Chi-Stimulated Recombination between Phage λ and the Plasmid λdv

Chi promotes Rec-mediated recombination between phage lambda DNA and the homologous plasmid lambda dv. In the absence of Chi, some of the interactions splice lambda dv into lambda, whereas others patch information from lambda dv into lambda. When Chi is in the phage DNA, splices and patches are increased in frequency by the same factor. This result strengthens the analogy between Chi and recombination-promoting elements in fungi. It also rules out one model for the previously reported orientation dependence of Chi phenotype.     

Role of the tof gene in the production and perpetuation of the λdv plasmid

Molecular Genetics and Genomics - A series of λ derivatives carrying tof mutations were tested for their ability to give rise to plasmid λ dv. Phages carrying tof mutations that distorted...     

Bilayer polarity and its thermal dependency in the ?o and ?d phases of binary phosphatidylcholine/cholesterol mixtures

Diverse variations in membrane properties are observed in binary phosphatidylcholine/cholesterol mixtures. These mixtures are nonideal, displaying single or phase coexistence, depending on chemical composition and other thermodynamic parameters. When compared with pure phospholipid bilayers, there are changes in water permeability, bilayer thickness and thermomechanical properties, molecular packing and conformational freedom of phospholipid acyl chains, in internal dipolar potential and in lipid lateral diffusion. Based on the phase diagrams for DMPC/cholesterol and DPPC/cholesterol, we compare the equivalent polarity of pure bilayers with specific compositions of these mixtures, by using the Py empirical scale of polarity. Besides the contrast between pure and mixed lipid bilayers, we find that liquid-ordered (?_o) and liquid-disordered (?_d) phases display significantly different polarities. Moreover, in the ?_o phase, the polarities of bilayers and their thermal dependences vary with the chemical composition, showing noteworthy differences for cholesterol proportions at 35, 40, and 45 mol%. At 20 °C, for DMPC/cholesterol at 35 and 45 mol%, the equivalent dielectric constants are 21.8 and 23.8, respectively. Additionally, we illustrate potential implications of polarity in various membrane-based processes and reactions, proposing that for cholesterol containing bilayers, it may also go along with the occurrence of lateral heterogeneity in biological membranes.     

Interaction between the Sbcc Gene of Escherichia Coli and the Gam Gene of Phage λ

gam mutants of phage lambda carrying long palindromes fail to form plaques on wild-type Escherichia coli but do grow on strains that are mutant in the sbcC gene. gam + lambda carrying the same palindrome grow on both hosts and on a host deleted for the recB, C and D genes. These results suggest that the Gam protein of lambda, known to interact also with E. coli's recBCD protein, can interact with the product of the sbcC gene.     

Structural and Functional Characterization of the Redβ Recombinase from Bacteriophage λ

The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure.     

Complementation and characterization of the nested Rz and Rz1 reading frames in the genome of bacteriophage λ

Transposon insertions in the Rz gene of bacteriophage λ block lysis if the medium contains divalent cations at concentrations greater than 5?mM, but otherwise cause no change in phenotype. The Rz protein is thought to have an endopeptidase activity, previously reported in λ lysates, which might be involved in cleavage of oligopeptide crosslinks between glycosidic strands in the peptidoglycan and the Lpp lipoproteins of the outer bacterial membrane. Recently, a small lipoprotein has been reported as the product of a short reading frame, designated Rz1, in the +1 register within Rz. This protein has been detected in membranes of induced λ lysogens. To determine whether Rz1 has a function in the λ vegetative cycle, amber nonsense alleles of Rz and Rz1 have been constructed by site-directed mutagenesis and used for complementation and suppression analysis. Both Rzam and Rz1am alleles have phenotypes identical to those of the original Rz insertion alleles, and complement and are fully suppressed in a supE host, indicating that the two genes are independent, trans-acting genes encoding proteins required for lysis in the presence of cations. Moreover, supF suppresses Rzam but not the Rz1am mutation, and the defective Rz1am product in the supF host shows a partially dominant character and significantly retards lysis even in the absence of additional cations in the medium. Rz and Rz1 represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway.     

RNA Synthesis Startpoints in Bacteriophage λ: Are the Promoter and Operator Transcribed?

Hybridization and fingerprint analysis of in vitro synthesized λ RNA shows that four chains are initiated at sites corresponding to those seen in vivo and that each molecule starts with a specific sequence. In one case examined, the major leftward operon, the promoter and operator and not transcribed into RNA.     

Cleavage-resistant fusion proteins of the M2 muscarinic receptor and Gαi1. Homotropic and heterotropic effects in the binding of ligands

Background

G protein-coupled receptors fused to a Gα-subunit are functionally similar to their unfused counterparts. They offer an intriguing view into the nature of the receptor–G protein complex, but their usefulness depends upon the stability of the fusion.

Methods

Fusion proteins of the M₂ muscarinic receptor and the α-subunit of G_i1 were expressed in CHO and Sf9 cells, extracted in digitonin–cholate, and examined for their binding properties and their electrophoretic mobility on western blots.

Results

Receptor fused to native α_i1 underwent proteolysis near the point of fusion to release a fragment with the mobility of α_i1. The cleavage was prevented by truncation of the α-subunit at position 18. Binding of the agonist oxotremorine-M to the stable fusion protein from Sf9 cells was biphasic, and guanylylimidodiphosphate promoted an apparent interconversion of sites from higher to lower affinity. With receptor from CHO cells, the apparent capacity for N-[³H]methylscopolamine was 60% of that for [³H]quinuclidinylbenzilate; binding at saturating concentrations of the latter was inhibited in a noncompetitive manner at low concentrations of unlabeled N-methylscopolamine.

Conclusions

A stable fusion protein of the M₂ receptor and truncated α_i1 resembles the native receptor–G protein complex with respect to the guanyl nucleotide-sensitive binding of agonists and the noncompetitive binding of antagonists.

General significance

Release of the α-subunit is likely to occur with other such fusion proteins, rendering the data ambiguous or misleading. The properties of a chemically stable fusion protein support the notion that signaling proceeds via a stable multimeric complex of receptor and G protein.     

Evidence for 6-keto-PGF1α in adrenal cortex of the rat and effects of 6-keto-PGF1α and PGI2 on adrenal cAMP levels and steroidogenesis

Both intact cortical tissue and isolated cortical cells from the adrenal gland of the rat were analyzed for 6-keto-PGF_1α, the hydrolysis metabolite of PGI₂, using high-performance liquid chromatography and gas chromatography-mass spectrometry. 6-Keto-PGF_1α was present in both incubations of intact tissue and isolated cells of the adrenal cortex, at higher concentrations than either PGF_2α or PGE₂. Thus, the cortex does not depend upon vascular components for the synthesis of the PGI₂ metabolite. Studies $\text{in vitro}$, using isolated cortical cells exposed to 6-keto-PGF_1α (10^?6-10^?4M), show that this PG does not alter cAMP levels or steroidogenesis. Cells exposed to PGI₂ (10^?6-10^?4M), however, show a concentration-dependent increase of up to 4-fold in the levels of cAMP without altering corticosterone production. ACTH (5–200 μU/ml) increased cAMP levels up to 14-fold, and corticosterone levels up to 6-fold, in isolated cells. ACTH plus PGI₂ produced an additive increase in levels of cAMP, however, the steroidogenic response was equal to that elicited by ACTH alone. Adrenal glands of the rat perfused $\text{in situ}$ with PGI₂ showed a small decrease in corticosterone production, whereas ACTH greatly stimulated steroid release. Thus, while 6-keto-PGF_1α is present in the rat adrenal cortex, its precursor, PGI₂, is not a steroidogenic agent in this tissue although it does stimulate the accumulation of cAMP.     

DNA Packaging by λ-Like Bacteriophages: Mutations Broadening the Packaging Specificity of Terminase,the λ-Packaging Enzyme

The DNA-packaging specificities of phages λ and 21 depend on the specific DNA interactions of the small terminase subunits, which have support helix-turn-recognition helix-wing DNA-binding motifs. λ-Terminase with the recognition helix of 21 preferentially packages 21 DNA. This chimeric terminase''s ability to package λDNA is reduced ∼20-fold. Phage λ with the chimeric terminase is unable to form plaques, but pseudorevertants are readily obtained. Some pseudorevertants have trans-acting suppressors that change codons of the recognition helix. Some of these codons appear to remove an unfavorable base-pair contact; others appear to create a novel nonspecific DNA contact. Helper-packaging experiments show that these mutant terminases have lost the ability to discriminate between λ and 21 during DNA packaging. Two cis-acting suppressors affect cosB, the small subunit''s DNA-binding site. Each changes a cosB^λ-specific base pair to a cosB²¹-specific base pair. These cosB suppressors cause enhanced DNA packaging by 21-specific terminase and reduce packaging by λ-terminase. Both the cognate support helix and turn are required for strong packaging discrimination. The wing does not contribute to cosB specificity. Evolution of packaging specificity is discussed, including a model in which λ- and 21-packaging specificities diverged from a common ancestor phage with broad packaging specificity.VIRUSES must package viral chromosomes from nucleic acid pools that include host-cell nucleic acids, so specific recognition of the viral nucleic acid is essential during virion assembly. For large DNA viruses, including the tailed double-strand DNA (dsDNA) bacteriophages, the herpesviruses, and the adenoviruses, DNA-packaging proteins recognize specific sequences on the viral chromosomes (reviewed in Baines and Weller 2005 and Ostapchuk and Hearing 2005, respectively). For the dsDNA viruses that produce virion chromosomes by processing concatemeric DNA, a viral terminase enzyme functions in the recognition and cutting of concatemeric DNA and subsequently sponsors DNA translocation. λ-Terminase is a heterooligomer of large and small subunits, gpA and gpNu1, respectively. Cutting of concatemeric DNA is carried out by gpA''s endonuclease activity (Becker and Gold 1978; Davidson and Gold 1992; Hwang and Feiss 1996). Three DNA subsites, cosQ, cosN, and cosB, are contained in the ∼200-bp-long cos site and orchestrate DNA packaging through interactions with terminase (Figure 1A; reviewed in Feiss and Catalano 2005). gpA introduces staggered nicks in cosN to generate the 12-bp cohesive ends of mature λDNA molecules. Efficient and accurate nicking of cosN requires anchoring of gpA by gpNu1, which binds to the adjacent cosB subsite (Higgins and Becker 1994b; Hang et al. 2001).Open in a separate windowFigure 1.—The cos and terminase region of the λ-chromosome. (A) (Top) Map of cos and the terminase-encoding Nu1 and A genes. The black bar indicates the location of the winged helix-turn-helix DNA-binding motifs in the N-terminal domain of gpNu1. (Bottom) cos subsites: cosQ is required for termination of DNA packaging; cosN is the site where the large terminase subunit, gpA, introduces staggered nicks to generate the cohesive ends of virion DNA molecules; and cosB contains the gpNu1-binding sites R1, R2, and R3 along with the IHF-binding site I1. (B) (Top) Schematic of gpNu1 residues 1–42, including the support (blue) and recognition (red) α-helixes and the wing loop (magenta). β1 and β2 are short β-strands flanking the DNA-binding elements. (Bottom) Sequences are a comparison of residues of λ''s gpNu1 and phage 21''s gp1, with conserved resides indicated by vertical lines. Note that the recognition helixes of gpNu1 and gp1 differ by four residues, all likely solvent-exposed (Becker and Murialdo 1990; de Beer et al. 2002). (C) Three-dimensional structure of the winged helix-turn-helix-containing, N-terminal domain of gpNu1 (residues 1–68) (de Beer et al. 2002). Side groups of solvent-exposed residues of the recognition helix are displayed. Color coded as in B.λ''s cosB (cosB^λ) is a complex subsite containing three copies of a gpNu1-binding sequence, the R sequence, plus a site, I1, for the integration host factor (IHF), the Escherichia coli DNA-bending protein. The order of sites is cosN–R3–I1–R2–R1. The amino-terminal half of gpNu1 contains a winged helix-turn-helix DNA-binding motif (Figure 1, B and C; Gajiwala and Burley 2000) that interacts with the R sequences. Further, the amino-terminal domain of gpNu1 is a tight dimer (Figure 1C, de Beer et al. 2002). The IHF-induced bend at I1 creates a DNA hairpin in cosB that positions the major grooves of R3 and R2 to face inward, so that the helix-turn-helix motifs of dimeric gpNu1 can be docked into them. The wing loops are positioned to make minor groove contacts with R3 and R2. Thus it is proposed that gpA is positioned to nick cosN by assembly of a bent structure with dimeric gpNu1 bound to R3 and R2 (Becker and Murialdo 1990; de Beer et al. 2002). A variety of studies indicate that the positioning of gpNu1 at R3 is crucial and that the other interactions function to create and/or stabilize the R3–gpNu1 interaction (Cue and Feiss 1993a; Higgins and Becker 1994a; Hang et al. 2001).DNA packaging initiates when terminase binds and nicks a cos. Following cosN nicking and separation of the cohesive ends, terminase remains bound to the cosB-containing chromosome end (Becker et al. 1977; Yang et al. 1997). The DNA-bound terminase docks on the portal vertex of a prohead, the empty, immature virion head shell. Assembly of the ternary prohead–terminase–DNA complex activates gpA''s potent translocation ATPase, and the viral DNA is translocated into the prohead (Yang and Catalano 2003; Dhar and Feiss 2005). Translocation brings the next cos along the concatemer to the portal-docked terminase (Feiss and Widner 1982). The downstream cos is cleaved by terminase, completing packaging of the chromosome. Recognition of the downstream cos requires cosQ and cosN (Cue and Feiss 2001). Following DNA packaging, terminase undocks from the filled head. Attachment of a tail to the DNA-filled head completes virion assembly. The undocked terminase remains bound to and sponsors the packaging of the next chromosome along the concatemer.The interactions between the recognition helix of gpNu1 and an R sequence are typical for helix-turn-helix proteins, as shown by genetic studies of chimeras between λ and its relative, phage 21, as follows: λ and 21 have similarly organized cos sites; the cosB of 21 also has the R3–I1–R2–R1 structure. Nevertheless, the two phages have distinct packaging specificities. Base-pair differences in the R sequences account for packaging specificity (Becker and Murialdo 1990; Smith and Feiss 1993). cosN and cosQ are interchangeable between λ and 21 (Feiss et al. 1981). The consensus R sequences are 5′-CGTTTCCtTTCT-3′ for cosB^λ and 5′-CaTGTCGGncCT-3′ for cosB²¹, where capitalized residues are conserved in all three R sequences of both phages; underlined and capitalized are two residues conserved in all three R sequences of both phages, but which differ between cosB^λ and cosB²¹ (Becker and Murialdo 1990). These two conserved but phage-specific base pairs are likely to be of major importance for specificity. Similarly, the recognition helixes of the helix-turn-helix motifs of the small subunits of λ (gpNu1) and 21 (gp1) terminases differ in four amino acid residues that account for packaging specificity (Figure 1; Becker and Murialdo 1990).In earlier work (de Beer et al. 2002), we showed that modifying λ-terminase by replacing the gpNu1 recognition helix with that of 21''s gp1 created a terminase (gpNu1^hy1 terminase) that was specific for the cosB of phage 21 (designated cosB²¹). That is, λ cosB²¹ Nu1^hy1 was viable, but λ cosB^λ Nu1^hy1 was inviable due to the specificity mismatch between cosB^λ and the cosB²¹-specific recognition helix of the chimeric small terminase subunit, gpNu1^hy1. The Nu1^hy1 terminase packages cosB²¹ chromosomes ∼10-fold more efficiently than it does cosB^λ chromosomes. This 10-fold discrimination between cosB²¹ and cosB^λ chromosomes is much weaker than the >10⁴-fold discrimination shown by wild-type λ and 21 terminases (de Beer et al. 2002). Because of the modest discrimination of Nu1^hy1 terminase, the yield of λ cosB^λ Nu1^hy1 is only slightly below the yield required for plaque formation. Lysates of λ cosB^λ Nu1^hy1 contain plaque-forming pseudorevertants at a level expected for single mutations. A number of these pseudorevertants were sequenced and found to contain mutations in cosB^λ or in the Nu1^hy1 gene. Here we report on in vivo packaging studies on the effects of these Nu1^hy1 and cosB^λ suppressor mutations on packaging specificity.     

Influence of prostaglandins (PG) E2 and F2α on the inflammatory process

PGF_2^α, but not PGE₂, induces a slight pedal edema when given alone. Both compounds were equipotent in the carrageenin-induced rat paw edema. Locally administered, PGE₂ and PGF_2^α did not exacerbate, but rather inhibited inflammations induced by various agents such as 1% carrageenin or 1% egg white. The administration of PGE₂ directly into cotton pellets or into the rat's hind paw in combination with M. butyricum significantly inhibited, respectively, granuloma formation and the polyarthritis. Subcutaneously, both prostaglandins inhibited the adjuvant induced polyarthritis. Neither PGE₂ nor PGF_2^α inhibited the anti-edema properties of non-steroidal or steroidal anti-inflammatory standards. A greater anti-edema activity was observed with the combination treatment than with the anti-inflammatory standards alone. We were unable to decrease the anti-inflammatory activity of the steroidal and non-steroidal standards or increase the inflammatory potential of the phlogistic agents.     

Effect of PGD2, PGE2, PGF2α and PGI2 on blood pressure,heart rate and plasma catecholamine responses to spinal cord stimulation in the rat

The following experiments were designed in order to examine the inter-relationships of various prostaglandins (PG's) and the adrenergic nervous system, in conjunction with blood pressure and heart rate responses, $\text{in vivo}$. Stimulation of the entire spinal cord (50v, 0.3–3 Hz, 1.0 msec) of the pithed rat increased blood pressure, heart rate and plasma epinephrine (EPI) and norepinephrine (NE) concentration (radioenzymatic-thin layer chromatographic assay). Infusion of PGE₂(10–30 μg/kg. min, i.v.) suppressed blood pressure and heart rate responses to spinal cord stimulation while plasma EPI (but not NE) was augmented over levels found in control animals. PGI₂ (0.03–3.0 μg/kg. min, i.v.) suppressed the blood pressure response to spinal cord stimulation without any effect on heart rate or the plasma catecholamine levels. PGE₂ and PGF_2α(10–30 μg/kg. min, i.v.) did not change the blood pressure, heart rate or plasma EPI and NE responses to the spinal cord stimulation although PGF_2α disclosed an overall vasopressor effect during the pre-stimulation period. At the pre-stimulation period it was also observed that PGE₂, PGF_2α and PGI₂, had a positive chronotropic effect on the heart rate, the cardiac accelerating effect of PGE₂ was not abolished by propanolol. These $\text{in vivo}$ studies suggest that in the rat, PGE₂ and PGI₂ modulate sympathetic responses, primarily by interaction with the post-synaptic elements — PGE₂ on both blood vessels and the heart and PGI₂ by acting principally on blood vessels.     

Critical evaluation of electron transfer kinetics in P700–FA/FB, P700–FX, and P700–A1 Photosystem I core complexes in liquid and in trehalose glass

This work aims to fully elucidate the effects of a trehalose glassy matrix on electron transfer reactions in cyanobacterial Photosystem I (PS I). Forward and backward electron transfer rates from A_1A^? and A_1B^? to F_X, and charge recombination rates from A₀^?, A_1B^?, A_1A^?, F_X^?, and [F_A/F_B]^? to P₇₀₀⁺ were measured in P₇₀₀–F_A/F_B complexes, P₇₀₀–F_X cores, and P₇₀₀–A₁ cores, both in liquid and in a trehalose glassy matrix at 11% humidity. By comparing CONTIN-resolved kinetic events over 6 orders of time in increasingly simplified versions of PS I at 480?nm, a wavelength that reports primarily A_1A^?/A_1B^? oxidation, and over 9 orders of time at 830?nm, a wavelength that reports P₇₀₀⁺ reduction and A₀^? oxidation, assignments could be made for nearly all of the resolved kinetic phases. Trehalose-embedded PS I samples demonstrated partially arrested forward electron transfer. The fractions of complexes in which electron transfer did not proceed beyond A₀, A₁ and F_X were 53%, 16% and 22%, respectively, with only 10% of electrons reaching the terminal F_A/F_B clusters. The ~10?μs and ~150?μs components in both liquid and trehalose-embedded PS I were assigned to recombination between A_1B^? and P₇₀₀⁺ and between A_1A^? and P₇₀₀⁺, respectively. The kinetics and amplitudes of these resolved kinetic phases in liquid and trehalose-embedded PS I samples could be well-fitted by a kinetic model that allowed us to calculate the asymmetrical contribution of the A_1A^? and A_1B^? quinones to the electrochromic signal at 480?nm. Possible reasons for these effects are discussed.     

Comparison of the effects of prostaglandins D2, F2α and E1 on spontaneous contractions of rabbit oviduct

The effects of PGD₂, PGF_2α and PGE₁ were studied on the circular muscle of post-ovulatory rabbit oviducts $\text{in vitro}$. PGE₁ inhibited spontaneous contractile activity. Lower concentrations of PGD₂ and PGF_2α were stimulatory and higher concentrations were inhibitory. Since PGD₂ may be produced in the oviduct, any hypothesis concerning the role of prostaglandins in the control of oviductal motility and ovum transport should include PGD₂ as well as PGFs and PGEs.