties of AmpR were exploited to selectively precipitate and resolubilize the protein in a nearly homogenous state. AmpR was then purified by a single gel-filtration chromatography step which demonstrated that AmpR exists in solution as a monodisperse homodimeric protein. Several milligrams of purified AmpR could be obtained routinely from a 1-1 culture of induced bacteria. A DNA-binding assay buffer containing 300 mM potassium glutamate and 30% glycerol was found to stabilize AmpR and used to demonstrate sequence-specific DNA-binding. Additionally, purified AmpR binds a half-operator DNA with an inverted-repeat sequence which competes with binding by the wild-type operator. These findings are discussed in terms of the helix-turn-helix DNA-binding motif, whereby AmpR is proposed to interact with its wild-type operator as a dimer of dimers.

Coordinate regulation of murein peptidase activity and AmpC beta-lactamase synthesis in Escherichia coli.

In the periplasmic space of Escherichia coli, the (L)-m-A2pm-(D)-m-A2pm peptide, the lipoprotein, and the AmpC beta-lactamase are controlled by growth rate. To explain this coordinate regulation, it is proposed that the AmpC protein functions as an LD-endopeptidase in addition to its known function as a beta-lactamase. As LD-peptides, DD-peptides and beta-lactams are structurally similar, LD-peptidases may belong to the larger family of DD-peptidases and serine beta-lactamases. In contrast to E. coli, many related bacteria possess an inducible AmpC protein. Several gene systems necessary for AmpC induction are known to affect various aspects of peptidoglycan metabolism. It is proposed that AmpC induction occurs indirectly via a recyclable cell wall peptide.

Positional effects on the structure and stability of abbreviated H-ras DNA sequences containing O6-methylguanine residues at codon 12.

Activation of the H-ras protooncogene in rats by methylating carcinogens results from a G-to-A transition mutation at the second position of codon 12 (GGA), presumably due to formation of an O6-methylguanine (m6G) at this position. A similar transition at the first position of codon 12 appears not to occur in vivo. To study the possible structural basis for this bias in mutation, we synthesized a series of 11-base H-ras sequences [e.g., 5'-d(CGCTG*G*AGGCG)-3' and two complementary strands] containing an m6G at the first, second, or both positions of codon 12 (i.e., G* = m6G). The results of solution chemical studies indicated that the individual strands formed stable hairpin structures among which that containing m6G at the second position of codon 12 was most stable. Further, the DNA duplex with m6G at the second position was significantly more stable than that with m6G at the first position, and under certain conditions, it was more stable than the unmodified duplex as well. It is possible that such a difference in stability might lead to more ready recognition of an m6G at the first position by repair proteins, and this could contribute to the apparent site specificity of mutation by methylating carcinogens at codon 12 of the H-ras gene.

Vitamin B6 and cancer: a novel pyridoxal 5-phosphate conjugate in tumor cells and blood of cancer patients.

Studies on the metabolic transformations of labeled pyridoxine showed that its utilization by tumor animals and tumor cells differs greatly from that seen in control animals. When [3,4-14C] and/or tritium labeled pyridoxine at the 6th ring carbon is administered i.p. to tumor-bearing animals and its fate is subsequently determined at different time intervals (using HPLC separation of the labeled metabolites following acid extraction from tissues), in addition to other differences, synthesis of a novel labeled product occurs which begins with the onset of tumor growth. It is either absent or present only at minimal levels in normal animals and regenerating rat liver. It is present in all tumor sources examined to date, i.e. serum of tumor rats, a spectrum of rat hepatomas, solid human tumors, tumor cells in culture and plasma of cancer patients. The novel product is a conjugate of pyridoxal 5'-phosphate with the structure Adenosine-N6-Diethylthioether-N1- Pyridoximine-5'-phosphate. This communication reports on the occurrence and distribution of the novel product in different tumor tissues and cells as well as the blood of cancer patients with active disease and in remission, and in normal volunteers. The results show significantly higher levels of this product in the blood of patients with different malignancies and in the active state. The novel vitamin B6 compound may be a good candidate as a marker for tumor presence and/or metastasis.

Synthesis of adenosine-N6-methyl, propylthioether-N-pyridoxamine: an analog of a novel vitamin B6 tumor product.

Studies on the time-course utilization of radiolabeled pyridoxine in rats with hepatomas led to the discovery of a novel vitamin B6 product. It is found in a spectrum of tumor lines but it is absent or occurs minimally in normal tissues. Hepatomas incorporate up to 20-30% of labeled pyridoxine into the novel product. Its structure was tentatively identified as adenosine-N6-methyl, propylthioether-N-pyridoximine-5'-PO4. However, results of tests on the incorporation of labeled precursors into the novel product by 3B3 hybridoma or HL-60 cells support an N6-diethylthioether bridge linking the adenosyl and pyridoxyl moieties. The synthesis of adenosine-N6-methyl, propylthioether-N-pyridoxamine is reported in this paper. The mass spectrum of this analog is similar to that of the tumor product as seen by its fragmentation in further support of the structure of the tumor product. Whether the latter may be part of tumor RNA is questionable. RNA was isolated for 3B3 or HL-60 cells after incubation with tritiated or 14C-pyridoxine using SDS-phenol repeated extractions in the presence of RNase inhibitors. Centrifugation of cRNA on 5-20% linear sucrose density gradients showed practically all the label at the top of the gradient. RNase treatment resulted in a labeled product which coeluted with the tumor product on reverse phase paired-ion HPLC and chromatographed as dinucleotide on paper. These results suggest that the novel tumor product may occur as a short oligonucleotide.

Biosynthesis of a novel form of vitamin B-6 by tumor cells.

Studies on the time-course utilization of radiolabeled pyridoxine in hepatoma-bearing rats led to the discovery of a novel vitamin B-6 product. It is present in a spectrum of tumor lines, but it is absent or occurs minimally in normal tissues. Hepatomas incorporate up to 20-30% of labeled pyridoxine into the novel species. Its structure was tentatively identified as adenosine-N6-methyl, propylthioether-N-pyridoximine-5'-phosphate. In the present study, 3B3 mouse-human hybridoma cells were incubated with radiolabeled precursor molecules, perchloric acid cell extracts were analyzed by high performance liquid chromatography (HPLC), and radioactivity in effluent fractions was measured. The results show that [G-3H]pyridoxine, [2,8-3H]adenosine, L-[35S]cysteine and L-[U-14C]serine are incorporated into the novel tumor product. These findings are interpreted to indicate that the correct structure of the novel product is adenosine-N6-diethylthioether-N'-pyridoximine-5'-phosphate. Further, these data demonstrate that tumor cells have evolved novel enzymatic steps for metabolism of vitamin B-6. The potential use of the novel metabolite as a marker for tumor genesis and establishment is especially significant, as the compound is peculiar to the neoplastic state.

Purification and properties of Escherichia coli dimethyl sulfoxide reductase, an iron-sulfur molybdoenzyme with broad substrate specificity.

Dimethyl sulfoxide reductase, a terminal electron transfer enzyme, was purified from anaerobically grown Escherichia coli harboring a plasmid which codes for dimethyl sulfoxide reductase. The enzyme was purified to greater than 90% homogeneity from cell envelopes by a three-step purification procedure involving extraction with the detergent Triton X-100, chromatofocusing, and DEAE ion-exchange chromatography. The purified enzyme was composed of three subunits with molecular weights of 82,600, 23,600, and 22,700 as identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The native molecular weight was determined by gel electrophoresis to be 155,000. The purified enzyme contained 7.5 atoms of iron and 0.34 atom of molybdenum per mol of enzyme. The presence of molybdopterin cofactor in dimethyl sulfoxide reductase was identified by reconstitution of cofactor-deficient NADPH nitrate reductase activity from Neurospora crassa nit-I mutant and by UV absorption and fluorescence emission spectra. The enzyme displayed a very broad substrate specificity, reducing various N-oxide and sulfoxide compounds as well as chlorate and hydroxylamine.