Finding a basis for flipping bases

Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ('base flipping') was first observed in the structure of a DNA methyltransferase. There is now evidence that a variety of proteins use base flipping in their interactions with DNA. Though the mechanism for base flipping is still unclear, we propose a three-step pathway: recognizing the target site and increasing the interstrand phosphate-phosphate distance nearby, initiating base flipping by protein invasion of the DNA, and trapping the flipped DNA structure.

Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis

Restriction endonuclease PvuII plays a central role in restriction fragment length polymorphism analysis of Mycobacterium tuberculosis complex isolates with IS6110 as a genetic marker. We have investigated the basis for an apparent dichotomy in PvuII restriction fragment pattersn observed among strains of the M. tuberculosis complex. The chromosomal regions of two modified PvuII restriction sites, located upstream of the katG gene and downstream of an IS1081 insertion sequence, were studied in more detail. An identical 10-bp DNA sequence (CAGCTGGAGC) containing a PvuII site was found in both regions, and site-directed mutagenesis analysis revealed that this sequence was a target for modification. Strain-specific modification of PvuII sites was identified in DNA from over 80% of the nearly 800 isolates examined. Furthermore, the proportion of modifying and nonmodifying strains differs significantly from country to country.

Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes

Previous X-ray crystallographic studies have revealed that the catalytic domain of a DNA methyltransferase (Mtase) generating C5-methylcytosine bears a striking structural similarity to that of a Mtase generating N6-methyladenine. Guided by this common structure, we performed a multiple sequence alignment of 42 amino-Mtases (N6-adenine and N4-cytosine). This comparison revealed nine conserved motifs, corresponding to the motifs I to VIII and X previously defined in C5-cytosine Mtases. The amino and C5-cytosine Mtases thus appear to be more closely related than has been appreciated. The amino Mtases could be divided into three groups, based on the sequential order of motifs, and this variation in order may explain why only two motifs were previously recognized in the amino Mtases. The Mtases grouped in this way show several other group-specific properties, including differences in amino acid sequence, molecular mass and DNA sequence specificity. Surprisingly, the N4-cytosine and N6-adenine Mtases do not form separate groups. These results have implications for the catalytic mechanisms, evolution and diversification of this family of enzymes. Furthermore, a comparative analysis of the S-adenosyl-L-methionine and adenine/cytosine binding pockets suggests that, structurally and functionally, they are remarkably similar to one another.

Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association

The PvuII restriction-modification system has been found to contain three genes which code for a DNA methyltransferase (MTase), a restriction endonuclease (ENase) and a small protein required for expression of the ENase-encoding gene. In addition, there is a small open reading frame (ORF) within and opposite to the MTase-encoding gene. The region containing this ORF is transcribed, and the ORF has an excellent Shine-Dalgarno sequence with an ATA start codon. A closely related ORF is present in the SmaI system. The 28-amino-acid (aa) predicted peptide from the PvuII ORF resembles a region of the PvuII ENase at the dimer interface. We have cloned this ORF, giving it an ATG start codon and putting it under the control of an inducible promoter: induction leads to a slight but significant decrease in restriction of bacteriophage lambda. We also have obtained the 28-aa synthetic peptide, and are exploring the possibility that it modulates ENase subunit association. While this peptide has no detectable effect on dimeric PvuII ENase, it inhibits renaturation of urea-denatured ENase in a concentration-dependent manner. The ORF may represent an additional safeguard during establishment of the PvuII restriction-modification system in a new host cell, helping to delay the appearance of active ENase dimers, while the MTase accumulates and protects the host chromosome.

Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system

Plasmid pPvu1 from Proteus vulgaris carries the genes of the PvuII restriction-modification system [Blumenthal et al., J. Bacteriol. 164 (1985) 501-509]. This report focuses on physical and functional features of the 4.84-kb plasmid, which shows a composite genetic architecture. Plasmid pPvu1 has a replication origin and an incompatibility locus that each function in Escherichia coli, and an apparent cer recombination site. The replication origin includes a possible RNA I gene, and the incompatibility locus closely resembles a rom gene. These loci show substantial sequence similarity to corresponding loci from the E. coli plasmids P15A, ColEI and pSC101, and closely flank the PvuII genes. The close association between a recombinational locus and the PvuII genes has implications for their mobility.

The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF

The two major porins of Escherichia coli K-12 strains, OmpC and OmpF, are inversely regulated with respect to one another. The expression of OmpC and OmpF has been shown to be influenced by the leucine-responsive regulatory protein (Lrp): two-dimensional gel electrophoresis of proteins from strains with and strains without a functional Lrp protein revealed that OmpC expression is increased in an lrp strain, while OmpF expression is decreased. In agreement with these findings, we now present evidence that transcriptional (operon) fusions of lacZ+ to ompC and micF are negatively regulated by Lrp. Lrp binds specifically to the intergenic region between micF and ompC, as indicated by mobility shift assays and by DNase I footprinting. The expression of an ompF'-lacZ+ gene (translational) fusion is increased 3.7-fold in an lrp+ background compared with an lrp background, but expression of an ompF-lacZ+ operon fusion is not. Studies of in vivo expression of the outer membrane porins during growth on glucose minimal medium showed that the OmpF/OmpC ratio is higher in lrp+ strains than it is in isogenic lrp strains. The effect of Lrp was not seen in a strain containing a deletion of micF. Our studies suggest that the positive effect of Lrp on OmpF expression stems from a negative effect of Lrp on the expression of micF, an antisense RNA that inhibits ompF translation.

Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein?

The regulon controlled by the leucine-responsive regulatory protein (Lrp) of Escherichia coli consists of over 40 genes and proteins whose expression is regulated, either positively or negatively, by Lrp. The gltBDF operon, encoding glutamate synthase, was originally identified as a member of the Lrp regulon through a two-dimensional electrophoretic analysis of polypeptides from isogenic strains containing or lacking a functional Lrp protein. We have now demonstrated that Lrp regulates the transcription of gltBDF::lacZ operon fusions. Relative to expression in glucose minimal 3-(N-morpholino)propanesulfonic acid (MOPS) medium, gltBDF::lacZ expression in an lrp+ strain is repressed 2.2-fold in the presence of 10 mM exogenous leucine and 16-fold in Luria broth. Repression of gltBDF::lacZ expression by leucine or Luria broth is not seen for an isogenic strain containing a Tn10 insertion in lrp, and expression of gltBDF::lacZ is 44-fold lower than in the lrp+ strain when both are grown in glucose minimal MOPS medium. Lrp binds specifically to DNA fragments containing the gltBDF promoter region. Saturating levels of leucine do not abolish binding of Lrp upstream of gltBDF but merely increase its apparent dissociation constant from 2.0 to 6.9 nM. Electrophoretic analysis of the Lrp regulon established that target proteins differ greatly in the degree to which the effect of Lrp on their expression is antagonized by leucine. On the basis of our present results, we present a model for positive regulation of target genes by Lrp. Insensitivity to leucine would be expected when the effective intracellular concentration of Lrp is high relative to the affinity of Lrp binding sites required for transcription of the target gene. At lower concentrations of Lrp, transcription of the target gene should be sensitive to leucine. This model suggests that regulation of the concentration of active Lrp is critical to control of the Lrp regulon.

Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli

Cobalamin-dependent methionine synthase catalyzes methyl group transfer from methyltetrahydrofolate to homocysteine to form tetrahydrofolate and methionine, and the cobalamin prosthetic group serves as an intermediate methyl carrier. Enzyme possessing cobalamin in the cobalt(II) oxidation state is inactive, and this form is activated by one-electron reduction coupled to methylation by S-adenosylmethionine (AdoMet). The enzyme from Escherichia coli has been divided into separable fragments by limited proteolysis with trypsin, and the contribution of each of these fragments to substrate binding and catalysis has been evaluated. The 37.7-kDa carboxyl-terminal domain binds AdoMet, and this was demonstrated through covalent modification with radiolabeled AdoMet during ultraviolet irradiation. Following reductive activation with AdoMet, the enzyme was digested with trypsin and a 98.4-kDa amino-terminal fragment was isolated. It retained at least 70% of the activity of the intact enzyme and must therefore possess determinants sufficient for the binding of methyltetrahydrofolate and homocysteine, as well as residues required for catalysis. However, when the cobalamin was oxidized to the cob(II) alamin state, the 98.4-kDa fragment could not be reductively remethylated with AdoMet. A purified, 28-kDa domain within the 98.4-kDa fragment retained bound cobalamin and therefore must play a central role in catalysis, but the isolated 28-kDa domain retained no catalytic activity. Because AdoMet binds to a different domain of the protein than methyltetrahydrofolate and homocysteine, the enzyme probably uses conformational flexibility to allow the cobalamin access to the required methyl donor or acceptor at the appropriate time in catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)

The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region

The DNA methyltransferase of the AluI restriction-modification system, from Arthrobacter luteus, converts cytosine to 5-methylcytosine in the sequence AGCT. The gene for this methyltransferase, aluIM, was cloned into Escherichia coli and sequenced. A 525-codon open reading frame was found, consistent with deletion evidence, and the deduced amino acid sequence revealed all ten conserved regions common to 5-methylcytosine methyltransferases. The aluIM sequence predicts a protein of M(r) 59.0k, in agreement with the observed M(r), making M.AluI the largest known methyltransferase from a type II restriction-modification system. M.AluI also contains the largest known variable region of any monospecific DNA methyltransferase, larger than that of most multispecific methyltransferases. In other DNA methyltransferases the variable region has been implicated as the sequence-specific target recognition domain. An in-frame deletion that removes a third of this putative target-recognition region leaves the Alu I methyltransferase still fully active.

Analysis of macromolecular biosynthesis to define the quinolone-induced postantibiotic effect in Escherichia coli

Quinolones inhibit DNA gyrase, and the major effects of this inhibition are on replication and transcription of DNA. The postantibiotic effect (PAE) refers to continued inhibition of cell division, in terms of the viable count, following transient exposure to an antibiotic. Previous work has shown that quinolone-treated cells have not fully recovered by the time the classically defined PAE has ended. We describe the PAE of the quinolones CI-960, enoxacin, and ciprofloxacin on macromolecular biosynthesis in the clinical isolate Escherichia coli J96 in an attempt to relate the PAE to the time that it actually takes for the cells to recover fully. DNA synthesis was inhibited immediately upon exposure to these quinolones at 0.5x or 0.75x the MIC. This inhibition continued for several hours following quinolone removal. The effects of these quinolones on RNA and protein synthesis varied; enoxacin treatment at 0.5x the MIC resulted in an increase of over 60% in both RNA and protein synthesis per unit of cell mass, while ciprofloxacin and CI-960 at that level had no significant effects on either RNA or protein synthesis. The effects of enoxacin and ciprofloxacin on bacterial protein profiles were also distinguishable, and these changes corresponded to their PAE on DNA synthesis. Throughout the study, all measures of the physiological status of the cells returned to normal by the time DNA synthesis per unit of cell mass did so. These results suggest that DNA synthesis per unit of cell mass provides an accurate measure of the time required for quinolone-treated cells to recover fully.

Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene

An open reading frame partially overlaps pvuIIR, and genetic evidence implies that this open reading frame, named pvuIIC, specifies a positive regulator of pvuIIR (T. Tao, J. C. Bourne, and R. M. Blumenthal, J. Bacteriol. 173:1367-1375, 1991). Inducible constructs of pvuIIC produced a protein of the expected size. The site of C.PvuII action appears to lie within pvuIIC itself; thus, pvuIIC may be a self-contained regulatory cassette.

Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II

The base sequence of the pvuIIM gene has been determined. This gene codes for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. The base sequence contains a single large open reading frame that predicts a 38.3kDa polypeptide, consistent with experimental data. The pvuIIM gene contains some sequences common to DNA methyltransferases in general, but includes none of the sequences specifically conserved among DNA-(cytosine 5)-methyltransferases. The pvuIIM sequence also reveals an internal homology at the amino acid level, each half of which spans over 100 amino acids and is itself homologous to the sequences of some DNA-(adenine N6)-methyltransferases. A derivative of the pvuIIM plasmid was constructed to allow high-level production of M.Pvu II. Specifically, the composite Ptac promoter was inserted 5' to pvuIIM, intervening DNA was deleted, and the resulting construct was used to transform an mcrB laclq strain of Escherichia coli. When this transformant was induced with isopropyl-B-D-galactopyranoside (IPTG), growth rapidly ceased and M.Pvu II accumulated to the point of comprising over 10% of the total soluble protein.

Isolation of mutants in a DNA methyltransferase through mcrB-mediated restriction

A procedure has been developed that permits the positive selection of mutants in a DNA methyltransferase (MTase) gene. The stringency of this selection can be varied so as to yield null mutants only, or a mixture of null and partially defective mutants. The procedure was developed with the PvuII MTase gene (pvuIIM), which was subcloned into a bacteriophage lambda vector. Growth of this lambda pvuIIM construct on an mcrB+ host selected for non-methylating mutants, and the stringency of selection was proportional to the number of consecutive lytic cycles. Many cytosine MTases have been found to generate substrates for mcrB-mediated restriction, and this procedure should be applicable to a number of cytosine MTase genes.

McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning

The McrA and McrB (modified cytosine restriction) systems of E. coli interfere with incoming DNA containing methylcytosine. DNA from many organisms, including all mammalian and plant DNA, is expected to be sensitive, and this could interfere with cloning experiments. The McrA and B phenotypes of a few strains have been reported previously (1-4). The Mcr phenotypes of 94 strains, primarily derived from E. coli K12, are tabulated here. We briefly review some evidence suggesting that McrB restriction of mouse-modified DNA does occur in vivo and does in fact interfere with cloning of specific mouse sequences.

Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli

A 4.84-kilobase-pair plasmid was isolated from Proteus vulgaris (ATCC 13315) and cloned into the plasmid vector pBR322. Plasmid pBR322 contains substrate sites for the restriction endonucleases PvuI and PvuII. The recombinant plasmids were resistant to in vitro cleavage by PvuII but not PvuI endonuclease and were found to cause production of PvuII endonuclease or methylase activity or both in Escherichia coli HB101. The approximate endonuclease and methylase gene boundaries were determined through subcloning, Bal 31 resection, insertional inactivation, DNA-dependent translation, and partial DNA sequencing. The two genes are adjacent and appear to be divergently transcribed. Most E. coli strains tested were poorly transformed by the recombinant plasmids, and this was shown by subcloning and insertional inactivation to be due to the PvuII methylase gene. At a low frequency, stable methylase-producing transformants of a methylase-sensitive strain were obtained, and efficiently transformed cell mutants were isolated from them.

Occurrence and expression of imipemide (N-formimidoyl thienamycin) resistance in clinical isolates of coagulase-negative staphylococci

More than 500 clinical isolates were screened for resistance to a number of antibiotics, including imipemide (N-formimidoyl thienamycin [MK0787]). Of the 25 coagulase-negative staphylococcal isolates present in the screening sample, almost one-third showed one of two patterns of imipemide resistance. One pattern apparently involves constitutive expression of drug resistance, whereas the other pattern seems to result from an inducible resistance having an apparent induction threshold higher than the minimal inhibitory concentration of imipemide. The mechanism(s) responsible for this imipemide resistance is unclear, but may be distinct from the more common staphylococcal mechanisms of resistance to beta-lactam antibiotics. Only two of the patients from whom imipemide-resistant staphylococci were cultured had actually been treated with the antibiotic.

The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene

The E. coli dam (DNA adenine methylase) enzyme is known to methylate the sequence GATC. A general method for cloning sequence-specific DNA methylase genes was used to isolate the dam gene on a 1.14 kb fragment, inserted in the plasmid vector pBR322. Subsequent restriction mapping and subcloning experiments established a set of approximate boundaries of the gene. The nucleotide sequence of the dam gene was determined, and analysis of that sequence revealed a unique open reading frame which corresponded in length to that necessary to code for a protein the size of dam. Amino acid composition derived from this sequence corresponds closely to the amino acid composition of the purified dam protein. Enzymatic and DNA:DNA hybridization methods were used to investigate the possible presence of dam genes in a variety of prokaryotic organisms.

Computer programs for nucleic acid sequence manipulation

Computer programs are described which help during the collection and analysis of nucleic acid sequence data. They are written in FORTRAN and have been implemented on a PDP 11/60 computer.

Proteins Specified by bovine herpesvirus 1 (infectious bovine rhinotracheitis virus)

An electrophoretic analysis of radioactively labeled, purified, "empty" and DNA-containing infectious bovine rhinotracheitis virions revealed the presence of 25 to 33 structural (virion) polypeptides. A total of 11 of these polypeptides could be labeled with [3H]glucosamine and were identified as glycoproteins. In addition to the 25 structural polypeptides, infectious bovine rhinotracheitis virus infected cells also contained at least 15 nonstructural (nonvirion) polypeptides that were not present in purified virions. Expression of the viral polypeptides in infected cells was controlled temporally. Thus, most viral polypeptides could be categorized as "alpha" (immediate early), "beta" (early), or "gamma" (late) on the basis of their order of appearance in infected cells and whether their syntheses were dependent upon prior viral protein or DNA synthesis. None of the glycoproteins belongs to the alpha class, although at least one (GVP11) was synthesized in the absence of viral DNA synthesis. Serum from a cow in which infectious bovine rhinotracheitis virus lesions were reactivated by dexamethasone precipitated both structural and nonstructural polypeptides.

Regulation of ribonucleic acid polymerase synthesis during restriction of an Escherichia coli mutant temperature sensitive for transcription factor sigma

An Escherichia coli mutant temperature sensitive for the sigma subunit of ribonucleic acid polymerase was shifted to restrictive temperatures. In response to these restrictions the transcription of rpoBC increased markedly, and the synthesis rates of the beta and beta' subunits of ribonucleic acid polymerase increased. The ratio of the beta and beta' synthesis rates (beta/beta') decreased.