Magnetic Circular Dichroism of Molecules in Dense Media: Relation Between Magnetic Circular Dichroism and Hammett's Constants

The linear relation between the magnetic circular dichroism (benzene ¹A_1g → ¹B_2u transition) of monosubstituted and 1,4-disubstituted benzenes and the substituent constants σ and σ_R are compared. In all cases, better linear correlations were found between the magnetic circular dichroism and σ_R. Three series of 1,4-disubstituted benzenes, XC₆H₄I, XC₆H₄NO₂, and XC₆H₄CO₂H, have been chosen for the magnetic circular dichroism measurements.     

Magnetic Circular Dichroism Studies XXV. A Preliminary Investigation of Microsomal Cytochromes

The application of magnetic circular dichroism as an optical probe for simultaneous identification and determination of at least two microsomal cytochromes is demonstrated. The assignments of the bands in the spectra of microsomal suspensions are made from the spectra of soluble preparations of cytochrome P-450 obtained from Pseudomonas putida and of cytochrome b(5) obtained from rat livers.     

Structure of the Replicating DNA from Bacteriophage T4

At an early stage of replication, parental T4 DNA shows a loop structure often displaying two 3'-ended, single-stranded "whiskers", located in trans configuration at the branching-points. Several such loops have been observed within a single T4 molecule. Occasionally, reinitiation occurred in the middle of a loop, which suggests that the loop was growing in both directions.     

Coordinated DNA Replication by the Bacteriophage T4 Replisome

The T4 bacteriophage encodes eight proteins, which are sufficient to carry out coordinated leading and lagging strand DNA synthesis. These purified proteins have been used to reconstitute DNA synthesis in vitro and are a well-characterized model system. Recent work on the T4 replisome has yielded more detailed insight into the dynamics and coordination of proteins at the replication fork. Since the leading and lagging strands are synthesized in opposite directions, coordination of DNA synthesis as well as priming and unwinding is accomplished by several protein complexes. These protein complexes serve to link catalytic activities and physically tether proteins to the replication fork. Essential to both leading and lagging strand synthesis is the formation of a holoenzyme complex composed of the polymerase and a processivity clamp. The two holoenzymes form a dimer allowing the lagging strand polymerase to be retained within the replisome after completion of each Okazaki fragment. The helicase and primase also form a complex known as the primosome, which unwinds the duplex DNA while also synthesizing primers on the lagging strand. Future studies will likely focus on defining the orientations and architecture of protein complexes at the replication fork.     

Isolation of Heterogeneous Circular DNA from Induced Lysogens of Bacteriophage Mu-1

Covalently-closed circular DNA molecules are formed after induction of phage Mu cts4 and after infection with phage Mu cts4. The circular molecules obtained after induction have a molecular length range from 36.5 to 156.7 kilobases as measured by electron microscopic techniques. These heterogeneous molecules have no consistent correlation to exact multiples of a Mu genome equivalent (37.3 +/- 1.2 kilobases). Direct evidence is given that these molecules contain phage Mu DNA that is covalently linked to other DNA sequences.     

Detection of Bacteriophage T4- and T5-Coded Transfer RNAs

A hybridization procedure using mixtures of radioactive aminoacyl-tRNA is described for detecting new phage-induced tRNA species. Five phage-coded tRNA species have been identified from T4 phage infected bacteria and 14 from T5 phage infected cells.     

Magnetic Circular Dichroism Studies XXXV. A Comparison of Cytochromes P-450 and P-448

Cytochromes P-450 and P-448 in microsomal suspensions have been shown to be spectrally distinct by magnetic circular dichroism spectroscopy. Furthermore, this technique can be used to measure induction of these two cytochromes by phenobarbital and 3-methyl-cholanthrene. Magnetic circular dichroism spectroscopy is thus at least as useful as difference spectroscopy for the investigation of P-450 and P-448 and more informative because the presence of cytochrome b₅ and hemoglobin can be detected concurrently. We have also shown that the molar magnetic ellipticity for reduced + CO treated cytochrome P-450 of Pseudomonas grown on camphor is of similar value to that of reduced + CO treated microsomal P-450 and P-448.     

The Three Dimensional Structure of the Lysozyme from Bacteriophage T4

The three dimensional structure of the lysozyme from bacteriophage T4 has been determined from a 2.5 A resolution electron density map. About 60% of the molecule is in a helical conformation and there is one region consisting of antiparallel beta-structure. The polypeptide backbone folds into two distinct lobes linked in part by a long helix. In the region between the two lobes, there is a cleft which deepens into a hole or cavity, about 6-8 A in diameter, extending from one side of the molecule to the other. This opening is closed off by side chains which extend to within 3-5 A of each other. A number of mutant lysozymes in which residues in the vicinity of the opening are modified have markedly reduced catalytic activity, suggesting that this region of the molecule may be catalytically important. The three dimensional structure of T4 phage lysozyme is quite different from that of hen egg-white lysozyme although it is not clear at this time whether or not the mechanisms of catalysis of the respective enzymes are related.     

Self-Association of Gene-32 Protein of Bacteriophage T4

The self-association of gene-32 protein has been studied by sedimentation equilibrium centrifugation and polyacrylamide gel electrophoresis, in order to better understand its role in DNA replication and genetic recombination. The monomer molecular weight of gene-32 protein is 38,000 in guanidine hydrochloride and 34,000 in sodium dodecyl sulfate, in agreement with the results of Alberts and coworkers. Stable dimers of gene-32 protein occur under various conditions, among which are high ionic strength and pH 10. The occurrence of stable dimers under some conditions and higher aggregates under others indicates there are two types of protein-protein interactions occurring in gene-32 protein self-association. The association that occurs above about 0.1 mg/ml concentration of protein produces at least decamers.A model for the DNA replication fork is postulated that requires the two different interactions that occur in gene-32 protein aggregation. In the model, gene-32 protein holds the two strands of the DNA duplex in a conformation that prevents their reannealing and, therefore, facilitates replication and recombination.     

Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs

The bacteriophage T4-encoded RegB endoribonuclease is produced during the early stage of phage development and targets mostly (but not exclusively) the Shine-Dalgarno sequences of early genes. In this work, we show that the degradation of RegB-cleaved mRNAs depends on a functional T4 polynucleotide kinase/phosphatase (PNK). The 5'-OH produced by RegB cleavage is phosphorylated by the kinase activity of PNK. This modification allows host RNases G and E, with activity that is strongly stimulated by 5'-monophosphate termini, to attack mRNAs from the 5'-end, causing their destabilization. The PNK-dependent pathway of degradation becomes effective 5 min postinfection, consistent with our finding that several minutes are required for PNK to accumulate after infection. Our work emphasizes the importance of the nature of the 5' terminus for mRNA stability and depicts a pathway of mRNA degradation with 5'- to 3'-polarity in cells devoid of 5'-3' exonucleases. It also ascribes a role for T4 PNK during normal phage development.     

The Temporal Expression of T2r+ Bacteriophage Genes In Vivo and In Vitro

The kinetic order of synthesis of deoxycytidylate deaminase (EC 3.5.4.12), deoxycytidylate hydroxymethylase (EC 2.1.2.b), dihydrofolate reductase (EC 1.5.1.3), 5-hydroxymethyldeoxycytidylate kinase (EC 2.7.4.4), and thymidylate synthetase (EC 2.1.1.b) after infection of Escherichia coli with T2r(+) bacteriophage was found not to correlate with their order of synthesis in an in vitro protein-synthesizing preparation. The in vivo and in vitro synthesis of enzyme-specific messenger RNA measured in the protein-synthesizing preparation preceded each enzyme by about 1 min. Through the use of sheared DNA, it was shown that the thymidylate synthetase gene was most susceptible to a loss in template activity, which suggests that this gene is further removed from its promoter than the other genes are from theirs. With a DNA segment of 2.5 x 10(5) daltons, the synthesis of dihydrofolate reductase alone was obtained, but at a much reduced rate. Translation of the RNA from phage-infected cells treated with chloramphenicol yielded amounts of dihydrofolate reductase and deoxycytidylate hydroxymethylase activities similar to those obtained with RNA from untreated infected cells. These results suggest that the chloramphenicol RNA, which consists primarily of immediate-early RNA, may contain most, if not all, of the information required for the synthesis of phage dihydrofolate reductase and deoxycytidylate hydroxymethylase.     

Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation.

The bacteriophage T4 regA protein is a translational repressor of a subset of phage mRNAs. We show here that purified regA protein binds specifically to target mRNAs near the initiating AUG and occludes binding of ribosomes. Translational repression by regA protein diminishes expression of many genes whose mRNA sequences around the initiating AUG codons are different. A comparison of nucleotide sequences from several regA-repressed mRNAs suggests that the initiating AUG is an important, but not sufficient, sequence for regA binding.     

Purification and Properties of Bacteriophage T4-Induced RNA Ligase

An enzyme, purified 300-fold from Escherichia coli infected with bacteriophage T4, catalyzes the conversion of 5'-termini of polyribonucleotides to internal phosphodiester bonds. The reaction requires ATP and Mg(++). For every 5'-(32)P terminus rendered resistant to alkaline phosphatase, an equal amount of AMP and PPi are formed. Various polyribonucleotides are substrates in the reaction; to date, the best substrate is [5'-(32)P]polyriboadenylate. With the latter substrate, no evidence of intermolecular reaction was obtained. However, the 5'-(32)P termini of poly(A) rendered resistant to alkaline phosphatase are also resistant to attack by RNase II, polynucleotide phosphorylase, and low concentrations of venom phosphodiesterase. Since the product formed with poly(A) lacks 3'-hydroxyl ends, as measured with these exonucleases, the enzyme appears to convert linear molecules of polyriboadenylate to a circular form by the intramolecular covalent linkage of the 5'-phosphate end to the 3'-hydroxyl terminus.     

In Vivo Repair of the Single-Strand Interruptions Contained in Bacteriophage T5 DNA

Bacteriophage T5 is known to contain several unique single-strand interruptions in only one strand of the duplex DNA. Analysis of labeled parental phage DNA from infected Escherichia coli shows that these nicks are repaired in vivo to yield intact double-stranded molecules. Sealing begins at about 6 min after infection and is independent of DNA replication. Repair may be an ordered process that starts at a unique end of the molecule.     

Packaging and Maturation of DNA of Bacteriophage T7 In Vitro

We have developed an in vitro complementation assay to demonstrate packaging and maturation of DNA of phage T7. Cells of Escherichia coli B infected with an appropriate T7 amber mutant are concentrated 200-fold and lysed by freezing and thawing. Two extracts from cells infected with different amber mutants are mixed and incubated at 30 degrees . Positive complementation results in a 100-fold increase in phage titer.Using this assay we have demonstrated the packaging of phage DNA from an extract that contains no phage heads (gene 9(-), 10(-)), within head structures present in an extract that contains no phage DNA (gene 5(-)). We have also demonstrated an activity in extracts that contain no phage DNA or heads (gene 5(-), 9(-), 10(-)), which complements gene 19(-)-infected cells. We have proven that this activity is due to the gene-19 product by showing that the activity is temperature-sensitive if the extract is made from cells infected with a mutant having a temperature-sensitive mutation in gene 19. This assay should be useful in elucidating the mechanism of packaging and maturation of DNA of phage T7.     

Changes in Intrinsic Circular Dichroism of Several Homogeneous Anti-Type III Pneumococcal Antibodies on Binding of a Small Hapten

Three homogeneous antibodies against the capsular polysaccharide of Type III pneumococci of similar specificities and affinities were purified from a single bleeding of an individual rabbit and fractionated by isoelectric focusing. A comparison of the circular dichroic spectra of the three antibodies revealed differences among them, although the spectra were generally similar to those obtained previously for heterogeneous rabbit antibodies [Cathou, R. E., Kulcycki, A., Jr. & Haber, E. (1968) Biochemistry 7, 3958].On binding of the hexasaccharide, -[-->3)-beta-D-glucuronic acid-(1-->4)-beta-D-glucose-(1-](3)-->, significant changes in all three circular dichroic spectra were observed. Since the oligosaccharide alone shows no transitions above 220 nm, these spectral changes can be attributed to changes in the intrinsic optical activity of the antibodies. Calculated difference circular dichroism spectra (of antibody minus that of antibody-hapten complex) of the three antibodies are different from each other, and resemble spectra of tryptophan and tyrosine derivatives. These changes in optical activity can be ascribed to changes in the asymmetric environments of aromatic chromophores directly in the combining site and/or to changes in orientation inside or beyond the site.Since the hapten-antibody interactions are different in the three antibodies, as shown by the difference spectra, the structures of the combining sites are presumably also different. We have interpreted these observations to mean that a relatively simple ligand may be bound by several different complementary sites.     

The Beauty of Bacteriophage T4 Research: Lindsay W. Black and the T4 Head Assembly

Viruses are biochemically complex structures and mainly consist of folded proteins that contain nucleic acids. Bacteriophage T4 is one of most prominent examples, having a tail structure that contracts during the infection process. Intracellular phage multiplication leads to separate self-directed assembly reactions of proheads, tails and tail fibers. The proheads are packaged with concatemeric DNA produced by tandem replication reactions of the parental DNA molecule. Once DNA packaging is completed, the head is joined with the tail and six long fibers are attached. The mature particles are then released from the cell via lysis, another tightly regulated process. These processes have been studied in molecular detail leading to a fascinating view of the protein-folding dynamics that direct the structural interplay of assembled complexes. Lindsay W. Black dedicated his career to identifying and defining the molecular events required to form the T4 virion. He leaves us with rich insights into the astonishingly precise molecular clockwork that co-ordinates all of the players in T4 assembly, both viral and cellular. Here, we summarize Lindsay’s key research contributions that are certain to stimulate our future science for many years to come.     

Regions of Single-Stranded DNA in the Growing Points of Replicating Bacteriophage T7 Chromosomes

In partially replicated T7 chromosomes, the points where parental strands are separating and new DNA is being synthesized can be seen in the electron microscope to contain regions of single-stranded template DNA. The single-stranded regions are located on only one of the two daughter arms of the replicating chromosome. Inman and Schnös observed such single-stranded regions in 50% of the growing points of replicating lambda DNA, and, as reported in this paper, we find them in about 85% of the growing points of T7 DNA. Both studies support the conclusion that DNA synthesis involves the direct elongation of one daughter strand in the growing point. Evidently, this elongation is accompanied by the unwinding of the parental double helix to expose a region of single-stranded DNA which is then converted to the duplex state by a discontinuous mechanism involving the synthesis of DNA fragments.