Conformational dynamics of a transposition repressor in modulating DNA binding

Can Lucifer Yellow Indicate Correct Permeability of Biological Cell Membrane under An Electric and Magnetic Field?

The effect of external magnetic and electric fields, in the range of electroporation and magnetoporation, on Lucifer Yellow (LY) fluorescence in the absence of cells is studied. Electric-field-induced quenching and magnetic field-induced increase are observed for fluorescence intensity of LY. Regard to the fact that the variation of field-induced fluorescence, even in the absence of cells, can be observed, the application of LY, as a marker, is debatable in electroporation and magnetoporation techniques.

Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility

The C-terminal domain (CTD) of bacteriophage Mu immunity repressor (Rep) regulates DNA binding by the N-terminal domain and degradation by ClpXP protease. Five residues at the Rep C terminus (CTD5) can serve as a ClpX recognition motif, but it is dormant unless activated, a state that can be induced by the presence of dominant-negative mutant repressors (Vir). Conversion of Rep to ClpXP-sensitive form was associated with not only increased exposure of CTD5 to solvent but also increased CTD motion or flexibility as measured by fluorescence anisotropy. CTD mutations (V183S, K193S, and V196S) promoting ClpXP resistance without destroying the recognition motif prevented increased CTD motion induced by Vir. Suppression of ClpXP protease resistance conferred by the V196S mutation also correlated with restoration of CTD motion. The temperature-sensitive R47Q mutation present in cis within the DNA-binding domain restored ClpXP protease sensitivity to the V196S mutant, and anisotropy analysis indicated that R47Q allows the V196S CTD to gain increased flexibility when Vir was present. The results indicate that the CTD functions to turn the recognition motif on and off, most likely by modulating flexibility of the domain that harbors the ClpX recognition motif, suggesting a general mechanism by which proteins can regulate their own degradation.

Environmental factors that influence the transition from lysogenic to lytic existence in the phiHSIC/Listonella pelagia marine phage-host system

The marine phage varphiHSIC has been previously reported to enter into a pseudolysogenic-like interaction with its host Listonella pelagia. This phage-host system displays behaviors that are characteristic of both pseudolysogeny and lysogeny including a high rate of spontaneous induction and chromosomal integration of the prophage. To determine what parameters may influence the transition from lysogenic to lytic existence in the varphiHSIC/L. pelagia phage-host system, cultures of this organism were incubated under different environmental conditions, while host cell growth and bacteriophage production were monitored. The environmental parameters tested included salinity, temperature, a rapid temperature shift, and degree of culture aeration. The highest titers of phage were produced by HSIC-1a cells grown in high-salinity nutrient artificial seawater media (67 ppt with a natural salinity equivalent of 57 ppt) or those cultured in highly aerated nutrient artificial seawater media (cultures shaken at 300 rpm). Conversely, the lowest titers of phage were produced under low salinity or rate of aeration. In general, conditions that stimulated growth resulted in greater lytic phage production, whereas slow growth favored lysogeny. These results indicate that elevated salinity and aeration influenced the switch from lysogenic to lytic existence for the phage varphiHSIC. These results may have implications for environmental controls of the lysogenic switch in natural populations of marine bacteria.

Control of Bacteriophage Mu Lysogenic Repression

The transposable and temperate phage Mu infects Escherichia coli where it can enter the lytic life-cycle or reside as a repressed and integrated prophage. The repressor protein Rep is the key element in the lysis-lysogeny decision. We have analyzed the fate of Rep in different mutants by Western blotting under two conditions that can induce a lysogen: high temperature and stationary phase. We show that, unexpectedly, Rep accumulates under all conditions where the prophage is completely derepressed, and that this accumulation is ClpX-dependent. An analysis of the degradation kinetics shows that Rep is a target of two protease systems: inactivation of either the clpP or lon gene results in a stabilization of Rep. Such a reaction scheme explains the counterintuitive observation that derepression is correlated with high repressor concentration. We conclude that under all conditions of phage induction the repressor is sequestered in a non-active form. A quantitative simulation accounts for our experimental data. It provides a model that captures the essential features of Mu induction and explains some of the mechanisms by which the physiological signals affecting the lysis-lysogeny decision converge onto Rep.

A context-dependent ClpX recognition determinant located at the C terminus of phage Mu repressor

The bacteriophage Mu immunity repressor is a conformationally sensitive sensor that can be interconverted between forms resistant to and sensitive to degradation by ClpXP protease. Protease-sensitive repressor molecules with an altered C-terminal sequence promote rapid degradation of the wild-type repressor by inducing its C-terminal end to become exposed. Here we determined that the last 5 C-terminal residues (CTD5) of the wild-type repressor contain the motif required for recognition by the ClpX molecular chaperone, a motif that is strongly dependent upon the context in which it is presented. Although attachment of the 11-residue ssrA degradation tag to the C terminus of green fluorescent protein (GFP) promoted its rapid degradation by ClpXP, attachment of 5-27 C-terminal residues of the repressor failed to promote degradation. Disordered peptides derived from 41 and 35 C-terminal residues of CcdA (CcdA41) and thioredoxin (TrxA35), respectively, activated CTD5 when placed as linkers between GFP and repressor C-terminal sequences. However, when the entire thioredoxin sequence was included as a linker to promote an ordered configuration of the TrxA35 peptide, the resulting substrate was not degraded. In addition, a hybrid tag, in which CTD5 replaced the 3-residue recognition motif of the ssrA tag, was inactive when attached directly to GFP but active when attached through the CcdA41 peptide. Thus, CTD5 is sufficient to act as a recognition motif but has requirements for its presentation not shared by the ssrA tag. We suggest that activation of CTD5 may require presentation on a disordered or flexible domain that confers ligand flexibility.

Trans-targeting of the phage Mu repressor is promoted by conformational changes that expose its ClpX recognition determinant

Dominant negative forms of the phage Mu repressor, including the mutant Vir repressors, are not only rapidly degraded by the ClpXP protease but also promote degradation of the unmodified, wild-type repressor. This trans-targeting of the wild-type repressor depends upon a determinant within its C-terminal domain, which is needed for recognition by ClpX. An environmentally sensitive fluorescent probe (2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid (MIANS)) attached to the C terminus of the full-length repressor indicated that Vir induces the movement of this domain into a more exposed configuration. Vir also promoted attachment of MIANS to the C terminus of the repressor at an accelerated rate, and it greatly increased the rate of phosphorylation of a cAMP-dependent protein kinase motif attached to the repressor C terminus. While an excess of Vir was needed to promote repressor phosphorylation at maximal rates, the presence of ClpX could increase phosphorylation rates at lower Vir levels. trans-Targeting of the Mu repressor is therefore promoted by exposing its ClpX recognition determinant, and the action of ClpX can assist Vir in exposing these determinants.

Modulation of phage Mu repressor DNA binding and degradation by distinct determinants in its C-terminal domain

Rapid degradation of the bacteriophage Mu immunity repressor can be induced in trans by mutant, protease-hypersensitive repressors (Vir) with an altered C-terminal domain (CTD). Genetic and biochemical analysis established that distinct yet overlapping determinants in the wild-type repressor CTD modulate Vir-induced degradation by Escherichia coli ClpXP protease and DNA binding by the N-terminal DNA-binding domain (DBD). Although deletions of the repressor C-terminus resulted in both resistance to ClpXP protease and suppression of a temperature-sensitive DBD mutation (cts62), some cysteine-replacement mutations in the CTD elicited only one of the two phenotypes. Some CTD mutations prevented degradation induced by Vir and resulted in the loss of intrinsic ClpXP protease sensitivity, characteristic of wild-type repressor, and at least two mutant repressors protected Vir from proteolysis. One protease-resistant mutant became susceptible to Vir-induced degradation when it also contained the cts62 mutation, which weakens DNA binding but apparently facilitates conversion to a protease-sensitive conformation. Conversely, this CTD mutation was able to suppress temperature sensitivity of DNA binding by the cts62 repressor. The results suggest that determinants in the CTD not only provide a cryptic ClpX recognition motif but also direct CTD movement that exposes the motif and modulates DNA binding.

Characterization of the cts4 repressor mutation in transposable bacteriophage Mu

Mucts4 was isolated more than 30 years ago and was the first available thermoinducible derivative of transposable phage Mu. We have characterized the cts4 mutation and the corresponding mutant protein. Contrary to previously characterized thermoinducible Mu prophages (e.g., Mucts62), Mucts4 lysogenizes at reduced frequency even at 30 degrees C. The cts4 mutation (Leu129Val) was located in this central repressor region. The cts4 protein was thermosensitive for operator DNA binding in vitro. Temperature-dependent changes in protein-protein cross-linking patterns in the absence of DNA were detected for purified wild type, cts62 and cts4 repressor proteins. The cts4 protein exhibited a subtly different electrophoretic profile, which became more marked at higher temperatures, from both the wild type and cts62. In addition the cts4 repressor generated a significantly different pattern of binding to DNA fragments carrying the early operator region. Consistent with the predicted involvement of the central leucine-rich region of the Mu repressor in the formation of multimeric forms, the cts4 mutation thus appeared to affect protein-protein interactions.

Derepression of bacteriophage mu transposition functions by truncated forms of the immunity repressor

To trigger bacteriophage Mu transposition and replication in response to physiological signals, its immunity repressor must be synchronously inactivated. Two repressor mutants (Vir), which have an altered C-terminal domain and are highly susceptible to degradation by ClpXP protease, confer a dominant negative phenotype by promoting degradation of the wild-type repressor. To search for other modified repressors that can induce Mu derepression in vivo and to determine what part of the inducing repressor molecules are needed to target the unmodified repressor population, repressor peptides with nested deletions starting at the C-terminal end were constructed. Such peptides with a C-terminal ssrA degradation tag promoted a sharp reduction in cellular levels of full-length unmodified repressor, a process largely dependent upon the clpP protease function. Only the repressor DNA-binding domain, located at the N-terminal end, was required in tagged peptides to target unmodified repressor. In addition, some repressor peptides containing the DNA-binding domain promoted derepression without the clpP function, being able to promote repressor inactivation without promoting its degradation. None of the modified repressors could promote derepression if immunity was established by a mutant repressor lacking 18 residues at its C-terminal end. The results indicate that inducing repressor peptides influence the function of the C-terminal domain of the intact repressor, a domain that regulates its degradation and DNA binding. They suggest the possibility that tagged repressor molecules, produced by stalled ribosomes, can be inducers of transposition under starvation conditions.