Plasmid transformation of Escherichia coli and other bacteria

Resistance to quaternary ammonium compounds in Staphylococcus spp. isolated from the food industry and nucleotide sequence of the resistance plasmid pST827

The complete nucleotide sequence of the 2.8 kb plasmid pST827 involved in resistance to the quaternary ammonium compound (QAC) benzalkonium chloride in meat-associated staphylococci was determined. An open reading frame (ORF) similar to the QAC resistance genes qacC, ebr and smr previously reported from clinical staphylococcal strains was identified (qacC'). In addition an ORF coding for a protein (Rep827) showing extensive homology to reported replication proteins of Gram-positive organisms was found. The occurrence of known QAC resistance gene (qacA-C) among staphylococcal strains isolated from food processing plants was studied by hybridization analysis. Of 191 isolates, 25 were resistant to benzalkonium chloride. Five of these gave no hybridization signals to probes specific for qacA-C. Further hybridization analysis indicated that pST827 or closely related plasmids are widespread among QAC-resistant staphylococcal strains. The finding of resistant staphylococci in different areas of the food processing industry indicates that QAC resistance is a potential problem in the food processing industry.

Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo

A total of 5 conventional, directionally cloned plasmid cDNA libraries have been constructed from the entire embryonic region of the mid-gastrulation mouse embryo and from its four principal tissue constituents (ectoderm, mesoderm, endoderm and primitive streak). These libraries have been validated with respect to the number of independent clones, insert-size and appropriate representation of diagnostic marker genes. Subtractive hybridisation has been used to remove clones common to the Endoderm and Mesoderm cDNA libraries resulting in an Endoderm minus Mesoderm subtracted library. Probe prepared from this subtracted library has been hybridised to a grid containing approximately 18,500 Embryonic Region library clones. Three novel clones have been recovered as well as expected genes already known to be highly expressed in the primitive endoderm lineage at this stage of development. In situ hybridisation to early postimplantation embryos has revealed the expression patterns of these novel genes. One is highly expressed exclusively in visceral endoderm, one is expressed in ectodermal and endodermal tissues, and the third proves to be an early marker of prospective and differentiated surface ectoderm as well as being expressed in endoderm and its derivatives.

The gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae

We report the isolation, genomic mapping, and DNA sequence of the BPL1 gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae. The gene was isolated by complementation of an Escherichia coli birA (biotin-apoprotein ligase) mutant indicating that the expressed yeast protein modified the essential biotinated protein of the bacterial host. The BPL1 gene encodes a protein of 690 residues (M(r) 76.4 kDa) with strong sequence similarities to the E. coli and human biotin-apoprotein ligases. BPL1 was mapped to chromosome IV, is allelic to the previously described ACC2 gene, and encodes the major (if not the only) biotin-apoprotein ligase activity of S. cerevisiae.

Transformation of Escherichia coli with large DNA molecules by electroporation

We have examined bacterial electroporation with a specific interest in the transformation of large DNA, i.e. molecules > 100 kb. We have used DNA from bacterial artificial chromosomes (BACs) ranging from 7 to 240 kb, as well as BAC ligation mixes containing a range o different sized molecules. The efficiency of electroporation with large DNA is strongly dependent on the strain of Escherichia coli used; strains which offer comparable efficiencies for 7 kb molecules differ in their uptake of 240 kb DNA by as much as 30-fold. Even with a host strain that transforms relatively well with large DNA, transformation efficiency drops dramatically with increasing size of the DNA. Molecules of 240 kb transform approximately 30-fold less well, on a molar basis, than molecules of 80 kb. Maximum transformation of large DNA occurs with different voltage gradients and with different time constants than are optimal for smaller DNA. This provides the opportunity to increase the yield of transformants which have taken up large DNA relative to the number incorporating smaller molecules. We have demonstrated that conditions may be selected which increase the average size of BAC clones generated by electroporation and compare the overall efficiency of each of the conditions tested.

Conversion of Xenopus ectoderm into neurons by NeuroD, a basic helix-loop-helix protein

Basic helix-loop-helix (bHLH) proteins are instrumental in determining cell type during development. A bHLH protein, termed NeuroD, for neurogenic differentiation, has now been identified as a differentiation factor for neurogenesis because (i) it is expressed transiently in a subset of neurons in the central and peripheral nervous systems at the time of their terminal differentiation into mature neurons and (ii) ectopic expression of neuroD in Xenopus embryos causes premature differentiation of neuronal precursors. Furthermore, neuroD can convert presumptive epidermal cells into neurons and also act as a neuronal determination gene. However, unlike another previously identified proneural gene (XASH-3), neuroD seems competent to bypass the normal inhibitory influences that usually prevent neurogenesis in ventral and lateral ectoderm and is capable of converting most of the embryonic ectoderm into neurons. The data suggest that neuroD may participate in the terminal differentiation step during vertebrate neuronal development.

Genes that protect against the host-killing activity of the E3 protein of Bacillus subtilis bacteriophage SPO1

A cloned rpoB gene, specifying an apparently mutant RNA polymerase beta subunit, protected Escherichia coli against the cytocidal effects of the E3 protein of bacteriophage SPO1, suggesting that RNA polymerase is the primary cellular target of the E3 protein. Two segments of the wild-type E. coli genome, one of which specifies a suppressor of dnaK mutations, and thus, possibly, a molecular chaperone, also provided protection when overexpressed, but wild-type rpoB did not.

Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis

One step in de novo pyridoxine (vitamin B6) and pyridoxal 5'-phosphate biosynthesis was predicted to be an oxidation catalyzed by an unidentified D-erythrose-4-phosphate dehydrogenase (E4PDH). To help identify this E4PDH, we purified the Escherichia coli K-12 gapA- and gapB-encoded dehydrogenases to homogeneity and tested whether either uses D-erythrose-4-phosphate (E4P) as a substrate. gapA (gap1) encodes the major D-glyceraldehyde-3-phosphate dehydrogenase (GA3PDH). The function of gapB (gap2) is unknown, although it was suggested that gapB encodes a second form of GA3PDH or is a cryptic gene. We found that the gapB-encoded enzyme is indeed an E4PDH and not a second GA3PDH, whereas gapA-encoded GA3PDH used E4P poorly, if at all, as a substrate under the in vitro reaction conditions used in this study. The amino terminus of purified E4PDH matched the sequence predicted from the gapB DNA sequence. Purified E4PDH was a heat-stable tetramer with a native molecular mass of 132 kDa. E4PDH had an apparent Km value for E4P [Kmapp(E4P)] of 0.96 mM, an apparent kcat catalytic constant for E4P [kcatapp(E4P)] of 200 s-1, Kmapp(NAD+) of 0.074 mM, and kcatapp(NAD+) of 169 s-1 in steady-state reactions in which NADH formation was determined. From specific activities in crude extracts, we estimated that there are at least 940 E4PDH tetramer molecules per bacterium growing in minimal salts medium plus glucose at 37 degrees C. Thin-layer chromatography confirmed that the product of the E4PDH reaction was likely the aldonic acid 4-phosphoerythronate. To establish a possible role of E4PDH in pyridoxal 5'-phosphate biosynthesis, we showed that 4-phosphoerythronate is a likely substrate for the 2-hydroxy-acid dehydrogenase encoded by the pdxB gene. Implications of these findings in the evolution of GA3PDHs are also discussed. On the basis of these results, we propose renaming gapB as epd (for D-erythrose-4-phosphate dehydrogenase).

The genes involved in production of and immunity to sakacin A, a bacteriocin from Lactobacillus sake Lb706

Sakacin A is a small, heat-stable, antilisterial bacteriocin produced by Lactobacillus sake Lb706. The nucleotide sequence of a 8,668-bp fragment, shown to contain all information necessary for sakacin A production and immunity, was determined. The sequence revealed the presence of two divergently transcribed operons. The first encompassed the structural gene sapA (previously designated sakA) and saiA, which encoded a putative peptide of 90 amino acid residues. The second encompassed sapK (previously designated sakB), sapR, sapT, and sapE. sapK and sapR presumably encoded a histidine kinase and a response regulator with marked similarities to the AgrB/AgrA type of two-component signal-transducing systems. The putative SapT and SapE proteins shared similarity with the Escherichia coli hemolysin A-like signal sequence-independent transport systems. SapT was the HlyB analog with homology to bacterial ATP-binding cassette exporters implicated in bacteriocin transport. Frameshift mutations and deletion analyses showed that sapK and sapR were necessary for both production and immunity, whereas sapT and sapE were necessary for production but not for immunity. The putative SaiA peptide was shown to be involved in the immunity to sakacin A. The region between the operons contained IS1163, a recently described L. sake insertion element. IS1163 did not appear to be involved in expression of the sap genes. Northern (RNA) blot analysis revealed that the putative SapK/SapR system probably acts as a transcriptional activator on both operons. A 35-bp sequence, present upstream of the putative sapA promoter, and a similar sequence (30 of 35 nucleotides identical) upstream of sapK were shown to be necessary for proper expression and could thus be possible targets for transcriptional activation.

Use of a gene-targeted phage display random epitope library to map an antigenic determinant on the bluetongue virus outer capsid protein VP5

We describe the use of a gene-targeted random epitope library for the mapping of antigenic determinants. A DNA clone encoding the target antigen was digested randomly with DNase I to generate a population of DNA fragments of different sizes and sequences. After size fractionation, small DNA fragments (100-200 bp) were isolated and cloned into the phage expression vector fUSE2 to form an expression library displaying random polypeptide sequences as fusion proteins at the N terminus of the phage gene III protein. This library, termed a gene-targeted random epitope library to distinguish it from totally random synthetic epitope libraries, was then screened by affinity selection for recombinant phages which were specifically bound by the antibody of interest. Using this approach, we have mapped a monoclonal antibody (mAb)-defined epitope on the bluetongue virus outer capsid protein VP5. This epitope is not accessible on the intact virus surface, but is recognised by the immune system of sheep and cattle during virus infection. Although the example given here utilised a DNA fragment of known sequence and the library was screened for a mAb-defined epitope, the strategy described should be equally applicable to genes of unknown sequence and for screening of epitopes using polyclonal antibodies. The approach can also be extended to identify immunodominant epitope from much more complex genome-targeted random epitope library for virus, bacteria and eukaryotic organisms. Other applications of recombinant phages expressing defined immunodominant epitopes include serodiagnosis and vaccine development.

The site-specific recombination system regulating expression of the type 1 fimbrial subunit gene of Escherichia coli is sensitive to changes in DNA supercoiling

We have studied the effect of altering the in vivo level of DNA supercoiling on the phase-variable expression of the Escherichia coli fimA gene. Transcription from the fimA promoter was unaffected by changes in DNA supercoiling whether caused by the introduction of a topA::Tn10 mutation or by inhibition of DNA gyrase with the antibiotic novobiocin. However, inversion of the fimA promoter fragment was altered in response to perturbation of DNA supercoiling. Specifically, inactivation of topA reduced the rate of promoter fragment inversion in both the ON-to-OFF and the OFF-to-ON directions. This effect correlated with the loss of functional topA and not with the global level of DNA supercoiling. Inhibition of DNA gyrase introduced a bias in favour of the OFF-to-ON inversion; the ON-to-OFF inversion was affected only slightly. Changes in expression of fimB, the gene coding for the recombinase that catalyses fimA promoter fragment inversion in the strains used in this study, did not correlate with effects on fimA phase variation: we found that transcription of fimB was inhibited by loss of functional topA and was enhanced by inhibition of DNA gyrase in a manner that correlated well with the global level of in vivo DNA supercoiling. A model is presented to account for the effects of lost topoisomerase function on fimA gene expression.

Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor

The construction of representative large insert DNA libraries is critical for the analysis of complex genomes. The predominant vector system for such work is the yeast artificial chromosome (YAC) system. Despite the success of YACs, many problems have been described including: chimerism, tedious steps in library construction and low yields of YAC insert DNA. Recently a new E.coli based system has been developed, the bacterial artificial chromosome (BAC) system, which offers many potential advantages over YACs. We tested the BAC system in plants by constructing an ordered 13,440 clone sorghum BAC library. The library has a combined average insert size, from single and double size selections, of 157 kb. Sorghum inserts of up to 315 kb were isolated and shown to be stable when grown for over 100 generations in liquid media. No chimeric clones were detected as determined by fluorescence in situ hybridization of ten BAC clones to metaphase and interphase S.bicolor nuclei. The library was screened with six sorghum probes and three maize probes and all but one sorghum probe hybridized to at least one BAC clone in the library. To facilitate chromosome walking with the BAC system, methods were developed to isolate the proximal ends of restriction fragments inserted into the BAC vector and used to isolate both the left and right ends of six randomly selected BAC clones. These results demonstrate that the S. bicolor BAC library will be useful for several physical mapping and map-based cloning applications not only in sorghum but other related cereal genomes, such as maize. Furthermore, we conclude that the BAC system is suitable for most large genome applications, is more 'user friendly' than the YAC system, and will likely lead to rapid progress in cloning biologically significant genes from plants.

Detection and classification of mutagens: a set of base-specific Salmonella tester strains

A detection and classification system for mutagens has been developed that identifies the six possible base-pair substitution mutations. A set of six Salmonella typhimurium (TA7001 to TA7006) strains has been constructed, each of which carries a unique missense mutation in the histidine biosynthetic operon. In addition to the his mutation, these strains carry different auxiliary features that enhance the mutability of the target his mutation. These include the R factor pKM101, which has the SOS-inducible mucAB system; a deletion of the uvrB component of excision repair; and rfa mutations to increase the accessibility of bulky chemicals to the bacteria. Another set of strains (TA7041 to TA7046) contain a wild-type rfa gene. Reversion via the base substitution unique to each strain was verified by sequence analyses of > 800 revertants obtained from different types of mutagens. The strains have considerably lower spontaneous reversion frequencies and detect a variety of mutagens at a sensitivity comparable to the Salmonella tester strains TA100, TA102, and TA104. The low spontaneous frequency of reversion of a mixture of the six tester strains (approximately 10 revertants per plate) enables a single mutation assay with the mixture that is followed by classification of the type of mutation with the individual strains.

Isolation and 1H-NMR spectroscopic identification of poly(3-hydroxybutanoate) from prokaryotic and eukaryotic organisms. Determination of the absolute configuration (R) of the monomeric unit 3-hydroxybutanoic acid from Escherichia coli and spinach

Trace amounts of poly[(R)-3-hydroxybutanoate] were isolated from competent Escherichia coli, spinach, bovine serum albumin, beef heart mitochondria, and aortal tissues, all sources in which it is not accumulated as storage material. Its identity was in all cases proved by 1H-NMR spectroscopy. In some runs, the poly[(R)-3-hydroxybutanoate] isolated from competent E. coli also contained some 3-hydroxyvalerate, an observation confirmed by 1H-NMR spectroscopy and gas chromatography. The absolute configuration of the polymers isolated from E. coli and spinach was shown to be (all-R) by gas chromatography on chiral columns.

Systemic and mucosal immune responses in mice orally immunized with avirulent Salmonella typhimurium expressing a cloned Porphyromonas gingivalis hemagglutinin

Porphyromonas gingivalis produces a variety of virulence factors that may have a function in the periodontal disease process. Determination of the role of these various factors in pathogenesis and identification of a means for protecting the host from the destructive effects of this organism are areas of vigorous investigation. In this study we demonstrate the potential of avirulent Salmonella typhimurium strains to stimulate a specific systemic and mucosal immune response to a cloned P. gingivalis hemagglutinin (HagB). An avirulent strain of S. typhimurium, chi 4072, expressing the hagB gene of P. gingivalis 381 on the plasmid pDMD1 was intragastrically administered to BALB/c mice. These mice mounted a serum immunoglobulin G (IgG) and IgA primary response against the hagB gene product and a mucosal immune response as measured by evaluation of saliva. IgA antibodies were also detected in bile. These results demonstrate the feasibility of using attenuated S. typhimurium strains as carriers of P. gingivalis virulence factors for subsequent evaluation of the systemic and mucosal immune response against these antigens. This system will provide a means for evaluating the virulence factors of P. gingivalis for their suitability in the construction of potential vaccines.

The spv virulence operon of Salmonella typhimurium LT2 is regulated negatively by the cyclic AMP (cAMP)-cAMP receptor protein system

The cyclic AMP (cAMP) receptor protein (CRP) was found to play a role in the growth phase regulation of the spv operon on the high-molecular-weight virulence plasmid of Salmonella typhimurium LT2. By using a lacZ reporter transcriptional fusion to the spvB structural gene on the single-copy virulence plasmid, it was found that while spvB transcription was induced in stationary-phase cultures, the induced level of expression was lower than that reported for the spv system in other serovars of Salmonella. Surprisingly, inactivation of the gene encoding the positive activator SpvR resulted in only a threefold reduction in spvB transcription. In contrast, spvB transcription in stationary-phase cultures was enhanced by 10-fold in mutants deficient in crp-encoded CRP or cya-encoded adenylate cyclase. Wild-type (i.e., 10-fold-lower) levels of spvB expression were restored by providing active copies of crp or cya on recombinant plasmids. Enhanced spvB transcription was not seen in crp or cya mutants in the absence of a functional spvR positive regulatory gene, showing that the cAMP-CRP system acted on spvB expression either in conjunction with or via SpvR. A lacZ transcriptional fusion to spvR could not be induced in stationary-phase cultures in the absence of functional SpvR, regardless of the cAMP-CRP status of the cells. When SpvR was provided in trans, transcription of the spvR-lacZ fusion was induced to similar levels in stationary-phase cultures with and without cAMP-CRP. These data are consistent with spvR being poorly transcribed from the single-copy virulence plasmid in S. typhimurium LT2 and with a suppression of this defect via inactivation of the cAMP-CRP system. The physiological significance of cAMP-CRP involvement in spv expression is discussed.

A new bacteriophage P1-derived vector for the propagation of large human DNA fragments

We have designed a P1 vector (pCYPAC-1) for the introduction of recombinant DNA into E. coli using electroporation procedures. The new cloning system, P1-derived artificial chromosomes (PACs), was used to establish an initial 15,000 clone library with an average insert size of 130-150 kilobase pairs (kb). No chimaerism has been observed in 34 clones, by fluorescence in situ hybridization. Similarly, no insert instability has been observed after extended culturing, for 20 clones. We conclude that the PAC cloning system will be useful in the mapping and detailed analysis of complex genomes.

A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast

We report genetic and biochemical evidence that the RNA polymerase II carboxy-terminal domain (CTD) interacts with a large multisubunit complex that contains TATA-binding protein (TBP) and is an integral part of the transcription initiation complex. The isolation and characterization of extragenic suppressors of S. cerevisiae RNA polymerase II CTD truncation mutations led us to identify SRB2, SRB4, SRB5, and SRB6 as genes involved in CTD function in vivo. SRB2 was previously isolated and shown to encode a 23 kd TBP-binding protein. The four SRB proteins and a portion of cellular TBP are components of a high molecular weight multisubunit complex that is tightly bound to RNA polymerase II. This SRB-TBP complex binds specifically to recombinant CTD protein. In vitro transcription and template commitment assays confirm that SRB2 and SRB5 are components of a functional preinitiation complex and are required for efficient transcription initiation.

Molecular characterization of the 128-kDa immunodominant antigen of Helicobacter pylori associated with cytotoxicity and duodenal ulcer

Helicobacter pylori has been associated with gastritis, peptic ulcer, and gastric adenocarcinoma. We report the nucleotide sequence and expression of an immunodominant antigen of H. pylori and the immune response to the antigen during disease. The antigen, named CagA (cytotoxin-associated gene A), is a hydrophilic, surface-exposed protein of 128 kDa produced by most clinical isolates. The size of the cagA gene and its protein varies in different strains by a mechanism that involves duplication of regions within the gene. Clinical isolates that do not produce the antigen do not have the gene and are unable to produce an active vacuolating cytotoxin. An ELISA to detect the immune response against a recombinant fragment of this protein detects 75.3% of patients with gastroduodenal diseases and 100% of patients with duodenal ulcer (P < 0.0005), suggesting that only bacteria harboring this protein are associated with disease.

Genomic fingerprinting of "Haemophilus somnus" isolates by using a random-amplified polymorphic DNA assay

The random-amplified polymorphic DNA (RAPD) assay was used to generate DNA fingerprints for 16 isolates of "Haemophilus somnus," and one isolate each of "Haemophilus agni," "Histophilus ovis," "Actinobacillus seminis," Pasteurella haemolytica, and Escherichia coli. The RAPD assay differentiated among "H. somnus" isolates, which shared similarity coefficients of 0.46 to 1.00 on the basis of pairwise comparisons of RAPD markers produced with nine random decamer primers. Three virulent encephalitic "H. somnus" isolates exhibited identical banding patterns, suggesting a common clonal ancestry. The RAPD assay clearly distinguished between the "H. somnus"-"H. agni"-"H. ovis" group and the other bacterial species tested. The results of the present study suggest that DNA fingerprinting of "H. somnus" isolates by the RAPD assay could be valuable in revealing subspecific divisions within this largely unexplored species.

Turbo cloning: a fast, efficient method for cloning PCR products and other blunt-ended DNA fragments into plasmids

The method uses a novel plasmid vector, p9lox5, containing a site-specific recombination sequence lox from the lox/Cre recombinase system of bacteriophage P1. There are two distinct stages. Firstly, vector and fragment DNAs are ligated intermolecularly under conditions of macromolecular crowding (15% polyethylene glycol 6000) which accelerate blunt-end joining a thousandfold. Secondly, circular recombinant molecules are efficiently excised from the ligation products by Cre recombinase acting on pairs of lox sites within directly repeated vector molecules flanking insert DNA. Recombinants are introduced into cells conventionally by transformation or electroporation. In both a model system and the cloning of PCR products, yields approaching those obtainable in cohesive-end cloning were achieved. Applications of the technique to cDNA library generation and recovery of DNA from archive material are discussed.

Gene expression during preimplantation mouse development

To develop a resource for the identification and isolation of genes expressed in the early mammalian embryo, large and representative cDNA libraries were constructed from unfertilized eggs, and two-cell, eight-cell, and blastocyst-stage mouse embryos. Using these libraries, we now report the first stages at which the cytokines interleukin (IL)-6, IL-1 beta, and interferon (IFN)-gamma are transcribed in the developing embryo and the presence of IL-7 transcripts in the unfertilized egg. Transcripts for IL-1 alpha, -2, -3, -4, or -5 were not detected at these stages. To identify novel genes expressed on activation of the embryonic genome, the egg and eight-cell stage-specific cDNA libraries were subtracted from the two-cell library, yielding a specialized cDNA library enriched for transcripts expressed at the two-cell stage. Sequence and Southern blot analysis of several of these cDNAs expressed predominantly at the two-cell stage of embryogenesis revealed them to be from novel genes, thereby providing the first molecular tools with which to approach the study of gene expression in the early mammalian embryo.