On the internal structure of bacteriophage lambda

The structure of bacteriophage lambda has been studied by electron microscopy of negatively stained particles. The phage particles will eject their DNA if they are heated or dialyzed against a chelating agent. The ghost particles, so formed, have a channel running down their tails. Since the channel is not visible in normal particles, the channel may be filled with part of the DNA molecule. Up to 30% of the ghosts contain round objects about half the internal diameter of the head. The round objects, called "cores," have the same buoyant density as the coat protein. The core may be a protein spool about which the phage DNA is wound.     

Comparative study on the mechanisms of rotavirus inactivation by sodium dodecyl sulfate and ethylenediaminetetraacetate.

This report describes a comparative study on the effects of the anionic detergent sodium dodecyl sulfate and the chelating agent ethylenediaminetetraacetate on purified rotavirus SA-11 particles. Both chemicals readily inactivated rotavirus at quite low concentrations and under very mild conditions. In addition, both agents modified the viral capsid and prevented the adsorption of inactivated virions to cells. Capsid damage by ethylenediaminetetraacetate caused a shift in the densities of rotavirions from about 1.35 to about 1.37 g/ml and a reduction in their sedimentation coefficients. Sodium dodecyl sulfate, on the other hand, did not detectably alter either of these physical properties of rotavirions. Both agents caused some alteration of the isoelectric points of the virions. Finally, analysis of rotavirus proteins showed that ethylenediaminetetraacetate caused the loss of two protein peaks from the electrophoretic pattern of virions but sodium dodecyl sulfate caused the loss of only one of these same protein peaks.     

Comparative study on the mechanisms of rotavirus inactivation by sodium dodecyl sulfate and ethylenediaminetetraacetate

This report describes a comparative study on the effects of the anionic detergent sodium dodecyl sulfate and the chelating agent ethylenediaminetetraacetate on purified rotavirus SA-11 particles. Both chemicals readily inactivated rotavirus at quite low concentrations and under very mild conditions. In addition, both agents modified the viral capsid and prevented the adsorption of inactivated virions to cells. Capsid damage by ethylenediaminetetraacetate caused a shift in the densities of rotavirions from about 1.35 to about 1.37 g/ml and a reduction in their sedimentation coefficients. Sodium dodecyl sulfate, on the other hand, did not detectably alter either of these physical properties of rotavirions. Both agents caused some alteration of the isoelectric points of the virions. Finally, analysis of rotavirus proteins showed that ethylenediaminetetraacetate caused the loss of two protein peaks from the electrophoretic pattern of virions but sodium dodecyl sulfate caused the loss of only one of these same protein peaks.     

Bacteriophage T4 baseplate components. I. Binding and location of the folic acid.

Two different proteins with high affinities for the pteridine ring of folic acid have been used to determine the location of this portion of the folate molecule in the tail plate of T4D and other T-even bacteriophage particles. The two proteins used were (i) antibody specific for folic acid and (ii) the folate-binding protein from bovine milk. Both proteins were examined for their effect on various intact and incomplete phage particles. Intact T2H was weakly inactivated by the antiserum but not by the milk protein. No other intact T-even phage, including T4D, was affected by these two proteins. When incomplete T4D particles were exposed in an in vitro morphogenesis system, it was found that neither of the two proteins affected either the addition of the long tail fibers to fiberless particles or the addition of tail cores to tail plates. On the other hand, these two proteins specifically blocked the addition of T4D gene 11 product to the bottom of T4D baseplates. After the addition of the gene 11 protein, these two reagents did not inhibit the further addition of the gene 12 protein to the baseplate. It can be concluded that the phage folic acid is a tightly bound baseplate constituent and that the pteridine portion of the folic acid is largely covered by the gene 11 protein.     

The net hydration of phage lambda

The banding density of phage lambda varies with the activity of water when the phage particles are banded in a series of different cesium salts. The results are comparable to those Hearst and Vinograd for free DNA. Lambda phage ghosts show less net hydration than the phage particles and band in a fairly narrow range of densities in these cesium salts. The phage banding density may be predicted to a first approximation by a simple additive approximation: the total net hydration of the phage is approximately equal to the net hydrations of free λ DNA λ hosts, all measured at the same water activity. The simple additive approximation is not adequate, however, to explain the banding density differences between a deletion mutant and phage lambda in the different cesium salts. The density differences evidently are sensitive to second-order effects: they apparently are affected by a restriction of DNA hydration inside the phage head, which depends both on water activity and on DNA length (or free volume inside the phage head). This becomes a striking effect in Cs₂SO₄ solutions where the net DNA hydration is large. Changing the phage banding density by substituting 5-bromouracil for thymine, which increases the DNA mass while leaving the DNA volume relatively unchanged, gives results consistent with a restriction of the net DNA hydration that depends on the DNA volume. Data on the sedimentation velocity behavior that λ and λb₂ in diferrent salts are presented and discussed. It appears possible to estimate the size of a DNA deletion from the phage sedimentation coefficient.     

Effect of Culture Conditions on the Production of d-Galactose Oxidase by Dactylium dendroides

The effects on enzyme production of inoculum size and age, medium composition, and culture conditions were studied in shake flasks and in a pilot-plant fermentor. Using a medium consisting of glucose, yeast extract, and inorganic salts in deionized water, we found that the addition of Cu(++) was essential for the formation of active enzyme. Cultures grown in the absence of added copper produced an inactive enzyme protein which could be activated by 10(-3) M Cu(++). Thiamine fulfilled all requirements for exogenous vitamins for growth and enzyme production. Glucose concentrations higher than 1% markedly suppressed enzyme formation. The mycelium inactivated the enzyme on prolonged incubation of the culture. Mycelial autolysates and sonic extracts were found to contain a thermostable and slowly dialyzable galactose oxidase-inactivating factor. The experiments suggest that this factor operates as a chelating agent which forms complexes with the copper of the enzyme. Copper ions (10(-3) M) prevented enzyme inactivation and restored activity to samples previously inactivated by this factor.     

Studies on Temperate Phages of Lactobacillus salivarius

Twenty-three temperate phages of Lactobacillus salivarius isolated from human feces were studied as to their morphological, biological, and serological properties. (1) Among 30 strains of L. salivarius tested, 23 strains were lysed by induction with mitomycin C (MC). In all these lysates, phage particles were detected by electron microscopic examination. (2) These phages were morphologically divided into three groups: particles with a regular hexagonal head and a long flexible tail; particles having a regular hexagonal head with or without a short tail-like structure; particles with an elongated head and a long noncontractile tail. (3) Only two, phage 223 having an elongated head and phage 227 with a regular hexagonal head and a long noncontractile tail, produced tiny and very turbid plaques on several host bacteria. Six phages could produce only inhibition zones, ranging from complete inhibition through partial inhibition to normal growth by a serial dilution spot test. (4) All these killer particles could also inhibit the growth of their producer cells. (5) A serological relationship was observed between temperate phages and killer particles, and this was somewhat consistent with the morphological groupings.     

Identification of gene products required for in vitro formation of the internal peptides of bacteriophage T4.

In vitro formation of both bacteriophage T4 internal peptides (II and VII) from preexisting precursor protein was shown to require the product of T4 gene 21. The proteolytic factor was detectable in extracts of cells infected with certain phage mutants blocked in early steps of head assembly but could not be demonstrated in extracts of T4 wild-type infected cells. This finding suggests that the proteolytic factor is inactivated during normal phage assembly. The product of T4 gene 22 appears to be the precursor of peptide VII but not of peptide II.     

The stability of bacterial viruses in solutions of salts

1. The seven bacterial viruses of the T group, active against E. coli, are much more rapidly inactivated by heat when suspended in 0.1 N solutions of sodium salts than when suspended in broth. 2. The kinetics of this inactivation whether in salt solutions or in broth are those of a first order reaction. 3. The rate of inactivation of phage T5 in 0.1 N NaCl at 37 degrees C. can be greatly decreased by the addition of 10(-8)M concentrations of such divalent cations as Ca, Mg, Ba, Sr, Mn, Co, Ni, Zn, Cd, and Cu. 4. An increase in the cation concentration in the suspending medium results in an increase in the stability of phage T5 to the inactivating effects of temperature. 5. The hypothesis is proposed that the increase in stability of phage T5 in the presence of various cations is the result of complex formation between the phage and the metal ion.     

Dissociation by Chelating Agents and Substructure of the Thermophilic Bacteriophage TP84

The thermophilic bacteriophage TP84 is dissociated into its head, tail, and released deoxyribonucleic acid (DNA) by chelating agents such as ethylenediaminetetraacetic acid (EDTA) and phosphate. The phage is more sensitive to EDTA than to phosphate, and dialysis against either agent causes more effective dissociation than standing in their presence. The tail possesses a knobbed structure which is inserted into the head of the intact phage and to which the DNA appears to be attached. The method of dissociating TP84 described in this paper provides a source of undamaged structural components and intact strands of DNA for subsequent investigations. A possible mechanism of chelate inactivation is discussed.     

Functional Interaction of the tonA/tonB Receptor System in Escherichia coli

Host range mutants of phage T1 (T1h), which productively infected tonB mutants of Escherichia coli, were isolated. The phage mutants were inactivated by isolated outer membranes of E. coli in contrast to the wild-type phage, which only adsorbed reversibly. For the infection process, the tonB function is apparently only required for the irreversible adsorption of the phage T1, but not for the transfer of the phage DNA through the outer membrane and the cytoplasmic membrane of the cell. Mutants of the tonA gene expressing normal amounts of outer membrane receptor proteins were isolated and found to be partially sensitive to phage T5 and resistant to the phages T1 and T1h, colicin M, and albomycin and unable to take up iron as a ferrichrome complex. One tonA mutant remained partially sensitive to T5, colicin M, and albomycin and supported growth of T1h (not of T1) with the same plating efficiency as the parent strain. Only a small region of the tonA receptor protein seems to function for all the very different substrates. A newly isolated host range mutant of T5 (T5h) adsorbed faster to tonA(+) cells than did wild-type T5 and infected tonA missense mutants resistant to wild-type T5. The interplay of the tonA with the tonB function was observed with phage T5 infection, although T5 required only the tonA receptor. Ferrichrome inhibited plaque formation of T5 only when plated on tonB mutants. Adsorption of T5 to cells in liquid medium was influenced by ferrichrome as follows: complete inhibition by 0.1 muM ferrichrome with tonB mutants, not more than 35% inhibition by 1 to 100 muM ferrichrome with the tonB(+) parent strain in the presence of glucose as energy source, and 90% inhibition by 1 muM ferrichrome with partially starved parent cells. We conclude that there exist different functional states of the receptor protein that depend on the energy state of the cell and the tonB function. The latter seems to be required only for translocation processes with outer membrane proteins involved.     

Reversible precipitation of bovine serum albumin by metal ions and synthesis, structure and reactivity of new tetrathiometallate chelating agents

Independent research is an important component of any undergraduate chemistry program. This article reports the findings of two of many undergraduate research projects directed by Ed Stiefel in the hopes that the results will be inspiring and useful to the scientific community. The neurological disorders associated with insufficient copper in Menkes disease and an excess of copper in Wilson's disease are well established; however, recent evidence suggests that copper may also be involved in other disorders, such as Alzheimer's, angiogenesis, and prion diseases. The exact role of copper, however, is uncertain. This study examines the role of copper and zinc in the formation of protein deposits and the chelation and removal of the metal ions to reverse the process. The bovine serum albumin (BSA) protein forms a precipitate after the addition of approximately 6 copper(II) atoms or 8 zinc(II) atoms. Other metal ions, such as Ca(II), Al(III), Ni(II), and Co(II), did not precipitate the BSA even when the metal ion to BSA ratios were in excess of 1000. The copper and zinc protein precipitates returned to solution after addition of the chelating agents, ethylenediaminetetraacetic acid (EDTA) or tetrathiometallates [(MS(4)(2-)), where M=Mo, W]. Two new choline and acetylcholine tetrathiomolybdate and tetrathiotungstate chelating agents have been synthesized and characterized. The infrared (IR) and X-ray crystal structures of the complexes revealed that the (MS(4)(2-)) cores had approximate T(d) symmetry in the choline (Ch) salts and C(2v) symmetry in the acetylcholine (AcCh) salts. The AcCh salts hydrolyzed more slowly than the ammonium or Ch salts and the tetrathiotungstate salts hydrolyzed approximately two orders of magnitude more slowly than the tetrathiomolybdate salts. The slower hydrolysis of tetrathiotungstate may make it more useful as an inorganic reagent and therapeutic agent.     

The role of high ionic concentrations in protection against X-irradiation

Various levels of protection against x-irradiation damage in bacteriophage T1 may be obtained by the addition of inorganic salts to the aqueous virus suspensions during irradiation. The highest survival values are obtained with the nitrite salts, and their protective power is attributed primarily to their function as reducing agents. The nitrate ion shows greater protection than the corresponding sulfate or chloride ions. This may be due in part to the lower energy level of the nitrate ion, by reason of resonance. Since greater expenditure of incident energy is required to raise the ion from the ground state, the energy thus dissipated may be ineffective in the inactivation of virus particles. The ammonium salts exhibit protection of a different order of magnitude from that of the metallic salts. It is postulated that NH₄⁺ protects in a threefold way: (a) dehydration, (b) reduction, in which the ammonia is oxidized to nitrite and the nitrite to nitrate, and (c) stabilization of the virus protein. Metallic salts likewise protect, but a point of maximum protection is reached in lower concentrations than in the case of the ammonium salts. After this maximum protection is reached, there is a rapid decline in survival with increased concentration. This prevents protection of the order of magnitude that can be obtained with the ammonium salts. It is postulated that a specific cationic interaction with the phage may be responsible for the decreased protection. Bacteriophage is protected during x-irradiation by an alkaline pH, in the case of NH₄OH. This protection could not be produced with NaOH, presumably because of the greater hydrolysis of the protein components of the virus particle in solutions of NaOH, whereas NH₄OH stabilizes the protein.     

Phospholipase Activity in Bacteriophage-Infected Escherichia coli I. Demonstration of a T4 Bacteriophage-Associated phospholipase

Phospholipase activity has been found to be associated with T4 phage and T4 ghost particles. The attachment of the phospholipase to the phage persists during purification through cesium chloride gradients and dialysis, indicating that it is firmly bound. The presence of the enzymatic activity on T4 ghosts suggests that it is not normally packaged within the head of the virus. The enzyme has specificity for phosphatidylglycerol and its activity is stimulated by 0.1% Triton X-100 and 20% methanol. It does not have a requirement for Ca²⁺ and is inactivated at temperatures above 60 C. The association of the phospholipase with T4 phage grown in a phospholipase-deficient host and its absence on unsuppressed T4amtA3 suggests that it may be phage gene specific.     

Inactivation of T4D Bacteriophage by Antiserum Against Bacteriophage Dihydrofolate Reductase

Antiserum was prepared against highly purified T4D bacteriophage-induced dihydrofolate reductase (DFR). This serum not only inactivated the enzyme but also inactivated all strains of T4D examined. T6 was inactivated to a lesser extent, and T2L, T2H, and T5 were unaffected by the antiserum. The phage-killing power of the serum could be blocked by prior incubation with partially purified T4D dfr obtained from host cells unable to make phage structural proteins. These observations confirm earlier results that the phage dfr is a structural component of the phage particle, and they offer new evidence on the manner in which this enzyme in incorporated into the tail structure.     

Phage-inactivating Effect of Iron(II)-Ascorbate Complex

The effect of iron(II)-ascorbate complex on various phages was investigated. At 10- ⁶ M, the complex inactivated all nine phages examined. The mechanism of the inactivation was studied with phage J1, the most sensitive to the complex. The addition of H₂O₂ or Cu²⁺ to the reaction mixture increased the inactivation. Bubbling of nitrogen through the reaction mixture and the addition of Fe³⁺, a reducing agent, a chelating agent, or a radical scavenger prevented inactivation. These findings suggest the involvement of oxygen radicals in the inactivation. The complex had no effects on the SDS-PAGE pattern or amino acid composition of bovine serum albumin, or the structural protein of phage J1. The complex nicked the supercoiled form of pUC18 DNA, giving first single-stranded breaks (the open circular form) and then double-stranded breaks (the linear form). Strands of M13mp8 DNA, λDNA, and J1 DNA were also broken. The breaks could account for the inactivation.     

Head Proteins from T-Even Bacteriophage: I. Molecular Weight Characterization 1

T-even bacteriophage capsid proteins were separated on 6% agarose columns by use of 6 m guanidine hydrochloride containing 5 mm dithiothreitol both to dissociate and to elute the proteins. The head capsids of T2H, T4B, T4B01, T4D, and T6r(+) contained at least three structural proteins with molecular weights of 40,000, 18,000, and 11,000 daltons, amounting to 76, 2, and 8%, respectively, of the total capsid protein. On the other hand, T2L head capsids contained only two structural proteins with molecular weights of 40,000 and 18,000 daltons (81 and 2.5%, respectively, of the total protein). A discussion of the possible role of these structural head proteins and a T-even phage head model suggesting a structural arrangement of the 40,000 dalton subunit are presented.     

Introduction of a metal-dependent regulatory switch into an enzyme

A cysteine has been introduced into the hydrophobic binding pocket of staphylococcal nuclease via oligonucleotide-directed mutagenesis. The L89C mutation does not significantly alter the catalytic activity or specificity of the nuclease yet provides a metal-dependent switch for regulating enzymatic activity. The L89C mutant can be inactivated by addition of mercuric or cupric salts and subsequently reactivated by addition of chelating agents. This work may provide a general strategy for regulating the catalytic activity of other enzymes or the binding affinity of proteins to DNA or other proteins.     

A study of the action of phagolessin A58 on the T phages

Phagolessin A58, an antibiotic substance active against a number of bacterial viruses, was studied for activity against the seven T phages. Only three of the seven phages—T1, T3, and T7—proved to be sensitive to the antibiotic. The antibiotic caused a direct, apparently irreversible inactivation of free phage particles. A study of the properties of the inactivated phage particles showed that the particles retained the ability to kill host cells and to exert mutual exclusion against an unrelated phage after infectivity was lost. There was a progressive loss in these two properties when higher concentrations of antibiotic were used to inactivate the phage. Results with inactivated T3 and T7 revealed that these two properties—the ability to kill host cells and to exclude an unrelated phage—were lost at a different rate. They were, therefore, presumed to be different properties of these particular phage particles. The inactivation of phage by phagolessin A58 was inhibited by desoxyribose nucleic acid and to a lesser extent by ribose nucleic add. Cytosine, thymine, adenine, guanine, and cysteine failed to inhibit the reaction.     

Oxygen protection of bacteriophage T1 against ionizing radiations

Bacteriophage T1 was suspended in distilled water and in phosphate buffer, saturated with oxygen, nitrogen, hydrogen, and carbon monoxide, and irradiated with gamma rays and x-rays. Under the same conditions phage was exposed to hydrogen peroxide. Oxygen acted as a protective agent against both irradiation and hydrogen peroxide inactivation. As a protective agent against irradiation, oxygen was more efficient in distilled water than in buffer. The phage was much more sensitive to irradiation in the presence of hydrogen or nitrogen than in the presence of oxygen. Survivals of phage irradiated in suspensions saturated with hydrogen and with nitrogen did not differ significantly. From this it was concluded that oxygen did not protect T1 by removing atomic hydrogen from the irradiated medium, since the hydrogen-saturated medium increased the yield of atomic hydrogen but did not increase the yield of inactivated phage. It was presumed, therefore, that phage is sensitive to OH radicals and this was confirmed by irradiating phage with UV in the presence of hydrogen peroxide and comparing this survival with the survivals obtained from hydrogen peroxide alone and from UV alone. The combined effect of hydrogen peroxide and UV acting simultaneously was greater than the effect attributable to hydrogen peroxide and UV acting separately. Evidence for sensitivity to HO₂ radicals was considered, and the effect was attributed chiefly to an oxidizing action since phage sensitivity is greater at higher hydrogen ion concentrations, which favor oxidation by HO₂ radicals. Since the OH radical is a more efficient oxidizing agent than O^-, the former being favored in an acid medium, the latter in an alkaline medium, and since the phage is more sensitive in the first situation than in the second, the present tests proved the importance of oxidation as the mechanism of inactivation. Since some inactivation was encountered when phage was exposed to reducing agents, independently of irradiation, it was concluded that phage is somewhat sensitive to reducing agents, but the inactivation attributable to ionizing radiations is due chiefly to oxidation, against which these reducing agents are very efficient protectors. Under no circumstances did hydrogen peroxide protect T1, whether produced by irradiation in the medium or added beforehand to the medium to be irradiated. The first point was investigated by irradiating T1 in the presence of hydrogen and oxygen combined; this produced a higher yield of hydrogen peroxide but a lower survival of T1. In all these tests phage survival under irradiation was directly correlated with oxygen content of the medium rather than with production of hydrogen peroxide. It is proposed that the protective effect of oxygen is due to a reaction between the phage and oxygen, and this complex confers stability upon the phage.