Inactive X chromosome has the highest concentration of unmethylated Hha I sites.

A procedure enabling the highly sensitive detection of accessible restriction endonuclease sites on metaphase chromosomes is described. The procedure is based on the following: (i) a terminal deoxynucleotidyltransferase is used to add a biotinylated nucleotide (Bio-11-dUTP) tail to the 3' hydroxyl terminus generated by the action of a restriction enzyme and (ii) the biotinylated oligonucleotide is detected by a peroxidase-based immunocytochemical method. When used with the 5-methylcytosine-sensitive enzyme Hha I, it gives rise to a pattern close to R and T banding on autosomes. In addition, the staining of one X chromosome in females appears very unusual by its pattern and its strong intensity. This procedure, as applied on a case with a polysomy X chromosome, provides direct evidence of an overall hypomethylation of the inactive X chromosomes.     

The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication.

The terminus region of the chromosome of Escherichia coli contains two separate sites, called T1 and T2, that inhibit replication forks. T1 is located near 28.5 min, which is adjacent to trp, and T2 is located at 34.5-35.7 min on the opposite side of the terminus region, near manA. The sites act in a polar fashion, and replication forks traveling in a clockwise direction with respect to the genetic map are not inhibited as they pass through T1 but are inhibited at T2. Similarly, counterclockwise forks are not inhibited at T2 but are inhibited at T1. Consequently, forks are not inhibited until they have passed through the terminus region and are about to leave it. Studies with deletion strains have located T2 within a 58-kilobase interval, which corresponds to kilobase coordinates 387-445 on the physical map of the terminus region.     

Three tRNA binding sites on Escherichia coli ribosomes.

The binding of N-acetyl-Phe-tRNAPhe (an analogue of peptidyl-tRNA), Phe-tRNAPhe, and deacylated tRNAPhe to poly(U)-programmed tightly coupled 70S ribosomes was studied. The N-acetyl-Phe-tRNAPhe binding is governed by an exclusion principle: not more than one N-acetyl-Phe-tRNAPhe can be bound per ribosome, although this peptidyl-tRNA analogue can be present either at the aminoacyl-tRNA (A) site or the peptidyl-tRNA (P) site. Two Phe-tRNAPhe molecules are accepted by one ribosome in the presence of poly(U). This aminoacyl-tRNA binds enzymatically (in the presence of elongation factor Tu and GTP) and nonenzymatically to the A site and is then transferred to the P site, if that site is free. If this elongation factor G-independent movement is hampered, either by using an incubation temperature of 0 degrees C or by the addition of the translocation inhibitor viomycin, only one Phe-tRNAPhe per ribosome can be bound. The effect of the peptidyltransferase inhibitor chloramphenicol on the binding is similar to that of viomycin. In the absence of poly(U), Phe-tRNAPhe cannot bind to the ribosome. Deacylated [14C]tRNAPhe can bind in three copies to one ribosome. The new third tRNA binding site is called the "E" site. The sequence of filling the sites is P, E, and A. The apparent binding constants for the P and the E sites are both approximately 9 X 10(6) M-1 and that for the A site is 1.3 X 10(6) M-1. In the absence of poly(U), only one deacylated tRNAPhe can be bound per ribosome. This tRNAPhe most likely occupies the P site.     

Bacillus licheniformis penicillinase synthesized in Escherichia coli contains covalently linked fatty acid and glyceride.

DNA sequence analysis of the structural gene for Bacillus licheniformis penicillinase has revealed a tetrapeptide sequence of Leu-Ala-Gly-Cys within the NH2-terminal part of the precursor form of penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6). The same tetrapeptide occurs in the signal sequence of the prolipoprotein of Escherichia coli, and the cysteine residue in the tetrapeptide of prolipoprotein is modified to form glyceride-cysteine which becomes the NH2 terminus of Braun's lipoprotein. On the basis of labeling, with [2-3H]glycerol, [3H]palmitate, [35S]methionine, and [35S]sulfuric acid, of an E. coli strain lysogenic for a lambda vector containing the penicillinase gene from B. licheniformis and of immunoprecipitation with rabbit antisera against purified B. licheniformis penicillinase, we conclude that B. licheniformis penicillinase synthesized in E. coli contains covalently linked glyceride and fatty acid. These results strongly suggest the operation of a modification system in E. coli, and presumably in other Gram-negative bacteria, which results in the formation of a glyceride-cysteine residue if the proper peptide sequence is present in the signal sequence of membrane proteins.     

Enzymatic replication of the origin of the Escherichia coli chromosome.

An enzyme system that replicates plasmids bearing the origin of the Escherichia coli chromosomes (oriC) has the following physiologically relevant features. The system (i) depends completely on low levels of exogenously furnished supercoiled oriC plasmids, (ii) uses only those plasmids that contain the intact oriC region of about 245 base pairs, (iii) initiates replication within or near the oriC sequence and proceeds bidirectionally, (iv) proceeds linearly, after a 5-min lag, for 30-40 min to produce as much as a 40% increase over the input DNA, (v) depends on RNA polymerase and gyrase as indicated by total inhibition by rifampicin and nalidixate, (vi) depends on replication proteins (e.g., dnaB protein and single-stranded DNA binding protein) as judged by specific antibody inhibitions, (vii) operates independently from protein synthesis, and (viii) depends on dnaA activity, as suggested by the inactivity of enzyme fraction from each of two dnaA temperature-sensitive mutant strains, and complementation (with a 15-fold overproduction of complementing activity) by a fraction from a strain containing the dnaA gene cloned in a multicopy plasmid. Resolution and analysis of factors that control the initiation of a chromosome cycle should become accessible through its enzyme system.     

Left-handed Z-DNA and in vivo supercoil density in the Escherichia coli chromosome.

A system for studying Z-DNA formation in the Escherichia coli chromosome was developed. Prior investigations in recombinant plasmids showed that alternating (Pur-Pyr) sequences can adopt a left-handed Z-DNA conformation both in vitro and in vivo. We constructed mobile, transposon-based cassettes carrying cloned (Pur-Pyr) sequences containing an EcoRI site in the center. These cassettes were subsequently inserted into different locations in the E. coli chromosome in a random fashion. A number of stable insertions were characterized by Southern analysis and pulsed-field gel electrophoresis mapping. A cloned temperature-sensitive MEcoRI methylase was expressed in trans as the probe to study Z-DNA formation in vivo. In this system, the control EcoRI sites were quickly methylated when cells were placed at the permissive temperature. Strong inhibition of the methylation was observed, however, only for the EcoRI sites embedded in a 56-bp run of (C-G). In contrast, the shorter sequence of 32 bp did not show this behavior. Prior in vitro determinations revealed that the longer tract required less energy to stabilize the Z-helix than the shorter block. We conclude that the observed inhibition of methylation is due to Z-DNA formation in the E. coli chromosome. In vitro, these sequences undergo the B- to Z-DNA transition at a supercoil density of -0.026 for the 56-bp insert and -0.032 for the 32-bp block. Since only the longer (C-G) tract but not the shorter run adopted the left-handed conformation in the chromosome, we propose that these densities establish the boundaries in the different chromosomal loci investigated; these boundaries are in good agreement with the extremes found in plasmids.     

The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain.

The hflA (high frequency of lysogenization) locus of Escherichia coli governs the lysis-lysogeny decision of bacteriophage lambda by controlling stability of the phage cII protein. hflA contains three genes, hflX, hflK, and hflC, encoding polypeptides of 50, 46, and 37 kDa, respectively. We have determined the nucleotide sequence of 3843 base pairs containing hflA and have found three large open reading frames corresponding to hflX, hflK, and hflC. HflX contains the three sequence motifs typical of GTP-binding proteins and appears to be a member of a distinct family of putative GTPases. HflC and HflK appear to be integral membrane proteins which show some similarity to each other and to a human membrane protein. The C-terminal region of HflC contains a domain resembling the catalytic domain of ClpP, a bacterial ATP-dependent protease. We hypothesize that HflK and HflC constitute a distinct membrane-bound protease whose activity may be modulated by HflX GTPase.     

Escherichia coli contains a soluble ATP-dependent protease (Ti) distinct from protease La.

The energy requirement for protein breakdown in Escherichia coli has generally been attributed to the ATP-dependence of protease La, the lon gene product. We have partially purified another ATP-dependent protease from lon-cells that lack protease La (as shown by immunoblotting). This enzyme hydrolyzes [3H]methyl-casein to acid-soluble products in the presence of ATP and Mg2+. ATP hydrolysis appears necessary for proteolytic activity. Since this enzyme is inhibited by diisopropyl fluorophosphate, it appears to be a serine protease, but it also contains essential thiol residues. We propose to name this enzyme protease Ti. It differs from protease La in nucleotide specificity, inhibitor sensitivity, and subunit composition. On gel filtration, protease Ti has an apparent molecular weight of 370,000. It can be fractionated by phosphocellulose chromatography or by DEAE chromatography into two components with apparent molecular weights of 260,000 and 140,000. When separated, they do not show proteolytic activity. One of these components, by itself, has ATPase activity and is labile in the absence of ATP. The other contains the diisopropyl fluorophosphate-sensitive proteolytic site. These results and the similar findings of Katayama-Fujimura et al. [Katayama-Fujimura, Y., Gottesman, S. & Maurizi, M. R. (1987) J. Biol. Chem. 262, 4477-4485] indicate that E. coli contains two ATP-hydrolyzing proteases, which differ in many biochemical features and probably in their physiological roles.     

Terminus region of the chromosome in Escherichia coli inhibits replication forks.

Induction of prophage P2sig5 at 42 degrees caused replication of the bacterial chromosome in a dnaA mutant of Escherichia coli. The P2sig5 is integrated in this strain near the metG locus, which is at min 47 on the genetic map. The regions of the chromosome replicated after prophage induction have been determined by means of DNA-DNA hybridization with various DNAs obtained from Proteus mirabilis/E. coli F' merogenotes and from lambda specialized transducing phage. The replication was initiated at the prophage site and was bidirectional. Most of the replication occurred in a counterclockwise direction on the genetic map, and the replication quickly proceeded to the aroD locus (min 37). The replication forks were retarded between aroD and rac (min 31) loci, although the rac locus was finally replicated. A more severe inhibition of replication occurred between the rac and trp (min 27) loci. It is proposed that the replication terminus is near the rac locus and that the terminus inhibits replication forks.     

Escherichia coli ribosomal protein S1 has two polynucleotide binding sites.

The interaction of Escherichia coli ribosomal protein S1 with a variety of RNA and DNA oligomers and polymers has been studied, using both a sedimentation technique and the quenching of intrinsic protein fluorescence upon nucleic acid binding to obtain equilibrium binding parameters. Two polynucleotide binding sites have been detected on S1: site I binds either single-stranded DNA or RNA and does not discriminate between adenine- and cytidine-containing polynucleotides, while the II binding is highly specific for RNA over DNA and shows a marked preference for cytidine polynucleotides over the corresponding adenine-containing species. On the basis of the binding properties of S1 to denatured DNA cellulose and poly(rC)-cellulose, it is demonstrated that every S1 molecule carries both a site I and a site II. Some possible implications of these results for mechanisms of protein synthesis and phage Qbeta replication are briefly considered.     

Membrane attachment activates dnaA protein, the initiation protein of chromosome replication in Escherichia coli.

ADP and ATP are tightly bound to dnaA protein and are crucial to its function in DNA replication; the exchange of these nucleotides is effected specifically by the acidic phospholipids (cardiolipin and phosphatidylglycerol) present in Escherichia coli membranes [Sekimizu, K. & Kornberg, A. (1988) J. Biol. Chem. 263, 7131-7135]. We now find that phospholipids derived from membranes lacking an unsaturated fatty acid (e.g., oleic acid) are unable to promote the exchange. This observation correlates strikingly with the long-known effect of 3-decynoyl-N-acetylcysteamine, a "suicide analog" that prevents initiation of a cycle of replication in E. coli by inhibiting the synthesis of oleic acid, an inhibition that can be overcome by providing the cells with oleic acid. Profound influences on the specific binding of dnaA protein to phospholipids by temperature, the content of unsaturated fatty acids, and the inclusion of cholesterol can be explained by the need for the phospholipids to be in fluid-phase vesicles. These findings suggest that membrane attachment of dnaA protein is vital for its function in the initiation of chromosome replication in E. coli.     

Translation of RNA that contains polyadenylate from yeast mitochondria in an Escherichia coli ribosomal system.

RNA that contains poly(A) [poly(A)-RNA] has been isolated from yeast mitochondria by poly(U) Sepharose-4B column chromatography. Pulse-labeled poly(A)-RNA shows 8-10 discrete peaks by acrylamide gel electrophoresis. The specific activity of mitochondrial poly(A)-RAN is six to eight times greater than that of mitochondrial rRNA after pulse labeling of protoplasts with [3H-]uridine. Ethidium bromide inhibits incorporation by over 90%. The total mitochondrial RNA preparation was contaminated with 5-15% cytoplasmic rRNA as determined by gel electrophoresis, but RNA exhaustion hybridization experiments indicated little or no cytoplasmic contamination of the mitochondrial poly(A)-RNA. The poly(A)-RNA stimulates [3H]leucine incorporation into protein in an E. coli cell-free system. A fraction of the labeled product is precipitated with antibody directed toward yeast cytochrome oxidase, but not with antibody directed toward bovine serum albumin. Sodium dodecyl sulfate gel electrophoresis of the immunoprecipitated material reveals labeled peptides having the mobility of the three larger cytochrome oxidase peptides, which are known to be translated by mitochondrial ribosomes.     

Protein engineering of antibody binding sites: recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli.

A biosynthetic antibody binding site, which incorporated the variable domains of anti-digoxin monoclonal antibody 26-10 in a single polypeptide chain (Mr = 26,354), was produced in Escherichia coli by protein engineering. This variable region fragment (Fv) analogue comprised the 26-10 heavy- and light-chain variable regions (VH and VL) connected by a 15-amino acid linker to form a single-chain Fv (sFv). The sFv was designed as a prolyl-VH-(linker)-VL sequence of 248 amino acids. A 744-base-pair DNA sequence corresponding to this sFv protein was derived by using an E. coli codon preference, and the sFv gene was assembled starting from synthetic oligonucleotides. The sFv polypeptide was expressed as a fusion protein in E. coli, using a leader derived from the trp LE sequence. The sFv protein was obtained by acid cleavage of the unique Asp-Pro peptide bond engineered at the junction of leader and sFv in the fusion protein [(leader)-Asp-Pro-VH-(linker)-VL]. After isolation and renaturation, folded sFv displayed specificity for digoxin and related cardiac glycosides similar to that of natural 26-10 Fab fragments. Binding between affinity-purified sFv and digoxin exhibited an association constant [Ka = (3.2 +/- 0.9) x 10(7) M-1] that was about a factor of 6 smaller than that found for 26-10 Fab fragments [Ka = (1.9 +/- 0.2) x 10(8) M-1] under the same buffer conditions, consisting of 0.01 M sodium acetate, pH 5.5/0.25 M urea.     

The PapG adhesin of uropathogenic Escherichia coli contains separate regions for receptor binding and for the incorporation into the pilus.

Most uropathogenic strains of Escherichia coli produce heteropolymeric organelles, known as P pili, that bind to the globoseries of glycolipids present in the urinary tract. The formation of a P pilus is the result of a family of related proteins being coordinately assembled into the structure in a defined order with the adhesin located exclusively at the tip. The preassembled digalactoside alpha-D-galactopyranosyl-(1----4)-beta-D-galactopyranose-binding adhesin was purified to homogeneity from the periplasmic space in a complex with the periplasmic assembly protein PapD by affinity chromatography to alpha-D-galactopyranosyl-(1----4)-beta-D-galactopyranose-Sepharose. A receptor-binding domain was mapped to the amino-terminal half of the adhesin. The interaction of PapD with PapG, which was required for the incorporation of the adhesin into the pilus, was found to protect PapG from proteolytic cleavages and enhanced the processing of the PapG signal peptide. A preassembly domain necessary for forming a complex with PapD was mapped to the carboxyl terminus of PapG.     

Incompatibility of plasmids containing the replication origin of the Escherichia coli chromosome.

Plasmids containing the replication origin of the Escherichia coli chromosome (oriC plasmids) are unstable in certain recA strains of E. coli. However, they can be maintained more stably in other recA strains. This stable maintenance has allowed us to study the incompatibility properties of oriC plasmids. We have found that two oriC plasmids are incompatible: they cannot be stably coinherited in individual dividing cells. An oriC plasmid is excluded from growing bacteria at a much faster rate in the presence of a hybrid plasmid made from an oriC plasmid and a high-copy-number vector plasmid than in the presence of another oriC plasmid. By inserting various segments around the oriC region into high-copy-number vectors, we have shown that two different regions in the vicinity of the oriC region determine incompatibility. One region, which we named incA, includes the region essential for autonomous replication of the oriC plasmid. The other, incB, is adjacent to incA but is not required for autonomous replication.