The regulation and role of the periplasmic copper, zinc superoxide dismutase of Escherichia coli.

The discovery of superoxide dismutase (CuZnSOD) within the periplasms of several Gram-negative pathogens suggested that this enzyme evolved to protect cells from exogenous sources of superoxide, such as the oxidative burst of phagocytes. However, its presence in some non-pathogenic bacteria implies that there may be a role for this SOD during normal growth conditions. We found that sodC, the gene that encodes the periplasmic SOD of Escherichia coli, is repressed anaerobically by Fnr and is among the many antioxidant genes that are induced in stationary phase by RpoS. Surprisingly, the entry of wild-type E. coli into stationary phase is accompanied by a several-hour-long period of acute sensitivity to hydrogen peroxide. Induction of the RpoS regulon helps to diminish that sensitivity. While mutants of E. coli and Salmonella typhimurium that lacked CuZnSOD were not detectably sensitive to exogenous superoxide, both were killed more rapidly than their parent strains by exogenous hydrogen peroxide in early stationary phase. This sensitivity required prior growth in air. Evidently, periplasmic superoxide is generated during stationary phase by endogenous metabolism and, if it is not scavenged by CuZnSOD, it causes an unknown lesion that augments or accelerates the damage done by peroxide. The molecular details await elucidation.

The adenylate kinase genes of M. voltae, M. thermolithotrophicus, M. jannaschii, and M. igneus define a new family of adenylate kinases.

The adenylate kinase genes (adkA) were cloned from four closely related methanogenic members of the Archaea: the mesophile Methanococcus voltae (Mv), the thermophile M. thermolithotrophicus (Mt) and the hyperthermophiles M. jannaschii (Mj) and M. igneus (Mi). All four genes encode a protein of 192 amino acids (aa), and the four enzymes were closely related, with 68-81% aa identity in pairwise comparisons. It is anticipated that the enzyme set will provide the basis for studies that can establish the structural basis for ADK thermal stability. Mj and Mi contained a gene homologous to M. vannielii sec Y upstream of adkA, while Mv and Mt contained an unidentified, yet conserved, upstream open reading frame (ORF). Mt, Mj and Mi, but not Mv, contained an unidentified, yet highly conserved, ORF directly downstream of adkA. Based on their size, predicted secondary structure and phylogenetic relation to bacterial and eukaryotic adenylate kinases (ADK), it was concluded that the archaeal adkA genes encoded a unique class of ADK, and suggested that Euryarchaeotal and Crenarchaeotal branches of the Archaea contain separate subclasses of the enzyme.

Bradhyrhizobium japonicum hydrogen-ubiquinone oxidoreductase activity: quinone specificity, inhibition by quinone analogs, and evidence for separate sites of electron acceptor reactivity.

The purified H2-uptake hydrogenase of Bradyrhizobium japonicum, containing no cytochrome b, catalyzed efficient H2-ubiquinone oxidoreductase activity. Hydrogen-oxidizing membranes also catalyzed H2-ubiquinone oxidoreductase activity, and the site of ubiquinone reduction was localized to the He-quinone oxidoreductase complex based on comparative antimycin A and HQNO titrations of both H2-ubiquinone-1 oxidoreductase and ubiquinol-1 oxidase activities. A variety of quinones could function as electron acceptors of both pure or membrane-bound hydrogenase, including ubiquinone-0 (Q0), ubiquinone-1 (Q1), duroquinone and menadione, indicating relatively loose substrate specificity with regard to the quinone head group. Both the redox potential and the quinone structure determined the efficiency of hydrogenase turnover. Among short-chain ubiquinones, the isoprenoid chain length had a profound affect on Kin, with each additional isoprenoid unit resulting in the K m of the membrane-bound enzyme to decrease more than an order of magnitude. For pure enzyme, the K m values for Q0, Q1 and Q2 were 1.97 mM, 68.8 /xM and 3.1 /~M, respectively. Vma x was also influenced by the substrate isoprenoid chain length for the pure enzyme. The inhibition patterns of H2-dependent Q1 versus MB reduction by the quinone analogs (2-n-heptyl-4-hydroxyquinoline N-oxide and Antimycin A) were significantly different, and clear differences in pH optima for the two activities were observed. In addition, the two hydrogen-dependent electron acceptor activities (Q1 and MB) exhibited different time-dependent inactivation patterns by the chemical modification reagent diazobenzene sulfonate. Ubiquinone and MB therefore react by different mechanisms (perhaps at different sites) within the hydrogenase complex in situ. The inhibition pattern of hydrogen-ubiquinone oxidoreductase activity by antimycin A was clearly different than antimycin A inhibition of ubiquinol oxidation at the bc1 complex. This is, to our knowledge, the first report of antimycin A inhibition of a hydrogenase complex, and also of a quinone reducing site of a primary dehydrogenase. When pure hydrogenase is assayed in the absence of dithionite, a delay (lag phase) is observed prior to attainment of full activity. The length of this lag period (in minutes) was inversely dependent on ubiquinone concentration, and was greatly reduced (but not eliminated) at saturating ubiquinone levels. These effects were obtained with both Q1 and MB as electron acceptor, and the lag phases with Q1 were significantly longer than with MB. Electron acceptor binding to hydrogenase is thus required for reductive activation of hydrogenase during turnover.

Hydrogen-ubiquinone oxidoreductase activity by the Bradyrhizobium japonicum membrane-bound hydrogenase.

The Bradyrhizobium japonicum heterodimeric nickel-iron hydrogenase efficiently catalyzed H2-ubiquinone-1 oxidoreductase activity at rates up to 47% of the maximal rates obtained using the artificial electron acceptor methylene blue. Gel filtration chromatography and SDS-polyacrylamide gel electrophoresis experiments demonstrated that the purified enzyme was a heterodimer containing only the 65 kDa and 33 kDa subunits. Reduced minus oxidized absorption difference spectra demonstrated the absence of detectable cytochromes. The H2-ubiquinone-1 oxidoreductase activity of both the purified heterodimeric hydrogenase and membranes was significantly inhibited by 2-n-heptyl-4-hydroxyquinoline-N-oxide and antimycin A, inhibitors known to act in the quinone region of electron transport chains. Our results are the first report of H2-ubiquinone oxidoreductase activity by a purified hydrogenase.

Incorporation of a bacterial membrane-bound hydrogenase into proteoliposomes.

Membrane-bound nickel-iron hydrogenases from diverse genera of bacteria have been previously characterized and they are closely related. We report the reconstitution of purified Bradyrhizobium japonicum hydrogenase into proteoliposomes by a detergent dialysis method followed by two or three cycles of freeze-thaw. Sedimentation experiments revealed that more than 60% of the H2-uptake activity was particulate when reconstituted into Escherichia coli phospholipids. Sucrose-gradient centrifugation separated hydrogenase activity into two peaks, the less dense of which was phospholipid-associated and turbid, thereby showing successful incorporation. Purified enzyme did not bind to performed phospholipid vesicles, and 1.0 M NaCl failed to remove incorporated hydrogenase. The optimal micellar detergent:phospholipid ratio (rho) value for hydrogenase incorporation was 2.0. Proteoliposomes containing acidic phospholipids were the most effective for incorporation as well as for activity. The artificial electron acceptor specificity was similar for proteoliposomes and for H2-oxidizing membranes from B. japonicum. Proteoliposomes formed under optimal conditions had a broad size distribution centered around 400 nm diameter. Hydrogenase activity in proteoliposomes was partially protected from inactivation by the protein modification reagent diazobenzene sulfonate (DABS) (inactivation t1/2 = 30 min), whereas DABS rapidly inactivated the purified enzyme (t1/2 = 4 min). The latter result indicates protection of a catalytically important site by the phospholipid bilayer. This experimental system should be useful in addressing questions regarding the in vivo situation of bacterial membrane-bound hydrogenases.

Selection of amidases with novel substrate specificities from penicillin amidase of Escherichia coli.

To obtain amidases with novel substrate specificity, the cloned gene for penicillin amidase of Escherichia coli ATCC 11105 was mutagenized and mutants were selected for the ability to hydrolyze glutaryl-(L)-leucine and provide leucine to Leu- host cells. Cells with the wild-type enzyme did not grow in minimal medium containing glutaryl-(L)-leucine as a sole source of leucine. The growth rates of Leu- cells that expressed these mutant amidases increased as the glutaryl-(L)-leucine concentration increased or as the medium pH decreased. Growth of the mutant strains was restricted by modulation of medium pH and glutaryl-(L)-leucine concentration, and successive generations of mutants that more efficiently hydrolyzed glutaryl-(L)-leucine were isolated. The kinetics of glutaryl-(L)-leucine hydrolysis by purified amidases from two mutants and the respective parental strains were determined. Glutaryl-(L)-leucine hydrolysis by the purified mutant amidases occurred most rapidly between pH 5 and 6, whereas hydrolysis by wild-type penicillin amidase at this pH was negligible. The second-order rate constants for glutaryl-(L)-leucine hydrolysis by two "second-generation" mutant amidases, 48 and 77 M-1 s-1, were higher than the rates of hydrolysis by the respective parental amidases. The increased rates of glutaryl-(L)-leucine hydrolysis resulted from both increases in the molecular rate constants and decreases in apparent Km values. The results show that it is possible to deliberately modify the substrate specificity of penicillin amidase and successively select mutants with amidases that are progressively more efficient at hydrolyzing glutaryl-(L)-leucine.

Utilization of histidine by Caulobacter crescentus.

Caulobacter crescentus has an inducible pathway which is responsible for the degradation of histidine. Induction of this pathway occurs in the presence of both glucose and ammonia. Growth yield experiments indicate that only two of the three available nitrogens are used for growth suggesting that formamide may be produced as a waste product. However, formamide was not detected in the culture fluid and formate was formed instead. These results suggest that histidine may be degraded in a novel pathway which results in the production of 1 mol each of ammonia, glutamate and formate per mol of histidine. The third nitrogen from histidine appears to be sequestered in some kind of secondary metabolite.

Synthesis and assembly of flagellar components by Caulobacter crescentus motility mutants.

Cultures of wild-type Caulobacter crescentus and strains with fla mutations representing 24 genes were pulse-labeled with 14C-amino acids and analyzed by immunoprecipitation to study the synthesis of flagellar components. Most fla mutants synthesize flagellin proteins at a reduced rate, suggesting the existence of some mechanism to prevent the accumulation of unpolymerized flagellin subunits. Two strains contain deletions that appear to remove a region necessary for this regulation. The hook protein does not seem to be subject to this type of regulation and, in addition, appears to be synthesized as a faster-sedimenting precursor. Mutations in a number of genes result in the appearance of degradation products of either the flagellin or the hook proteins. Mutations in flaA, -X, -Y, or -Z result in the production of filaments (stubs) that contain altered ratios of the flagellin proteins. In some flaA mutants, other flagellin-related proteins were assembled into the stub structures in addition to the flagellins normally present. Taken together, these analyses have begun to provide insight into the roles of individual fla genes in flagellum biogenesis in C. crescentus.

Genetic mapping with Tn5-derived auxotrophs of Caulobacter crescentus.

Chromosomal insertions of Tn5 in Caulobacter crescentus displayed complete stability upon transduction and proved useful in strain building on complex media. RP4-primes constructed in vitro containing C. crescentus genomic sequences in the HindIII site of the kanamycin resistance gene failed to show enhanced or directed chromosome mobilization abilities. One of these kanamycin-sensitive RP4 derivatives, pVS1, was used as a mobilization vector in conjugation experiments on complex media where chromosomal Tn5 transfer to the recipient was selected. pVS1-mediated transfer of Tn5-induced auxotrophic mutations occurred at frequencies of 10(-6) to 10(-8) per donor cell. During conjugation with Tn5-encoded kanamycin resistance as the selected marker, Tn5 remained in its donor-associated locus in 85 to 100% of the transconjugants. A collection of eight temperature-sensitive donor strains bearing Tn5 insertion mutations from various regions of the C. crescentus genetic map were used to provide a rapid means for the determination of the map location of a new mutation. Use of the techniques described in this paper allowed an expansion of the C. crescentus genetic map to include the relative locations of 32 genes.

Construction of a genetic map for Caulobacter crescentus.

RP4-mediated conjugation has been used to transfer large fragments of chromosomal material in Caulobacter crescentus. In this system, conjugation proceeds from multiple origins, and haploid recombinants are recovered at frequencies of 10(-6) and 10(-7) per donor cell. The data from five-factor crosses were subjected to computer-assisted crossover analyses as a rapid method to determine marker order. Using this information and data from additional two- and three-factor crosses mediated by RP4 or the generalized transducing bacteriophage phi Cr30, we constructed the first genetic map for C. crescentus.

Mutations to tolerance and resistance to pesticin and colicins in Escherichia coli phi.

The universal colicin-indicator strain Escherichia coli phi, unlike E. coli strain K-12, is sensitive to pesticin, a bacteriocin produced by wild-type Yersinia pestis. Eleven distinct phenotypes of E. coli phi mutants were obtained by selection for insensitivity to pesticin, group B colicins, the group A colicin S4, or coliphage T5. Representative isolates from eight of these classes closely resembled resistant receptor mutants (Cir-, Fep-, and TonA-) or tolerant mutants (TonB-, ExbB-, ExbC-, Ivt-, and Cmt-) described in Escherichia coli K-12. The remainder were unique; of these, one resembled TonB- but was also tolerant to colicin S4 (TonB/S4-), and the others exhibited specific resistance to either colicin S4 (Sfr-) or to pesticin (Psr-). All receptor mutants except Psr- remained sensitive to pesticin, whereas TonB/S4, TonB-, ExbB-, and ExbC- isolates were highly tolerant to this bacteriocin.

Plasmids in Yersinia pestis.

Pesticinogenic and Ca2+-dependent strains of Yersinia pestis harbored plasmids of about 6 and 45 megadaltons, respectively. In addition, most isolates examined possessed a cryptic 65-megadalton plasmid.

Mode of action of pesticin: N-acetylglucosaminidase activity.

Homogeneous preparations of pesticin, a bacteriocin produced by Yersinia pestis, neither significantly inhibited net synthesis of deoxyribonucleic acid, ribonucleic acid, or protein in Escherichia coli phi nor caused detectable degradation of deoxyribonucleic acid in vivo. Accordingly, its mode of action does not resemble that of colicin E2 as suggested by others. However, incorporation of cell wall-specific label ([14C]diaminopimelic acid) into trichloroacetic acid-insoluble material of growing cells was inhibited by pesticin which also promoted release of such radioactivity from both resting cells and purified mureinlipoprotein. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of reaction mixtures containing appropriately labeled mureinlipoprotein showed that [3H]N-acetylglucosamine comigrated either with [14C]diaminopimelic acid in the murein peptide or with [14C]isoleucine of the Braun lipoprotein. As judged by these findings and pesticin-dependent release of reducing equivalents but not 4-hydroxy-2-acetamido sugars, the bacteriocin possesses N-acetylglucosaminidase activity. Hydrolysis of murein-lipoprotein occurred over a broad pH, with an optimum of 4.7. Mureinlipoproteins from a variety of pesticin-sensitive and -resistant organisms were hydrolyzed by the bacteriocin, indicating that its antibacterial specificity resides at the level of absorption.