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  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 51 (1997), S. 593-628 
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract This review attempts to substantiate the notion that nonlinear DNA structures allow prokaryotic cells to evolve complex signal integration devices that, to some extent, parallel the transduction cascades employed by higher organisms to control cell growth and differentiation. Regulatory cascades allow the possibility of inserting additional checks, either positive or negative, in every step of the process. In this context, the major consequence of DNA bending in transcription is that promoter geometry becomes a key regulatory element. By using DNA bending, bacteria afford multiple metabolic control levels simply through alteration of promoter architecture, so that positive signals favor an optimal constellation of protein-protein and protein-DNA contacts required for activation. Additional effects of regulated DNA bending in prokaryotic promoters include the amplification and translation of small physiological signals into major transcriptional responses and the control of promoter specificity for cognate regulators.
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  • 2
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 38 (2000), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: In the presence of toluene and other structural analogues, the enhancer binding protein XylR activates the σ54 promoter Pu of the TOL (toluene degradation) plasmid pWW0 of Pseudomonas putida. Introduction of amino acid changes Val-219Asp and Ala-220Pro, which enter a proline kink at the interdomain region (B linker) between the A (signal reception) module and the central portion of XylR, originated a protein with unforeseen properties. These included a minor ability to activate Pu in the absence of aromatic effectors, a much higher responsiveness to m-xylene and a significant response to a large collection of aromatic inducers. Such changes could not be attributed to variations in XylR expression levels or to the fortuitous creation of a novel promoter, but to a genuine change in the properties of the activator. Structural predictions suggested that the mutation entirely disrupted an otherwise probable coiled-coil structure. A second directed mutant within the same region consisting of a major replacement of amino acids A220–N221 by the peptide HHHR produced an even more exacerbated phenotype. These data support a model in which the linker B region influences the effector profile by modifying at a distance the operative shape of the effector pocket and fixing the protein in an intermediate step of the activation process.
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  • 3
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: To investigate the activation mechanism of the enhancer-binding protein XylR encoded by the TOL plasmid of Pseudomonas putida mt-2, a combinatorial library was generated composed of shuffled N-terminal A domains of the homologous regulators DmpR, XylR and TbuT, reassembled within the XylR structure. When the library was screened in vivo for responsiveness to non-effectors bulkier than one aromatic ring (such as biphenyl) or bearing an entirely different distribution of electronegative groups (e.g. nitrotoluenes), protein variants were found that displayed an expanded inducer range including the new effectors. Although the phenotypes endowed with the corresponding changes were largely similar, the modifications involved different sites within the A domain. The positions of the mutations within a structural model of the A domain suggest that expansion of the inducer profile can be brought about not only by changes in the effector pocket of the protein but also by unlocking steps of the signal transmission mechanism that follows effector binding. These results provide a rationale for evolving in vitro regulators à la carte that are responsive to predetermined, natural or xenobiotic chemical species.
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science, Ltd
    Molecular microbiology 40 (2001), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: In this work, we have investigated whether the bacterial type I secretion pathway, which does not have a periplasmic intermediate of the secreted protein, allows the formation of disulphide bridges. To this end, the formation of disulphide bonds has been studied in an antibody single-chain Fv (scFv) fragment secreted by the Escherichia coli haemolysin (Hly) transporter (a paradigm of type I secretion). The scFv antibody fragment was used as a disulphide bond and protein-folding reporter, as it contains two disulphide bridges that are required for its correct folding (i.e. to preserve its antigen-binding activity). We show that an scFv–HlyA hybrid secreted by Hly type I transporter (TolC, HlyB, HlyD) is accumulated in the extracellular medium with the disulphide bonds correctly formed. Neither periplasmic and inner membrane-bound Dsb enzymes (e.g. DsbC, DsbG, DsbB and DsbD) nor cytoplasmic thioredoxins (TrxA and TrxC) were required for scFv–HlyA oxidation. However, a mutation of the thioredoxin reductase gene (trxB), which leads to the cytoplasmic accumulation of the oxidized forms of thioredoxins, had a specific inhibitory effect on the Hly-dependent secretion of disulphide-containing proteins. These data suggest that premature cytoplasmic oxidation of the substrate may interfere with the secretion process. Taken together, these results indicate not only that the type I system tolerates secretion of disulphide-containing proteins, but also that disulphide bonds are specifically formed during the passage of the polypeptide through the export conduit.
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  • 5
    Electronic Resource
    Electronic Resource
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 33 (1999), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The presence of intricate global cell regulation mechanisms may be one reason for the exceptional environmental and evolutionary success of microbes. Promoters, the cis-acting signals, are responsive to several stimuli related to growth, stress and substrate specificity. Their response is mediated by a wide variety of trans-acting regulators that sense the environment and the physiological state of the cell and adjust the transcription of specific genes. One of the main transcriptional regulation webs operates in the transition from affluent to barren conditions, with σS being the chief actor in a company of players that stage a competition for the sparsely available RNA polymerase molecules. In this role, σS may be assisted by several factors, including nucleoid-related proteins and metabolites. In addition, the levels of σS itself are regulated by mechanisms that include inactivation and degradation. Several transcription factors, belonging to different regulatory pathways, may operate in the same promoter. In such a case, the final transcriptional output depends both on the interplay of effectors and on the properties of the recruitment of the effector–RNA polymerase complex to the promoter. RNA polymerase itself is also capable of establishing selective interactions with activators and specific promoter regions through the carboxy-terminal domain of its alpha subunit (αCTD). Transcriptional regulation controls pervade such crucial events in the life of bacterial cells as Escherichia coli cell division, Bacillus subtilis sporulation and Caulobacter crescentus differentiation. These examples suggest that bacteria have been particularly inventive in adapting gene expression regulation to survive under a diversity of environments and have done so by exploiting the malleable molecular mechanisms involved in transcription, developing complexities that may match those found in eukaryotic cells.
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 31 (1999), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The effect of FtsH, an essential inner membrane-bound protease, in the regulation of the σ54-dependent Pu promoter has been examined in vivo. Escherichia coli cells lacking FtsH failed to activate a Pu–lacZ fusion in response to the cognate enhancer-binding protein XylR. However, the intracellular concentrations of XylR and σ54, as well as their apparent physical integrity were the same regardless of the presence or absence of the protease. The loss of Pu activity in FtsH-minus cells was not due to the imbalance between sigma factors caused by the lack of the protease. ftsH mutants could not grow in media with glutamine as the only nitrogen source and failed also to induce the σ54 promoters PnifH by NifA and PpspA by PspF. These lesions were fully complemented by a ftsH + plasmid. Therefore, part of the pleiotropic phenotype of FtsH-less cells corresponded to the lack of σ54 activity. Overproduction of σ54, however, restored both transcriptional activity of Pu and growth in glutamine of a ftsH strain. These observations suggested that the activity of σ54 is checked in vivo by an interplay of factors that ultimately determine the performance of cognate promoters under given physiological conditions.
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 33 (1999), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The mechanism of protein secretion mediated by the β-domain of the Neisseria gonorrhoeae IgA protease, a paradigm of a family of secreted polypeptides of Gram-negative bacteria called autotransporters, has been examined using a single-chain antibody (scFv) as a reporter passenger domain to monitor the translocation process. Fusion of a scFv to the β-module of the IgA protease allowed us to investigate the passage of the chimeric protein through the periplasm, its insertion into the outer membrane and the movement of the N-terminal moiety towards the cell surface. As the binding activity of the scFv to its target antigen is entirely dependent on the formation of disulphide bonds, the relationship between secretion, folding and formation of S–S bridges could be analysed in detail. In contrast to the current notion that only an unfolded N-passenger domain can be translocated through the β-domain, our results show that the scFv is able to pass through the outer membrane, albeit at a threefold reduced level, in an active conformation with its disulphide bonds preformed in the periplasm through the action of the DsbA product. These data call for a re-evaluation of the prevailing model for secretion of the N-domain of autotransporters.
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  • 8
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The mechanism by which XylR, the toluene-responsive activator of the σ54-dependent Pu and Ps promoters of the Pseudomonas TOL plasmid pWW0, downregulates its own σ70 promoter Pr has been examined. An in vitro transcription system was developed in order to reproduce the repression of Pr observed in cells of P. putida (pWW0) both in the presence and in the absence of the XylR inducer, benzyl alcohol. DNA templates bearing the two σ70-RNA polymerase (RNAP) binding sites of Pr, which overlap the upstream activating sequences (UAS) for XylR in the divergent σ54 promoter Ps, were transcribed in the presence of a constitutively active XylR variant deleted of its N-terminal domain (XylRΔA). The addition of ATP, known to trigger multimerization of the regulator at the UAS, enhanced the repression of Pr by XylR. Furthermore, we observed activation of the divergent σ54 promoter Ps during Pr downregulation by XylRΔA. These results support the notion that activation of XylR by aromatic inducers in vivo triggers a transcriptional switch between Pr and PsSuch a switch is apparently caused by the ATP-dependent multimerization and strong DNA binding of the protein required for activation of the σ54 promoter. This device could reset the level of XylR expression during activation of the σ54Pu and Ps promoters of the TOL plasmid.
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 21 (1996), S. 0 
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The lateral transfer of genetic information among microorganisms is a major force driving the outstanding adaptability of microbial communities to environmental changes. Until now little information has been obtained on gene transfer in natural ecosystems. We present here a genetic circuit for detecting and quantifying horizontal gene transfer from a defined donor microorganism to recipient organisms in the absence of selection for a recipient-specific phenotype. The system consists of an engineered lacZ (encoding β-galactosidase) reporter gene whose expression is controlled by a synthetic regulatory element based on a fusion between the Pr promoter-operator from lambda bacteriophage and the 5′ non-coding leader region of the tnp gene encoding the IS10 transposase function. Expression of this reporter cassette in the recombinant microorganism is completely shut down by two chromosomally encoded trans-acting repressors working at the level of transcription (the CI-EK117 protein from the lambda phage), and at the level of translation (the antisense RNA-OUT of the IS10 element). When the reporter element is transferred to a different host by any mechanism, it escapes repression and becomes expressed. The system was validated with Pseudo-monas putida, and conjugational transfer frequencies of the reporter element as low as 10−6 were detected. The modular design and broad host range of the genetic circuit, in combination with biomarkers which permit real-time in situ detection, will facilitate the monitor-ing of gene flow in a non-disruptive manner within the environment.
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  • 10
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: A subgenomic array of structural and regulatory genes of the TOL plasmid pWW0 of Pseudomonas putida mt-2 has been constructed to sort out the interplay between m-xylene catabolism and the environmental stress brought about by this aromatic chemical. To this end, xyl sequences were spotted along with groups of selected P. putida genes, the transcription of which become descriptors of distinct physiological conditions. The expression of the TOL pathway in response to pathway substrates was thus profiled, uncovering a regulatory network that overcomes and expands the predictions made by projecting known data from individual promoters. First, post-transcriptional checks appear to mitigate the burden caused by non-productive induction of the TOL operons. Second, the fate of different segments of the polycistronic mRNAs from the upper and lower TOL operons varies depending on the metabolism of their inducers. Finally, m-xylene triggers a noticeable heat shock, the onset of which does interfere with optimal expression of catabolic genes. These results reveal a degree of regulatory partnership between TOL plasmid-encoded functions and host physiology that go beyond transcription initiation control.
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