Marta Herrero

Metal ion regulation of gene expression. Fur repressor-operator interaction at the promoter region of the aerobactin system of pColV-K30.

Transcription of the iron-controlled aerobactin operon of the enterobacterial plasmid pColV-K30 is negatively regulated through the interaction of a Fe2+-binding repressor (the Fur protein) with operator sequences within the promoter region of the operon. The DNA sequences essential for interaction with the repressor were located by site-directed mutagenesis of specific regions within the 31 base-pair protected by the repressor from DNase I nicking. Occupation of two contiguous repressor-binding sites appears to be required for the complete repression of the system. Contacts of the Fur repressor with the corresponding operator sequences were analyzed with hydroxyl radical footprint and methylation protection experiments. These indicate that DNA-protein contacts approach a symmetrical mode and take place at all sides of the DNA helix.

An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid.

Transcription from promoter Pu of the upper catabolic operon of the Pseudomonas putida TOL plasmid which specifies conversion of toluene/xylenes to benzoate/toluates is activated by the TOL‐encoded regulator XylR protein in the presence of substrates of the catabolic pathway and in conjunction with the sigma 54(NtrA)‐containing form of RNA polymerase. This regulatory circuit was faithfully reproduced in Escherichia coli in single copy gene dosage by integrating the corresponding controlling determinants into the chromosomes of several K12 derivatives by means of specialized transposons. In vivo monitoring of the activity of a Pu‐lacZ fusion in E. coli strains with different genetic backgrounds demonstrated that integration host factor (IHF) is involved in Pu regulation and that hyperproduction of the XylR protein leads to a decrease of Pu activity in a manner in which deletion of the putative DNA‐binding domain of the XylR does not impair its inhibitory effect when hyperproduced. One discrete IHF binding site and two potential XylR sites (consensus sequence 5′‐TTGANCAAATC‐3′), bracketted by short stretches of DNase I‐hypersensitive bonds, were detected upstream of the transcription initiation site. A model accounting for the features found is proposed which includes the IHF‐promoted looping of upstream XylR‐DNA complexes so that they contact the sigma 54(NtrA)‐RNA polymerase bound at ‐12/‐24 positions.

Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways of Pseudomonas.

Four recombinant mini-Tn5 transposons are described which contain outward-facing Pm, Pu or Psal promoters from the catabolic plasmids TOL and NAH of Pseudomonas putida, along with their cognate wild-type regulatory genes (xylS, xylR, nahR) or mutant varieties (xylS2). Transcription from such promoters is activated when the host bacteria encounters certain aromatic compounds, such as alkyl- and halobenzoates (XylS, XylS2), alkyl- and halotoluenes (XylR) or salicylates (NahR). These transposons enable the generation of conditional phenotypes dependent on the presence of specific effectors, as well as the engineering of strains expressing heterologous genes that are regulated by aromatic inducers. A mini-Tn5 xylS/Pm::luxAB, was used to construct Pseudomonas strains emitting light upon exposure to concentrations of m-toluate as low as 5-10 microM. The broad-host-range transposition system of Tn5 and the stability of the inserted genes due to the loss of the transposase-encoding gene during delivery of the mobile element make these transposons particularly well suited for the construction of stable strains exhibiting halo/alkyl aromatic-regulated conditional phenotypes in the absence of antibiotic selection, as is required for some uncontained bioremediation and biomonitoring applications.

Mini-transposons in microbial ecology and environmental biotechnology

Abstract Mini‐transposon is the generic name given to the members of a collection of genetic assets derived from transposons Tn10 and Tn5, in which the naturally occurring functional segments of DNA have been rearranged artificially to originate shorter mobile elements. In the most widespread design (that known as the pUT system), any heterologous DNA segment can be conveniently cloned within the boundaries of a mini‐Tn5 vector and finally inserted into the chromosome of target Gram‐negative bacteria after a few simple genetic manipulations. The large variety of antibiotic, non‐antibiotic and excisable selection markers available has been combined at ease with DNA fragments encoding one or more phenotypes of interest for ecological or biotechnological applications. These include the tagging of specific strains in a community with selectable and/or optical marker genes, the production of stable gene fusions for monitoring transcriptional regulation in single cells, the metabolic engineering of strains destined for bioremediation, the non‐disruptive monitoring of gene transfer and the assembly of gene containment and strain containment circuits for genetically manipulated microorganisms.

A T7 RNA polymerase-based system for the construction of Pseudomonas strains with phenotypes dependent on TOL-meta pathway effectors.

A general method to construct recombinant Pseudomonas putida (and related bacteria), which transcribe specific genes inserted into their chromosome in response to the presence of alkyl- and halobenzoates, has been developed. The system is based on the ability of the T7 RNA polymerase (T7pol) to initiate transcription from cognate promoter sequences located upstream from cloned genes. A specialized transposon, mini-Tn5 xylS/Pm::T7pol, was constructed which contains the structural T7 gene 1 downstream from the XylS protein/benzoate-regulated Pm promoter of the meta-operon of the TOL catabolic plasmid. This transposon was stably inserted into the chromosome of a P. putida target strain so that gene 1 is transcribed upon exposure of the bacteria to benzoate effectors of the XylS regulator. Genes whose expression is to be mediated by T7pol are cloned in mini-Tn5 transposons containing T7 promoter sequences upstream from the cloning site and then the hybrid transposons are inserted into different positions in the same chromosome. In this way, expression of the genes cloned within the mini-Tn5 vectors is dependent on the T7pol/XylS/Pm system. This expression device is particularly well suited for applications in which the expression of two or more genes is to take place in response to a single chemical signal, i.e., exposure to certain aromatic compounds.

Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions.

The activation of the Pm promoter of the meta operon of the TOL plasmid of Pseudomonas putida by its cognate XylS activator protein in the presence and absence of benzoate inducers has been examined in specialized Escherichia coli strains carrying Pm-lacZ fusions and the xylS gene in different configurations in which all controlling elements are present in near native conditions and stoichometry. Expression of a chromosomal Pm-xylX::lacZ fusion was primarily dependent on the addition of an effector at a low xylS gene dosage, but such dependency decreased with increasing levels of the regulator, to the point that hyperproduced XylS could, in the absence of any aromatic effector, raise expression to a level 10(4)-fold higher than normal basal levels. Pm activity never reached a defined saturation level within the range of intracellular concentrations permitted by the intrinsic solubility of the protein, thus suggesting a low degree of occupancy of the OmR and OmL (Om right and left half-sites, respectively) operator sequences by XylS. This was confirmed by transcription interference experiments, which indicated that the frequency of occupation of Pm by active XylS is low. This property permits a fine tuning of Pm activity in vivo through changes in intracellular XylS concentrations, as is predicted in current models to account for the coordinated regulation of TOL operons.

IS1-mediated mobility of the aerobactin system of pColV-K30 in Escherichia coli

SummaryGenes determining the high affinity iron transport system mediated by the siderophore aerobactin are flanked in the enterobacterial plasmid pColV-K30 by inverted repeats of IS1 sequences, suggesting that the aerobactin genes are part of a transposon. To study this possibility, the entire region between the two IS1 sequences was cloned as an 18 kb HindIII-BamHI restriction fragment in pUC8 giving plasmid pMO1. A number of derivatives of pMO1, in which aerobactin genes were tagged with a kanamycin resistance gene, were prepared in order to assess the ability of both IS1s to promote the formation of cointegrates with pCJ105, an F derivative devoid of insertion sequences. Mating-out assays indicated that both flanking IS1s were active in cointegrate formation at detectable frequencies. In some cases, the cointegrates could be resolved, the final result being a transposition-like event for the entire aerobactin system.