Characterization of the alpha-peptide released upon protease activation of pyruvate oxidase

The pyruvate oxidase of Escherichia coli is a homo-tetrameric enzyme which can be activated greater than 500-fold (kcat/Km) by limited proteolytic digestion with alpha-chymotrypsin in the presence of pyruvate and thiamine pyrophosphate. The cleavage produces an Mr 2000 peptide (the alpha-peptide) from each subunit and mimics the physiologically important activation of the enzyme by phospholipids. Moreover, the proteolytic cleavage results in the loss of the high affinity lipid-binding site of the enzyme. We now report the isolation and characterization of the alpha-peptide fragment which is cleaved from the carboxyl terminus of each subunit by protease activation. Both the site of cleavage and the sequence of the alpha-peptide have been determined by a combination of Edman degradation of the purified peptide and DNA sequence analysis of the gene encoding the oxidase. The cleavage site lies within a sequence of hydrophobic amino acids predicted to form a beta-sheet. Another segment of the alpha-peptide is predicted to form an amphipathic alpha-helix. Quantitative assessment of the amphipathic nature of this alpha-helix (Eisenberg, D. (1984) Annu. Rev. Biochem. 53, 595-623) gives a value very similar to the values for several helical peptides which spontaneously bind to the surface of phospholipid vesicles. From these analyses, we propose that the alpha-peptide may play a role in binding pyruvate oxidase to cell membrane phospholipids in vivo.

An alkyl imidate labeling study of the organization of phospholipids and proteins in the lipid-containing bacteriophage PR4

The structure of the lipid-containing bacteriophage PR4 was studied using two alkyl imidates, ethyl acetimidate (EAI), a reagent permeant to lipid bilayers and isethionyl acetimidate (IAI), which is impermeant to membranes. The virion is an icosahedral particle consisting of a protein coat surrounding a membrane of phospholipid and protein which in turn encloses the DNA genome. Upon exposure to the permeant reagent, EAI, 50% of the phosphatidylethanolamine (PE) molecules reacted rapidly (half-life less than 10 min). A similar fraction of the PE also reacted with IAI, the impermeant reagent. The remaining half of the PE molecules reacted slowly with EAI (half-life of 80 min) and failed to react with IAI. All of the phage proteins reacted with both EAI and IAI (except a DNA-associated protein which reacted only with EAI). These labeling results indicate that the phage membrane consists of a lipid bilayer and that at least a portion of each phage protein (except the DNA-associated protein) is exposed on the external face of the lipid bilayer. Several of the membrane proteins could be cross-linked either to the phage membrane PE after EAI treatment or to phage phosphatidylglycerol after periodate treatment. The major structural protein of the phage was readily cross-linked to PG but failed to cross-link to PE suggesting that the protein specifically interacts with PG.

Selection for the transfer of phenotypically nonselectable chromosomal mutations to recombinant plasmids through introduction of an altered restriction site

We describe a simple method to select for transfer of mutant alleles from the Escherichia coli chromosome to a plasmid which formerly carried the wild-type (wt) allele. The wt allele on the plasmid is modified by introduction of a unique restriction site (e.g., XhoI) and transformed into a rec+ strain carrying the mutant allele on the chromosome. Upon homogenotization, the efficiency of which was increased by UV irradiation of the transforming plasmid [Chattoraj et al., Gene 27 (1982) 213-222], plasmids carrying the mutant allele are formed which are resistant to XhoI. These plasmids are selected from the population by resistance to XhoI digestion coupled with the low transformation efficiency of linear DNA molecules in recA- strain. The method is efficient and rapid and has particular advantages in situations where the mutant allele is difficult to detect by its phenotype.

Molecular cloning of the gene (poxB) encoding the pyruvate oxidase of Escherichia coli, a lipid-activated enzyme

The pyruvate oxidase structural gene (poxB) of Escherichia coli was cloned into derivatives of plasmid pBR322. The gene was first cloned into a cosmid vector by selection for the tetracycline resistance determinant of a closely linked Tn10 insertion (no direct selection for the gene was available). Subsequent subcloning resulted in localization of the gene to a 3.1-kilobase-pair DNA segment. Two of the smaller poxB plasmids were shown to cause the overproduction of oxidase activity (by six- to eightfold), and one of these plasmids was shown to encode a protein having the size and antigenic determinants of pyruvate oxidase. Introduction of poxB plasmids into strains (aceEF) lacking pyruvate dehydrogenase activity relieved the aerobic growth requirement of the strains for exogenous acetate.

Genetic characterization of the Escherichia coli cyclopropane fatty acid (cfa) locus and neighboring loci

The phenotypically silent cyclopropane fatty acid synthesis (cfa) gene of Escherichia coli K-12 has been located on the genetic linkage map. This was accomplished by integrating (via homologous recombination) the selectable marker of a recombinant plasmid into the host chromosome near the cfa locus. This integration allowed the subsequent isolation of a cfa-linked transposon Tn10 insertion. Genetic mapping of the Tn10 insertion, using conventional techniques, placed the cfa locus at min 36.5 on the linkage map in the vicinity of several other non-selectable markers. We ordered cfa and these other loci by three-factor transductional analyses. Selection for excision of the Tn10 element resulted in several types of mutants which harbor mutations of cfa and of neighboring genes, presumably as a consequence of Tn10-catalyzed chromosomal rearrangements.

Evidence that incorporation of exogenous fatty acids into the phospholipids of Escherichia coli does not require acyl carrier protein

Cells of an Escherichia coli acpS mutant were prepared with decreased intracellular concentrations (to 10% of the normal level) of the holo form of acyl carrier protein. These cells incorporated exogenous oleic acid into phospholipid at a normal rate.

Mini-Mu-duction as a test for genetic complementation in Escherichia coli

In mini-Mu-duction, segments of host DNA bracketed between two copies of an internally deleted Mu phage (a mini-Mu) can be packaged within Mu phage particles. Upon infection of a second host strain, the DNA injected by these particles can insert into the chromosomal DNA in a reaction catalyzed by the phage A gene product (transposase), which is independent of homologous recombination. This results in a partially diploid host strain in which the duplicated host DNA is bracketed by two copies of the mini-Mu phage (Faelen et al., Mol. Gen. Genet. 176:191-197, 1979). The frequency of mini-Mu-duction reported previously was low (10(-8) to 10(-9) per recipient cell) thus limiting its use to rather stable mutational lesions. I have increased the frequency of mini-Mu-duction 10- to 100-fold by use of a helper phage lacking the kil gene and by UV irradiation of the phage stocks. I have also shown that mini-Mu-duction is a reliable complementation assay in rec+ as well as recA recipient strains. This genetic complementation test does not require prior gene localization and (due to the extended host range of phage Mu) should be applicable to many enterobacterial species.

Cloning and manipulation of the Escherichia coli cyclopropane fatty acid synthase gene: physiological aspects of enzyme overproduction

Like many other eubacteria, cultures of Escherichia coli accumulate cyclopropane fatty acids (CFAs) at a well-defined stage of growth, due to the action of the cytoplasmic enzyme CFA synthase. We report the isolation of the putative structural gene, cfa, for this enzyme on an E. coli-ColE1 chimeric plasmid by the use of an autoradiographic colony screening technique. When introduced into a variety of E. coli strains, this plasmid, pLC18-11, induced corresponding increases in CFA content and CFA synthase activity. Subsequent manipulation of the cfa locus, facilitated by the insertion of pLC18-11 into a bacteriophage lambda vector, allowed genetic and physiological studies of CFA synthase in E. coli. Overproduction of this enzyme via multicopy cfa plasmids caused abnormally high levels of CFA in membrane phospholipid but no discernable growth perturbation. Infection with phage lambda derivatives bearing cfa caused transient overproduction of the enzyme, although pL-mediated expression of cfa could not be demonstrated in plasmids derived from such phages. CFA synthase specific activities could be raised to very high levels by using cfa runaway-replication plasmids. A variety of physiological factors were found to modulate the levels of CFA synthase in normal and gene-amplified cultures. These studies argue against several possible mechanisms for the temporal regulation of CFA formation.

Facile and gentle method for quantitative lysis of Escherichia coli and Salmonella typhimurium

Garrett et al. (Mol. Gen. Genet. 182:326-331, 1981) constructed strains of Escherichia coli harboring derivatives of plasmid pBR322 that carry the lysis genes (S, R, and Rz) of phage lambda. The plasmid construction placed the genes under control of the lactose operon operator-promotor (and thus of lac repressor). Induction of E. coli strains carrying these plasmids resulted in rapid lysis of the culture unless the S gene was defective, in which case the cells grew normally. A freeze-thaw treatment of induced cells carrying an S- plasmid gave quantitative lysis of either E. coli or Salmonella typhimurium cells under exceptionally gentle conditions. The method was equally effective on exponential phase cells and stationary phase cells and was readily extended to a large number of independent cultures.

Beta-hydroxydecanoyl thio ester dehydrase does not catalyze a rate-limiting step in Escherichia coli unsaturated fatty acid synthesis

The intracellular level of beta-hydroxydecanoyl thio ester dehydrase, the product of the fabA gene of Escherichia coli, was increased by isolation of a putative promotor mutant (termed fabAup) or by molecular cloning of the wild-type fabA gene into plasmid pBR322. The fabAup and plasmid-carrying strains overproduced dehydrase by about 15- and 10-fold, respectively. The phospholipids of all strains that overproduced the dehydrase contained significantly higher levels of saturated fatty acids than isogenic strains producing a normal level of dehydrase. No increased levels of unsaturated fatty acids were observed. This result indicates that, although the dehydrase is required for unsaturated fatty acid synthesis, the level of dehydrase activity in wild-type cells does not limit the rate of unsaturated fatty acid synthesis. The introduction of a plasmid carrying the structural gene for beta-ketoacyl acyl carrier protein synthase I into a fabAup strain overcame the effect of dehydrase overproduction on fatty acid composition.

Role for fadR in unsaturated fatty acid biosynthesis in Escherichia coli

Escherichia coli K-12 mutants constitutive for the synthesis of the enzymes of fatty acid degradation (fad) synthesize significantly less unsaturated fatty acid (UFA) than do wild-type (fadR+) strains. The constitutive fadR mutants synthesize less UFA than do fadR+) strains both in vivo and in vitro. The inability of fadR strains to synthesize UFAs at rates comparable to those of fadR+ strains is phenotypically asymptomatic unless the fadR strain also carries a lesion in fabA, the structural gene for beta-hydroxydecanoyl-thioester dehydrase. Unlike fadR+ fabA(Ts) mutants, fadR fabA(Ts) strains synthesize insufficient UFA to support their growth even at low temperatures and, therefore, must be supplemented with UFA at both low and high temperatures. The low levels of UFA in fadR strains are not due to the constitutive level of fatty acid-degrading enzymes in these strains. These results suggest that a functional fadR gene is required for the maximal expression of UFA biosynthesis in E. coli.

Genetic and biochemical analyses of Escherichia coli strains having a mutation in the structural gene (poxB) for pyruvate oxidase

Mutants of Escherichia coli K-12 deficient in pyruvate oxidase were isolated from an aceEF (pyruvate dehydrogenase-deficient) strain by selection for a complete absence of growth on medium lacking acetate. Extracts of two of the mutants were shown to contain normal levels of pyruvate oxidase antigen, although the enzymatic activities of the extracts were reduced or absent. The poxB locus was mapped by using closely linked transposon insertions to min 18.7 of the E. coli linkage map between the cmlA and aroA loci, a location far removed from that of the regulatory gene, poxA.

Nonsense mutants of the lipid-containing bacteriophage PR4

Thirty-three nonsense mutants of phage PR4 representing 12 complementation groups were isolated. One or two mutants of each group were grown on a suppressor-negative (Su-) host and characterized by the following criteria (i) proteins synthesized, (ii) level of phage DNA synthesis, and (iii) ability to assemble particles. We determined the protein and phospholipid compositions of the particles assembled in an Su- host, the presence of DNA in the particles, and the ability of the particles to adsorb to host cells. Finally each complementation group was tested for the ability to lyse an Su- host. We have identified one protein required for DNA synthesis, five proteins required for proper assembly of the protein coat and lipid membrane of the phage, two proteins required for stable insertion of DNA into the virion, a protein required for adsorption, a protein required for attachment of the adsorption protein to the virion, and a phage-encoded lytic enzyme.

Use of lambda phasmids for deletion mapping of non-selectable markers cloned in plasmids

A nonselectable gene carried on a poorly selectable recombinant plasmid has been physically mapped by deletion analysis. Our method involved cloning the plasmid into a coliphage lambda vector and treating the recombinant phage with a chelator. Virtually all particles surviving this treatment carried large deletions within the plasmid insert. Further deletion analysis was done by inserting a selectable lambda sequence into one such deletion derivative and repeating the chelator selection. Chelator selection was also used to isolate deletions constructed in vitro. The deleted phage are readily characterized by restriction mapping, and the gene in question scored after infection of a mutant host strain. These techniques have enabled us to physically assign the cyclopropane fatty acid synthase gene of Escherichia coli to 0.8 kb of a 16-kb segment after characterizing only a small number of isolates. This approach should be generally useful in the mapping of plasmids for which no convenient method exists for selecting or scoring the gene in question.

Genetic and biochemical analyses of Escherichia coli mutants altered in the temperature-dependent regulation of membrane lipid composition

We have previously studied two mutants of Escherichia coli altered in the regulation of membrane lipid composition by temperature. One class (represented by the fabFl allele) fails to regulate upon temperature shift and is defective in cis-vaccenic acid synthesis owing to the lack of the fatty acid elongation enzyme beta-ketoacyl-acyl carrier protein synthase II(EC 2.3.1.41). A second class of mutant, given the phenotypic designation Vtr, overproduces cis-vaccenic acid at all temperatures and hence is altered in temperature regulation. In this paper we report evidence for the following conclusions. (i) The Vtr and fabFl mutations show very tight genetic linkage. (ii) The Vtr lesion is allelic to the fabFl mutation since the presence of the fabFl mutation in merodiploid strains carrying the Vtr or fabF(+) alleles results in fatty acid compositions intermediate between those of the two monoploid strains. Merodiploids carrying both the fabF(+) and Vtr alleles likewise show an intermediate composition. These results indicate intra-allelic complementation. (iii) The two E. coli proteins recently discovered by Rock (J. Bacteriol. 152:1298-1300, 1982) that form mixed disulfide cross-links to acyl carrier protein are directly demonstrated to be beta-ketoacyl-acyl carrier protein synthases I and II. (iv) The fabFl strains produce a synthase II band of altered electrophoretic mobility, indicating that the fabF locus is the structural gene for synthase II. (v) The synthase II of Vtr strains is abnormally sensitive to cerulenin, an antibiotic that specifically inhibits synthases I and II. This increased sensitivity is readily demonstrated in vivo, but in vitro we failed to detect an increased sensitivity of the Vtr synthase II to cerulenin, nor have we detected any other kinetic or structural alteration in the enzyme. We interpret these results in terms of specific interactions of synthase II with other cellular components which occur in vivo but are not duplicated in vitro.

The lipid-containing bacteriophage PR4. Effects of altered lipid composition on the virion

Phage PR4 was grown on a variety of Escherichia coli mutants defective in fatty acid and phospholipid metabolism. The composition of the phage lipids was modified by changing the composition of the host membrane phospholipids. The compositions of both the polar and the acyl moieties of the phospholipids were altered. The proportion of saturated fatty acids in the phage phospholipids was increased in increments from 44% of the total fatty acids to 55%, 61% and 69% of the total fatty acids using a host mutant with a temperature-sensitive defect in unsaturated fatty acid biosynthesis. The increase in saturated fatty acids led to a pronounced loss of infectivity when the phage were incubated at temperatures between 2 degrees C and 30 degrees C (temperatures below those at which the phage were grown). The greater the level of saturated fatty acids in the phage phospholipids, the higher the temperature below which the phage were inactivated. Our results strongly suggest that the phage membrane undergoes a lipid phase transition, which can disrupt and inactivate the virion. The phospholipid composition of PR4 was also altered by using host mutants defective in phosphatidylethanolamine and/or cardiolipin synthesis. Phage PR4 grown on wild-type host strains contains 56% phosphatidylethanolamine, 37% phosphatidylglycerol, 4.6% cardiolipin and no detectable phosphatidylserine. However, in response to changes in the host, PR4 preparations were obtained with phospholipid compositions varying from 28% to 60% in phosphatidylethanolamine, from 22% to 39% in phosphatidylglycerol, from 1% to 15% in cardiolipin and containing as much as 35% phosphatidylserine. These changes in phospholipid composition did not affect the infectivity of the phage. Moreover, the increased level of phosphatidylglycerol in the phage relative to the host was not altered by these manipulations. It is concluded that the net charge of the phage membrane phospholipids is not involved in the selection or function of the viral phospholipids. We also present evidence suggesting that the phage and host membranes do not fuse during the course of infection.

Thermal regulation of membrane fluidity in Escherichia coli. Effects of overproduction of beta-ketoacyl-acyl carrier protein synthase I

Multicopy plasmids bearing the structural gene (fabB) for beta-ketoacyl-acyl carrier protein (ACP) synthase I were constructed in vitro and transformed into various Escherichia coli strains. Introduction of these plasmids into fabB strains resulted in a fabB+ phenotype and a large (8- to 10-fold) overproduction of synthase I activity. Strains carrying these plasmids were also unusually resistant to cerulenin (an antibiotic that specifically inhibits beta-ketoacyl-ACP synthase activity) and overproduced cis-vaccenic acid. Strains (fabF-) lacking beta-ketoacyl-ACP synthase II are deficient in both cis-vaccenic acid synthesis and thermal regulation. Introduction of the fabB plasmids into these strains resulted in the restoration of cis-vaccenic acid synthesis. However, the plasmid-engendered cis-vaccenic acid synthesis of these strains was unaffected by temperature. These results demonstrate that synthase II, the product of the fabF gene, is the sole enzyme regulating the temperature-dependent composition of the membrane phospholipid acyl chains.

Mapping nonselectable genes of Escherichia coli by using transposon Tn10: location of a gene affecting pyruvate oxidase

Mutants of Escherichia coli K-12 deficient in pyruvate oxidase were isolated by screening for the production of 14CO2 from [1-14C]pyruvate by the method of Tabor et al. (J. Bacteriol. 128:485-486, 1976). One of these lesions (designated poxA) decreased the pyruvate oxidase activity to 10 to 15% of the normal level but grew well. To map this nonselectable mutation, we isolated strains having transposon Tn10 inserted into the chromosome close to the poxA locus and mapped the transposon. These insertions were isolated by the following procedure: (i) pools of Tn10 insertions into the chromosomes of two different Hfr strains were prepared by transposition from a lambda::Tn10 vector; (ii) these Tn10-carrying strains were then mated with a poxA recipient strain, and tetracycline-resistant (Tetr) recombinants were selected; (iii) the Tetr recombinants were then screened for 14CO2 production from [1-14C]pyruvate. This method was shown to give a greater than 40-fold enrichment of insertions of Tn10 near the poxA gene as compared with transduction. Calculations indicate that a similar enrichment should be expected for other genes. The enrichment is due to the much greater map interval over which strong linkage between selected and unselected markers is found in conjugational crosses as compared with transductional crosses. The use of Hfr conjugative transfer allows isolation of transposon insertions closely linked to a nonselectable gene by scoring hundreds rather than thousands of colonies. Using a Tn10 insertion greater than 98% cotransduced with the poxA locus, we mapped the poxA gene on the E. coli genetic map. The poxA locus is located at 94 min, close to the psd locus. The clockwise gene order is ampA, poxA, psd, purA. The poxA mutation is recessive and appears to be a regulatory gene.

Overproduction of cis-vaccenic acid and altered temperature control of fatty acid synthesis in a mutant of Escherichia coli

A mutant of Escherichia coli has been characterized which overproduces cis-vaccenic acid in the temperature range of 30 to 42 degrees C. The mutational lesion acts within the fatty acid biosynthetic pathway rather than at the level of fatty acid incorporation into phospholipid.

Molecular properties of short chain acyl thioesters of acyl carrier protein

S-Acylated derivatives of the acyl carrier protein (ACP) of Escherichia coli were prepared by a specific chemical reaction. The properties of acetyl-ACP, butyryl-ACP, and hexanoyl-ACP were compared with those of long chain (greater than C8) acyl-ACPs. Acylation of ACP with long chain (greater than or equal to C8) acyl groups stabilizes the protein to alkaline pH-induced hydrodynamic expansion, the degree of stabilization being independent of acyl chain length (Rock, C. O., and Cronan, J. E., Jr. (1979) J. Biol. Chem. 254, 9778-9785). This was not true of the short chain length acyl-ACPs. We report that the C2, C4, and C6 acyl-ACPs showed a lower degree of stabilization (greater hydrodynamic radii) under alkaline conditions than the longer chain lengths. The degree of stabilization (assayed by polyacrylamide gel electrophoresis at pH 9.5) was a direct function of acyl chain length (C8 greater than C6 greater than C4 greater than C2 greater than ACP). Long chain (greater than C10) acyl-ACPs bind tightly to octyl-Sepharose whereas ACP does not bind. The strength of binding is a direct function of acyl chain length for C10 to C16 (Rock, C. O., and Garwin, J. L. (1979) J. Biol. Chem. 254, 7123-7128). In contrast to the result expected if the entire acyl chain was accessible, we report that neither acetyl-ACP nor butyryl-ACP binds to octyl-Sepharose. Moreover, both hexanoyl-ACP and octanoyl-ACP bind less tightly to octyl-Sepharose than expected from extrapolation of the data for the longer chain length acyl-ACPs. Both the pH stabilization data and the hydrophobic chromatographic data are interpreted as indicating the presence of an acyl chain binding site on ACP that binds the first 6 to 8 carbon atoms of the acyl chain.