Kenneth N. Timmis

Regulatory circuits controlling transcription of TOL plasmid operon encoding meta-cleavage pathway for degradation of alkylbenzoates by Pseudomonas

TOL plasmid PWWO of Pseudomonas putida contains two operons that specify a pathway for the degradation of aromatic hydrocarbons. The ‘upper’ operon encodes enzymes for the oxidation of toluene to benzoate and xylenes to toluates, whereas the meta‐cleavage operon specifies the further oxidation of benzoate and toluates. Transcription of the upper pathway operon (s positively regulated by the XylR protein, which is activated by toluene/xylenes and their alcohol catabolic products, in combination with the NtrA protein, a sigma factor. Expression of the meta‐operon is positively controlled by the XylS protein which is activated by meta‐pathway substrates, and is Independent of NtrA protein. Expression of the meta pathway is also Induced by toluene/xylene‐activated XylR protein via a cascade regulatory system in which this protein in combination with NtrA protein stimulates transcription from the xylS gene promoter. Hyper‐production of XylS protein in turn provokes high level expression of the meta‐operon, which is independent of meta‐pathway substrates. The two promoters, which are activated by the XylR and NtrA proteins, the upper pathway promoter and the xylS gene promoter, exhibit three regions of homology centred at –12(5′–TTGCTÃG–3′), –24(5′ ‐TGGCPuT –3) and –45(5′‐TTAAATÃGPuPuGCGPuTc‐3′), with respect to their principal transcription initiation points. The possible physiological significance of activated XylR‐protein‐induced expression of the meta‐operon through amplification of XylS protein levels is considered.

Cloning, nucleotide sequence, and expression of the gene encoding a novel dioxygenase involved in metabolism of carboxydiphenyl ethers in Pseudomonas pseudoalcaligenes POB310

Pseudomonas pseudoalcaligenes strain POB310 degrades 3-and 4-carboxydiphenyl ether. The initial reaction involves an angular dioxygenation yielding an unstable hemiacetal that spontaneously decays to phenol and protocatechuate. We cloned a DNA fragment containing the gene encoding the initial, dioxygenase from an unstable, self-transmissible plasmid. Sequence analysis revealed two open reading frames encoding proteins with putative molecular masses of 46.3 and 33.6 kDa. The deduced amino acid sequences showed homologies to oxygenase and reductase subunits of aromatic ring-activating dioxygenases, and contained regions identical to consensus sequences that bind chloroplast-like and Rieske-type [2Fe2S] clusters suggesting that the initial dioxygenase is a class IA aromatic ring-activating dioxygenase system. Intitial dioxygenase activity was induced in bacteria grown in M9 minimal medium containing 3-or 40-carboxydiphenyl ether or phenol as carbon source, indicating that the regulation is dependent on the phenol pathway. The maximal specific activity was measured at the beginning of the exponential growth phase.

Genetic analysis of a relaxed substrate specificity aromatic ring dioxygenase, toluate 1,2-dioxygenase, encoded by TOL plasmid pWW0 of Pseudomonas putida

SummaryToluate 1,2-dioxygenase is the first enzyme of a meta-cleavage pathway for the oxidative catabolism of benzoate and substituted benzoates to Krebs cycle intermediates that is specified by TOL plasmid pWW0 of Pseudomonas putida. A collection of derivatives harbouring Tn1000 insertions and defective in toluate dioxygenase have been isolated from pPL392, a pBR322-based hybrid plasmid carrying the TOL plasmid meta-cleavage pathway operon. In parallel, a series of N-methyl-N′-nitro-N-nitrosoguanidine-induced mutant plasmids defective in this enzyme activity were isolated from pNM72, a pKT231-based hybrid plasmid carrying the same operon. Pairs of mutant plasmids, consisting of one Tn1000 derivative and one nitrosoguanidine-induced derivative, were used for complementation analysis of toluate dioxygenase in Escherichia coli recA bacteria, in which the formation of 2-hydroxymuconic semialdehyde from benzoate was examined. Four cistrons for toluate 1,2-dioxygenase were thus identified. DNA fragments containing nitrosoguanidine-induced mutant cistrons plus the other meta-cleavage operon genes were cloned into pOT5, an R388-based vector, and complementation tests between different nitrosoguanidine-induced mutant cistrons were carried out in Pseudomonas putida cells, this time scoring for growth on p-toluate. This analysis also identified four cistrons. Examination of the products of these cistrons, by means of E. coli minicells containing pPL392 or its Tn1000 insertion derivatives, indicated that the first two cistrons of the operon comprise a single gene, xylX, which encodes a 57 kilodalton protein, and that the third cistron, xy/Y, encodes a 20 kilodalton protein.

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon

SummaryThe Pseudomonas putida TOL plasmid pWWO carries an operon that specifies a meta-cleavage pathway for the catabolism of benzoate and toluates whose transcription is positively regulated by the xylS gene product. Stimulation of transcription of the operon is thought to result from activation of this protein by pathway substrates/effectors. In the present study, overexpression of the xylS gene has led to identification of the regulator as a 33 kDa protein. Overexpression of xylS also resulted in partially constitutive, i.e. effector-independent expression of the meta-cleavage operon. Determination of the polynucleotide sequence of the xylS gene revealed amino acid sequence homology with several DNA binding proteins, particularly with the araC products of Escherichia coli and Salmonella typhimurium and with the nifA and ntrC products of Klebsiella pneumoniae. Homologous sequences were mainly located in an α-helix-turn-α-helix domain of the polypeptide. Interestingly, amino acid sequence homology was also found with sigma factors of E. coli (ntrA and htpR products) and Bacillus subtilis (spoIIG and phage SPOI Gp34 products) and other RNA polymerase core-interacting proteins, such as the E. coli nusA product.

Genetic and biochemical analysis of Shigella dysenteriae 1 O antigen polysaccharide biosynthesis in Escherichia coli K-12: structure and functions of the rfb gene cluster

The genetic organization and functions of the Shigella dysenteriae 1 rfb gene cluster, which specifies the somatic O antigen in this organism, have been studied in Escherichia coli K-12 by insertion and deletion mutagenesis of pSS9, a pBR322 hybrid containing the Shigella rfb genes. On the basis of the sensitivity/resistance to rough-specific bacteriophage T3 of E. coli K-12 derivatives containing mutant pSS9 plasmids, of the banding patterns and immunoreactivity of LPS isolated from such derivatives and electrophoresed on SDS-polyacrylamide gels, and of the sugar composition of the polysaccharide portion of the LPS determined by chemical analysis, six determinants for O antigen production were identified and localized. At least two determinants are involved in synthesis of TDP-rhamnose and the transfer of a rhamnose residue to the galactose-substituted core. One of these functions is probably TDP-rhamnose synthetase. A third function effects the transfer of a second rhamnose residue to the rha----gal-substituted core. A fourth function, for which evidence was obtained for two determinants (cistrons), is N-acetylglucosamine transferase, whereas a sixth determinant is necessary for extension of the first completed side chain repeat unit to the full O antigen polymer. These results confirmed the previously-determined chemical composition of the S. dysenteriae 1 O antigen and demonstrated that the order of the sugars is glcNAc----rha----rha----gal with gal as the first sugar linked to the core. Evidence was obtained for at least two transcriptional units in the rfb gene cluster and the approximate locations of two promoters are suggested. The detection of new electrophoretic species of LPS that may correspond to LPS biosynthetic intermediates, and the finding on the cell surfaces of structures corresponding to LPS core substituted with one or more O-specific sugars, appear to be novel findings.

The TraT lipoprotein as a vehicle for the transport of foreign antigenic determinants to the cell surface of Escherichia coli K12: structure–function relationships in the TraT protein

The TraT protein is a surface‐exposed lipoprotein, specified by plasmids of the IncF group, that mediates serum resistance and surface exclusion. The structure and function of the TraT protein determined by plasmid R6‐5 was probed by genetic insertion of a foreign antigenic determinant, the C3 epitope of polio virus, at residues 61, 125, 180, 200 or 216 of the protein. The chimaeric proteins were transported to the outer membrane and, in three cases, immunoassays with an anti‐C3 monoclonal antibody indicated that the C3 epitope was exposed on the cell surface. Three of the hybrids, with insertions at residues 125, 180 and 200, assembled into the trypsin‐resistant oligomeric form characteristic of the wild‐type protein, which suggested that these regions are not involved in TraT subunit:subunit interactions. Additionally, the hybrid protein carrying the C3 epitope at position 180 functioned in a genetic suppression assay and retained partial surface‐exclusion activity. Thus, its localization, folding and organization does not appear to be grossly altered from that of the wild‐type protein. Applications of the protein for the transport of foreign antigenic determinants to the cell surface are discussed.

Cloning of the rfb gene region of Shigella dysenteriae 1 and construction of an rfb-rfp gene cassette for the development of lipopolysaccharide-based live anti-dysentery vaccines

Recent studies have shown that determinants for the production of O antigen lipopolysaccharide in Shigella dysenteriae 1 are distributed over two distinct genetic elements, the chromosome and a 9 kb plasmid designated pHW400. In this communication, we describe the cloning of all determinants necessary for S. dysenteriae 1 O antigen production in E. coli K-12 and their combination in a single plasmid. An RP4::miniMu R-prime plasmid, R-prime 40, containing the his-rfb (histidine biosynthesis-lipopolysaccharide biosynthesis) gene region of the Shigella dysenteriae 1 chromosome was generated. E. coli K-12 bacteria containing R-prime 40 and pSS8, a transposon Tn5-tagged derivative of pHW400, produced lipopolysaccharide indistinguishable from that of S. dysenteriae 1. Small DNA fragments containing the rfb gene cluster and the rfp gene were subcloned from R-prime 40 and pSS8 and subsequently combined in vector pACYC184 to produce pSS37. This latter plasmid when introduced by transformation into E. coli K-12 provoked the formation of S. dysenteriae 1 O-specific lipopolysaccharide, a feature that suggests it may be useful in the construction of LPS-based live vaccines against the Shiga bacillus.

Broad‐host range expression vectors containing manipulated meta‐cleavage pathway regulatory elements of the TOL plasmid

The construction of pERD20 and pERD21, two broad‐host range expression vectors, is described. The vectors contain the Pm promoter of the meta‐cleavage pathway operon of the TOL plasmid pWWO; this promoter is present within a polylinker which provides a number of downstream cloning sites close to the transcription initiation site. Transcription from the Pm promoter in these vectors is controlled not by the natural positive regulator of Pm, the Xy1S protein, but by an Xy1S mutant analogue, Xy1S2tr6, which ??hibits an altered effector specificity and can mediate a 3–8‐fold higher level of transcription than can Xy1S in a wide range of temperatures. Controlled expression of cloned genes can be achieved in a broad spectrum of Gram negative bacteria grown at a wide range of temperatures.

Immunoblotting procedure for the analysis of electrophoretically-fractionated bacterial lipopolysaccharide

A procedure is described for the efficient transfer of fractionated bacterial lipopolysaccharide (LPS) from SDS-polyacrylamide gels to nitrocellulose filters, and its subsequent display by a peroxidase-linked antibody. The method is sensitive, and reveals and resolves high molecular weight LPS molecules having side chain lengths of up to and greater than 30 repeat units. It is also useful for the rapid analysis of LPS in bacterial outer membrane preparations.

Analysis and genetic manipulation of Shigella virulence determinants for vaccine development

Shigellosis is a major public health problem in developing countries. Current epidemics of Shigella dysenteriae serotype 1 strains are particularly serious and are characterized by high mortality rates. A high proportion of the isolates are resistant to many of the antibiotics currently in use in these countries, a feature which seriously compromises clinical treatment of the infections. Efficacious vaccines are thus urgently needed. Basic studies on Shigella virulence factors, infections in laboratory models, and host responses has led to the development of several strategies for the production of vaccines. All of these are live oral vaccines involving bacteria capable of at least limited survival in the animal intestine and of carrying selected antigens to the mucosal immune system. One type of vaccine involves non-pathogenic shigellae, attenuated either by introduction of a requirement for aromatic amino acids (aroD) or by loss of the large plasmid that specifies bacterial invasion of the mucosal epithelium. S. dysenteriae 1 strains under development as vaccines need to be engineered to eliminate high level Shiga toxin production, and a rapid and effective method to achieve this was recently elaborated. The second type of vaccine is represented by hybrid strains consisting of a carrier organism, such as an attenuated Salmonella or an Escherichia coli K-12 strain carrying the Shigella invasion plasmid, and the selected foreign antigen that it produces, in all cases so far the Shigella O antigen polysaccharide.