P1 plasmid replication. Role of initiator titration in copy number control

The copy number control locus incA of unit copy plasmid P1 maps in a region containing nine 19 base-pair repeats. Previous results from studies in vivo and in vitro indicated that incA interacts with the plasmid-encoded RepA protein, which is essential for replication. It has been proposed that the repeat sequences negatively control copy number by sequestering the RepA protein, which is rate-limiting for replication. Our results lend further support to this hypothesis. Here we show that the repeats can be deleted completely from P1 miniplasmids and the deletion results in an approximately eightfold increase in plasmid copy number. So, incA sequences are totally dispensable for replication and have only a regulatory role. The copy number of incA-deleted plasmids can be reduced if incA sequences are present in trans or are reincorporated at two different positions in the plasmid. This reduction in copy number is not due to lowered expression of the repA gene in the presence of incA. We show that one repeat sequence is sufficient to bind RepA and can reduce the copy number of incA-deleted plasmids. When part of the repeat was deleted, it lost its ability to bind as well as influence copy number. These results show a strong correlation between the capacity of incA repeats to bind RepA protein both in vivo and in vitro, and the function of incA in the control of copy number.     

Heat shock proteins DnaJ, DnaK, and GrpE stimulate P1 plasmid replication by promoting initiator binding to the origin.

Binding of the P1-encoded protein RepA to the origin of P1 plasmid replication is essential for initiation of DNA replication and for autoregulatory repression of the repA promoter. Previous studies have shown defects in both initiation and repression in hosts lacking heat shock proteins DnaJ, DnaK, and GrpE and have suggested that these proteins play a role in the RepA-DNA binding required for initiation and repression. In this study, using in vivo dimethyl sulfate footprinting, we have confirmed the roles of the three heat shock proteins in promoting RepA binding to the origin. The defects in both activities could be suppressed by increasing the concentration of wild-type RepA over the physiological level. We also isolated RepA mutants that were effective initiators and repressors without requiring the heat shock proteins. These data suggest that the heat shock proteins facilitate both repression and initiation by promoting only the DNA-binding activity of RepA. In a similar plasmid, F, initiator mutants that confer heat shock protein independence for replication were also found, but they were defective for repression. We propose that the initiator binding involved in repression and the initiator binding involved in initiation are similar in P1 but different in F.     

Further physical characterization of deletion and substitution mutants affecting the control of lysogeny in bacteriophage P2

Summary A deletion of phage P2, del6 (L.E. Bertani, 1980), thought to remove the structural gene int, and a deletion/substitution, vir94, thought to remove genes int, C and cox, were mapped by electron microscopy, using the heteroduplex technique.Four independent deletion/substitution mutations, all affecting the regulatory region of P2, were compared in all possible combinations with the same technique: two showed sequence homology in their substitution DNA. The results confirm the model proposed for the origin of these mutants, analogous to that for the origin of transducing variants in phage , but suggest in first approximation that the exchange between the P2 DNA and the chromosome of the host bacterium may occur at several different bacterial sites.A map of the regulatory region of P2, based on all data available from the study of deletions and insertions, is presented.     

Tandem pentuplication of a DNA segment in a derivative of bacteriophage P2: its use in the study of the mechanism of DNA annealing.

From a tandem duplication mutant of phage P2, triplication, quadruplication and pentuplication forms were derived. They were recognized by decreased virion heat stability resulting from the increase in DNA content, and were confirmed by electron microscope heteroduplex mapping. These forms of partially repeated DNA are quite stable in P2 because of the low level of recombination typical of this phage. Under conditions normally employed for full DNA renaturation, these high order repeat chromosomes gave often incomplete renaturation over the repeated segments. Based on current models for DNA renaturation, several predictions were made and tested. The results, although not quantitatively exhaustive, indicated that base pairing proceeding from a nucleation site was sufficiently slow to allow a second nucleation to occur with a fair probability over a length of a few thousand base pairs.     

Hydrophobic interactions of DNA with long-chain amines.

The binding ratio, Γ_a, for several long-chain amines to calf-thymus DNA was measured as function of the ligand concentration, C, using the equilibrium dialysis method. The different amines used in the binding experiments at constant temperature were dodecyl trimethyl ammonium bromide (DTAB), myristyl trimethyl ammonium bromide (MTAB), cetyl trimethyl ammonium bromide (CTAB), and cetyl pyridinium chloride (CPCL). The formation and dissociation of the saturated DNA–amine complex were reversible. The initial slope of the binding isotherm decreased sharply with the reduction of the electrostatic effect as a result of the increase of the ionic strength of the medium. A sharp inflexion region was noted in the binding isotherm where the ligands bound in significant numbers may undergo hydrophobic interactions with each other. Γ_a increased with C until a maximum value, Γ_a^m, was reached, beyond which binding slowly decreased with an increase of concentration. Both Γ_a^m and Γ_a increased significantly with the increase of the hydrocarbon chain length of a ligand. The free energy change ΔG^m for each saturated DNA–amine complex was evaluated on the basis of a thermodynamic relation and the standard state for binding was defined. The average free energy change for the binding per CH₂ group of the amine was found to be ?1550 cal/mol. The difference between ΔG^m for CTAB and CPCL was examined on the basis of the structural difference of their head groups. The binding isotherms for MTAB and CPCL were obtained from the binding data at 15, 30, and 45°C. The binding increased with increasing temperature. From the plot of ΔG^m/T vs 1/T, the changes in enthalpy and entropy due to the binding were evaluated for MTAB and CPCL. The binding reactions in these two cases were driven primarily by the entropy change due to the hydrophobic interaction. Standard free energy changes ΔG₀^m for the unsaturated complexes were close to ΔG^m for the saturated complexes. The binding isotherms also depended on the nature of the neutral salt of the medium. At a given salt concentration, the order of the binding of the inorganic salts was as follows: KCl > NaCl > LiCl > Na₂SO₄ > MgCl₂. The effect of pH on binding was also examined. The importance of these results on the formation of the reconstituted and natural nucleohistone complexes is discussed.     

Biopolymer - Surfactant Interaction: 4 Kinetics of Binding of Cetyltrimethyl Ammonium Bromide with Gelatin,Hemoglobin, β-lactoglobulin and Lysozyme

Abstract

The binding of CTAB with the proteins, gelatin, hemoglobin, β-lactoglobulin and lysozyme follow first order kinetics and occurs either in two or three distinct stages. The number of stages depends on the overall configuration of the biopolymers. The denatured protein, gelatin has shown three-stage kinetics under all conditions, whereas the native proteins, hemoglobinn, β-lactoglobulin and lysozyme have exhibited two stage kinetics. Heat treated lysozyme in 8 mol dm-³ urea medium has also shown a two-stage kinetics. On the basis of non interacting binding sites on the proteins and independent sequential binding, the rates of reaction have been observed to increase with temperature and follow the trend k₁ >> k₂ > k₃. The interaction of CTA⁺ with the proteins is both electrostatic and hydrophobic. Hemoglobin has shown maximum reaction rate whereas, β-lactoglobulin has shown a minimum. The activation parameters for the kinetic process have exhibited almost non-variant Δ G? and Δ H? < T Δ S? The formation of activation complex in the Eyring model is entropy controlled so also the overall kinetics. An isokinetic entropy-enthalpy compensation phenomenon has been observed for the respective kinetic stages.     

A point mutation at the C-terminal half of the repressor of temperate mycobacteriophage L1 affects its binding to the operator DNA

The wild-type repressor CI of temperate mycobacteriophage L1 and the temperature-sensitive (ts) repressor CIts391 of a mutant L1 phage, L1cIts391, have been separately overexpressed in E. coli. Both these repressors were observed to specifically bind with the same cognate operator DNA. The operator-binding activity of CIts391 was shown to differ significantly than that of the CI at 32 to 42 degrees C. While 40-95% operator-binding activity was shown to be retained at 35 to 42 degrees C in CI, more than 75% operator-binding activity was lost in CIts391 at 35 to 38 degrees C, although the latter showed only 10% less binding compared to that of the former at 32 degrees C. The CIts391 showed almost no binding at 42 degrees C. An in vivo study showed that the CI repressor inhibited the growth of a clear plaque former mutant of the L1 phage more strongly than that of the CIts391 repressor at both 32 and 42 degrees C. The half-life of the CIts391-operator complex was found to be about 8 times less than that of the CI-operator complex at 32 degrees C. Interestingly, the repressor-operator complexes preformed at 0 degrees C have shown varying degrees of resistance to dissociation at the temperatures which inhibit the formation of these complexes are inhibited. The CI repressor, but not that of CIts391, regains most of the DNA-binding activity on cooling to 32 degrees C after preincubation at 42 to 52 degrees C. All these data suggest that the 131(st) proline residue at the C-terminal half of CI, which changed to leucine in the CIts391, plays a crucial role in binding the L1 repressor to the cognate operator DNA, although the helix-turn-helix DNA-binding motif of the L1 repressor is located at its N-terminal end.     

Pairing of P1 plasmid partition sites by ParB

The mechanisms by which bacterial plasmids and chromosomes are partitioned are largely obscure, but it has long been assumed that the molecules to be separated are initially paired, as are sister chromatids in mitosis. We offer in vivo evidence that the partition protein ParB encoded by the bacterial plasmid P1 can pair cis-acting partition sites of P1 inserted in a small, multicopy plasmid. ParB was shown previously to be capable of extensive spreading along DNA flanking the partition sites. Experiments in which ParB spreading was constrained by physical roadblocks suggest that extensive spreading is not required for the pairing process.     

Control of plasmid DNA replication by iterons: no longer paradoxical

Replication origins of a family of bacterial plasmids have multiple sites, called iterons, for binding a plasmid-specific replication initiator protein. The iteron-initiator interactions are essential for plasmid replication as well as for inhibition of plasmid over-replication. The inhibition increases with plasmid copy number and eventually shuts plasmid replication off completely. The mechanism of inhibition appears to be handcuffing, the coupling of origins via iteron-bound initiators that block origin function. The probability of a trans-reaction such as handcuffing is expected to increase with plasmid copy number and diminish with increases in cell volume, explaining how the copy number can be maintained in a growing cell. Control is also exerted at the level of initiator synthesis and activation by chaperones. We propose that increases in active initiators promote initiation by overcoming handcuffing, but handcuffing dominates when the copy number reaches a threshold. Handcuffing should be ultrasensitive to copy number, as the negative control by iterons can be stringent (switch-like).     

Melatonin in the regulation of annual testicular events in carp Catla catla: evidence from the studies on the effects of exogenous melatonin, continuous light, and continuous darkness

The physiological significance of melatonin in the regulation of annual testicular events in a major carp Catla catla was evaluated through studies on the effects of graded dose (25, 50, or 100 µg/100 g body wt.) of melatonin exogenously administered for different durations (1, 15, or 30 days) and manipulation of the endogenous melatonin system by exposing the fish to constant darkness (DD) or constant light (LL) for 30 days. An identical experimental schedule was followed during the preparatory (February-March), pre-spawning (April-May), spawning (July-August), and post-spawning (September-October) phases of the annual cycle. Irrespective of the reproductive status of the carp, LL suppressed while DD increased the mid-day and mid-night values of melatonin compared to respective controls. Influences of exogenous melatonin varied in relation to the dose and duration of treatment and the reproductive status of the carp. However, testicular response to exogenous melatonin (at 100 µg, for 30 days) and DD in each reproductive phase was almost identical. Notably, precocious testicular maturation occurred in both DD and melatonin-injected fish during the preparatory phase and in LL carps during the pre-spawning phase. In contrast, testicular functions in both the melatonin-treated and DD fish were inhibited during the pre-spawning and spawning phases, while the testes did not respond to any treatment during the post-spawning phase. In conclusion, this study provided the first experimental evidence that melatonin plays a significant role in the regulation of annual testicular events in a sub-tropical surface-dwelling carp Catla catla, but the influence of this pineal hormone on the seasonal activity of testis varies in relation to the reproductive status of the concerned fish.