J Supramol Struct, 1979, 10(4), 457 - 65 Structure of the DNA binding cleft of the gene 5 protein from bacteriophage fd; McPherson A et al.; The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3-A resolution by X-ray diffraction techniques . The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface . The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft . Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place . The structure and binding mechanism as we visualize it appear to be fully consistent with evidence provided by physical-chemical studies of the protein in solution. Dev Biol Stand, 1979, 42, 87 - 91 Construction of hybrid viruses in vitro and their possible use for the production of specific viral or cellular proteins; Yaniv M; The use of plasmid and bacteriophage vectors for cloning of DNA segments from procaryotes and eucaryotes is described . A similar approach is being developed with DNA viruses like simian virus 40 or adenovirus 2 . Such hybrid viruses may permit the amplification of specific genes and the overproduction of the corresponding proteins. J Virol, 1979 Jan, 29(1), 322 - 7 Gene D5 product of bacteriophage T5: DNA-binding protein affecting DNA replication and late gene expression; McCorquodale DJ et al.; Gene D5 is not only necessary for replication of bacteriophage T5 DNA and for shutoff of expression of some early genes, but has been found to be necessary also for the expression of late T5 genes . The polypeptide product of gene D5 has been identified, an intragenic map of gene D5 has been constructed, and the direction of transcription of gene D5 has been established . The polypeptide coded by gene D5 has been shown to be a DNA-binding protein with affinity for both double- and single-stranded DNA. Z Allg Mikrobiol, 1979, 19(5), 325 - 32 {Effect of the detergent Metaupon on replication of various phages}; Menzel G et al.; As several other surfactants do, the detergent Metaupon acts on the multiplication of bacteriophages . We investigated the influence of Metaupon on the phages phi and lambda, the cyanophage LPP-1, and the RNA-phages f 2, M 12, and Q beta by means of the agar diffusion test, pour plate test, adsorption test, and one-step growth test . The action of Metaupon on the free phages was also tested . Metaupon inhibits the formation of plaques by the phages with exception of lambda . With the phages f 2 and M 12 the substance increases the amount of plaques depending on concentration . The main mode of action of Metaupon was found to be the inhibition of the adsorption of the phages to the host cells . Only in the case of phi 105 free phages were inactivated. Genetika, 1979, 15(10), 1719 - 23 {Characteristics of bacteriophage lambda and P1 modification-restriction in Escherichia coli strains controlled by factor R124}; Skavronskaia AG et al.; The specifities of restriction of bacteriophages P1 and lambda controlled by R plasmids in Escherichia coli have been investigated . The isogenic strains harbouring the plasmids pAS26 coding for restriction endonuclease R.EcoRI, R245 coding for restriction endonuclease R.EcoRII and and R124 have been investigated in the present work . Modification-restriction controlled by R124 has been found to differ in specificity from those controlled by R245 and pAS26 . Frequencies of restriction of bacteriophages P1vir and lambdavir specified by R124 pasmid differ from the frequencies in the strains harbouring pAS26 and R245 plasmids as well . The difference is due to the specifity of restriction-modification controlled by R124 plasmid . The data obtained are consistent with the determination of R124 specified restriction-modification activity as a novel one designated R.EcoRIII. Genetika, 1979, 15(8), 1351 - 9 {Transposition of the deo operon structural genes in Escherichia coli K-12 to plasmid RP4 using bacteriophage mu}; Grishchenkov VG et al.; Transposition of the structural genes of the deo operon of Escherichia coli K-12 into plasmid RP4 by means of temperate bacteriophage Mu was carried out . Some variants of composite RP4-deo-Mu plasmids were obtained and the expression of the deo genes integrated into the RP4 plasmid genome was studied . It was shown that the expression of these genes remains under the control of the chromosomal regulatory genes (deoR and cytR); although the activity of thymidine phosphorilase in the strain E . coli which contains hybrid plasmid is 4-6 fold greater than that in strains of E . coli with chromosomal localization of the deo operon. Genetika, 1979, 15(7), 1191 - 8 {Hybrid plasmid pSD1 containing the immunity region of bacteriophage lambda}; Dikarev SD et al.; Hybrid plasmid pSD1 carrying the immunity region of the coliphage lambda and bio operon have been obtained by means of studying the efficiency of transcription DNA fragments in the plasmid RSF2124 . The molecular weight of this plasmid is 17.2 Md . The growth inhibition of phage lambdavir has been observed in cells carrying the new hybrid plasma . The properties of the plasmid pSD1 and probable reasons of the growth inhibition of phage lambdavir are discussed . The hybrid plasmid pSD2 carrying genes R, A and J of phage lambda has been constructed on the basis of the plasmid RSF2124 . There are cohesive ends in this plasmid which make possible its packing in the phage lambda head . Hybrid plasmid pSD3 carrying genes P and Q of phage lambda has also been constructed. Cold Spring Harb Symp Quant Biol, 1979, 43 Pt 1, 165 - 78 Functional analysis of the replicator structure of lambdoid bacteriophage DNAs; Hobom G et al.; In our hybrid-plasmid reconstruction analysis of lambda (lambdoid) DNA signal structures involved in phage DNA replication, we have detected a dual system alternatingly able to initiate a first primer-RNA synthesis . Both of them--the major, primase-dependent ori system and the minor and usually suppressed, RNA-polymerase-dependent oop system--act in conjunction with a common signal structure for inception of DNA synthesis . It appears that in situations such as this, where one has to deal with the existence of regular as well as backup systems serving the same function, straightforward conclusions are no longer possible in their genetic analysis . For example, even though the oop-DNA segment can be deleted entirely from bacteriophage lambda DNA without disturbing its ability to replicate, it may not be valid to conclude that the oop system has no function in DNA replication . Dual systems of this type or organization in general have also been observed previously for some other replicons such as the R-factors R6-5 and R6K (Timmis et al . 1978; Crosa et al., this volume) or the F factor (Helinski et al., this volume), and they may be more common than presently expected. Rev Chir Orthop Reparatrice Appar Mot, 1979 Jan-Feb, 65(1), 33 - 7 {Bacteriophage therapy of septic complications of orthopaedic surgery (author's transl}; Lang G et al.; Seven septic cases have been treated by bacteriophage; two infections after insertion of a hip prosthesis, two septic arthritis of the knee, one osteomyelitis of the tibia, one septic non-union of the femur and one septic complication following Harrington rodding . Only specific phages were used in association with several types of surgical procedure . The technique of treatment is described . All cases were long-term infections with resistant organisms . Results were good in five, fair in one and one case was a failure . It is concluded that phage therapy may be helpful in the treatment of long-term infections. Z Naturforsch {C}, 1979 Jan-Feb, 34(1-2), 162 - 4 Methylmercury-induced sedimentation heterogeneity of T7 bacteriophage DNA; Gruenwedel DW et al.; Single-stranded and methylmercurated T7 DNA is composed of two species as evidenced from the sedimentation pattern displayed during band-sedimentation in self-generating density gradients as well as during equilibrium-sedimentation in CS2SO4 density gradients . Under the given experimental conditions, viz., at pH 9.18 and in presence of 0.1 mM CH3HgOH, the two species band in CS2SO4 with a density difference of 0.008 g/ml . The ratio of the sedimentation coefficients of the two species is sw, 20 (fast)/sw, 20 (slow) = 1.63 at pH 9.18 and in presence of 1.6 mM CH3HgOH . Both native and denatured T7 DNA behave as monodisperse systems in the absence of CH3HgOH. Rev Chir Orthop Reparatrice Appar Mot, 1979 Jan-Feb, 65(1), 33 - 7 {Bacteriophage therapy of septic complications of orthopaedic surgery (author's transl)}; Lang G et al.; Seven septic cases have been treated by bacteriophage ; two infections after insertion of a hip prosthesis, two septic arthritis of the knee, one osteomyelitis of the tibia, one septic non-union of the femur and one septic complication following Harrington rodding . Only specific phages were used in association with several types of surgical procedure . The technique of treatment is described . All cases were long-term infections with resistant organisms . Results were good in five, fair in one and one case was a failure . It is concluded that phage therapy may be helpful in the treatment of long-term infections. Acta Biol Med Ger, 1979, 38(11-12), 1627 - 37 Studies on the regulation of igm immune response . VII . changes in the affinity of antibodies and cell receptors after immunization with the T-cell independent antigen DNP-Ficoll; Fiebig H et al.; A/J-mice immunized by a single injection with DNP21-Ficoll respond on the humoral level exclusively with IgM antibodies . The intrinsic association constants (K0) of IgM anti-DNP to monovalent hapten E-DNP-L-lysine are within the range of 105-106 M-1 and do not change significantly during the immune response . On the other hand, the functional association constants (KF) of pentameric IgM to multivalent DNP-T4 bacteriophage increase from 1010 M-1 at 3rd day up to 1012 M-1 at 8th day . Subsequently, a decrease of KF to 1011 M-1 can be observed . This rise and fall of the affinity of IgM antibodies of multivalent DNP-conjugate can be detected at the cellular level also by inhibition of plaque formation . The concentration of DNP15-BSA needed for 50% inhibition of plaque formation (I50) decreases from second day to 8 th day by 4 orders, which represents a strong increase of functional affinity . In contrast, the I50 of E-DNP-L-lysine slightly decreases only until day 4 and does not change until day 21 . the inhibition of rosette formation by mono- and multivalent ligands was used to study the affinity of lymphocyte receptors . In the course of immunization antigen-binding cells carrying receptors with increasingly higher affinity for multivalent DNP-conjugates occur . These results are discussed with regard to the importance of functional affinity of lymphocyte receptors for the antigen-driven selection of high affinity anti-DNP-cell clones producing IgM antibodies. Acta Biol Med Ger, 1979, 38(11-12), 1615 - 25 {Regulations of IgM immune response . IV . Effect of the hapten: carrier ratio and the nature of the carrier on the intrinsic and functional affinity of carp DNP-antibodies}; Fiebig H et al.; Carp anti-DNP antibodies were raised by various DNP-carrier conjugates . Their intrinsic affinity (K0) to monovalent E-DNP-L-lysine and functional affinity (DF) for binding to the multivalent DNP-T4 bacteriophages were determined . The functional affinity of antibodies elicited by T-cell-dependent DMPn-HSA (n = 3, 15, 33) is relatively high (KF):1010-1012 M-1) . These KF values increase more than K0 during the immune response . The functional affinity is dependent on the molar KNP: HSA ratio . The mediate coupled DMP15-HSA elicits antibodies with the highest functional affinity . Carps immunized with T-cell-independent DNP-conjugates synthesize antibodies which have similar K0 as the antibodies elicited with DNP-HSA . However, the KF-values are in the range from 107 to 1010 M-1 only . The KF of antibodies raised with DNP-BA are 103-104 fold, those of DNP-S III and DNP-Ficoll elicited are only 4 . 101 to 4,7 . 102 fold higher than their corresponding K0-values . This means that these antibodies are not very effective in binding the multivalent DNP-T4 . Specifically purified antibodies have also such low functional affinities . These strong differences in the functional affinity of carp DNP-antibodies elicited by T-cell dependent and independent DNP-conjugates are discussed with regard to stimulation of different B-cell subpopulations. Ultramicroscopy, 1979, 4(1), 91 - 6 The reconstruction of a helical structure from projections applied to a phage tail; Cremers AF et al.; A procedure has been described for 3 D-image reconstruction for helical biological structures, if more than one projection will be required to determine the contributing helical density-waves . The method was tested with a helical protein aggregate derived from a bacteriophage . The results showed the feasibility of the proposed scheme and yielded a low resolution picture (about 2.5 nm) of the protein structure. Mol Gen Genet, 1979, 172(3), 295 - 301 Characterization of an amber suppressor in Pneumococcus; Gasc AM et al.; Partial revertant has been isolated, with resistance to aminopterin intermediate between wild type and mutant . This phenotype is the result of a mutation at a gene unlinked to the amiA locus . This suppressor mutation (su+) has no phenotypic characteristics by itself except a slow growth . 9 amiA mutants (belonging to 6 sites) are affected by su+ out of the 30 investigated mutants (i.e . 22 sites) . The efficiency of suppression is site dependent . Two sites out of 14 mutants belonging to the thymidylate synthetase gene are suppressible . Thymidylate synthetase activity is partially restored by su+ . Optochin mutants can also be suppressed . Thus su+ is not gene specific but site specific . Moreover when the str-41 allele conferring resistance to streptomycin is introduced by transformation, the suppression effect is restricted . All these properties are characteristic of an informational suppressor . The t-RNA extracted from the suppressor strain su+ but not the wild type restored the synthesis of coat protein coded by RNA from an amber mutant of bacteriophage f2 . Attempts to detect ochre suppression activity gave negative results . It is suggested that the su+ gene is amber specific . Thus su+ can provide insight into the nature of suppressible mutations which should be point mutations . Both low efficiency and high efficiency mutants are affected by su+; this is additional evidence that both categories contain point mutations. Z Allg Mikrobiol, 1979, 19(7), 473 - 80 {Host range relationship of bacteriophages T3 and T7 with Escherichia coli K 12 strains}; Kruger DH et al.; The closely related phages T3 and T7 exhibit different growth patterns on Escherichia coli W hosts cells (E . coli K12 derivatives) . T7 grows normally while T3 does not adsorb . T3hw mutants displaying a T7-like host range were isolated and described. Z Allg Mikrobiol, 1979, 19(6), 391 - 6 {Effect of temperature on RNA synthesis in Escherichia coli CRT 266 (dna Bts) following infection with bacteriophage T3}; Brux B et al.; Infection of the temperature-sensitive E . coli CRT 266 (dnaBts) with T3-phages at the temperature of 30 degrees C and 35 degrees C, respectively, induced T3-specific RNA synthesis with a maximum rate at 7 min (30 degrees C) and 4.5 min (35 degrees C) after infection . At temperatures above 40 degrees C no T3-induced RNA synthesis could be observed . Infection of E . coli CR 34--45 (dnaB+) with T3 phages at 30 degrees C, 35 degrees C and at temperatures above 40 degrees C, however, produced T3-specific RNA synthesis . The maximum of T3-induced RNA synthesis could be observed between 7 min and 3 min depending on the temperature during infection . The inability to form T3-specific RNA after infection of E . coli CRT 266 at nonpermissive temperatures may be a cause for the absence of the formation of T3 phages and lysis of the host cells. Acta Microbiol Pol, 1979, 28(3), 203 - 11 Aggregation deficient Escherichia coli K-12 female mutants with altered lipopolysaccharide; Heleszko H et al.; Two F- mutants deficient in conjugation with F-donors have been characterized . They map at about 83 minut position, show resistance to T3 and T7 bacteriophages, and form mating aggregates in the liquid medium with lowered efficiency . Mutants have no detectable alterations in their outer membrane protein composition. Mol Gen Genet, 1979, 172(3), 303 - 12 Physical mapping of the restriction fragments obtained from bacteriophage T4 dC-DNA with the restriction endonucleases SmaI, KpnI and BglII; Kiko H et al.; The cytosine-containing DNA of a mutant of bacteriophage T4 was digested with restriction endonucleases SmaI, KpnI and BglII producing 5, 7 and 13 fragments respectively . Complete physical maps of the T4 genome were constructed with the enzymes SmaI and KpnI and an almost complete map with the enzyme BglII. Mol Gen Genet, 1979, 172(3), 329 - 37 Aberrant immunity behaviour of hybrid lambda imm21 phages containing the DNA of ColE1-type plasmids; Windass JD et al.; Hybrid lambda and lambda imm21 bacteriophages carrying various ColE1-type plasmids have been constructed in vitro . The lambda imm21/plasmid recombinants display aberrant immunity behaviour, giving clear plaques under conditions where the parental phages give turbid ones and being able to grow on homoimmune lysogens . lambda imm lambda/plasmid recombinants show no such unusual behaviour . Studies with hybrids of a lambda imm21 cITS phage carrying pMB9 DNA showed the operation of the plasmid's replication system to be the basic cause of the aberrant immunity behaviour . The plasmid replication system could act as a complete alternative to the phage system during vegetative phage growth . The probable reason that lambda imm21 phages show such altered phenotypes when carrying a functional plasmid replication origin, whereas lambda imm lambda and lambda imm434 (Mukai et al., 1978) phages do not, is the relative ease of titration of the phage 21 repressor to allow transcription from pR21 . Various uses are considered for the altered phenotypic behaviour of lambda imm21/ColE1-type plasmid hybrids. Mol Gen Genet, 1979, 172(3), 271 - 9 Bacteriophage SPP1 polypeptides synthesized in infected minicells and in vitro; Mertens G et al.; Minicells produced by B . subtilis CU403divIVB1 and infected by SPP1 synthesize at least 46 polypeptides which can be separated by polyacrylamide gel electrophoresis . These polypeptides represent the expression of 86% of the SPP1 genome's coding capacity . Infection of minicells by sus mutants and deletion mutants of SPP1 has permitted a correlation of genetic location with gene product and has shown that SPP1 normally synthesizes at least 8 non-essential polypeptides . Restriction fragments of SPP1 produced by EcoRI digestion of SPP1 DNA have been purified and used as template DNA in a coupled transcription/translation system derived from E . coli to determine the polypeptides encoded by the individual fragments . SPP1 expression in minicells differs from SPP1 expression in nucleated cells (Esche, 1975) in that late syntheses are not dependent on phage DNA replication in infected minicells. J Supramol Struct, 1979, 11(2), 139 - 45 NMR of fd coat protein; Cross TA et al.; The conformations of the major coat protein of a filamentous bacteriophage can be described by nuclear magnetic resonance spectroscopy of the protein and the virus . The NMR experiments involve detection of the 13C and 1H nuclei of the coat protein . Both the 13C and 1H nuclear magnetic resonance (NMR) spectra show that regions of the polypeptide chain have substantially more motion than a typical globular protein . The fd coat protein was purified by gel chromatography of the SDA solubilized virus . Natural abundance 13C NMR spectra at 38 MHz resolve all of the nonprotonated aromatic carbons from the three phenylalanines, two tyrosines, and one tryptophan of the coat protein . The alpha carbons of the coat protein show at least two different classes of relaxation behavior, indicative of substantial variation in the motion of the backbone carbons in contrast to the rigidity of the alpha carbons of globular proteins . The 1H spectrum at 360 MHz shows all of the aromatic carbons and many of the amide protons . Titration of a 1H spectra gives the pKas for the tyrosines. J Bacteriol, 1979 Jan, 137(1), 556 - 67 Bacteriophage-associated gene transfer in pneumococcus: transduction or pseudotransduction? Porter RD, Shoemaker NB, Rampe G, Guild WR. Lysates of pneumococcal phage PG24 transferred genes from one host to another in a process with many of the properties of generalized transduction, in that the host genes were packaged in DNase-resistant particles that closely resembled infectious phage in physical properties, adsorbed to the recipient cells like phage, and were inhibited by antisera to the phage and by trypsin . However, phage processes did not complete the transfer of host DNA as they did phage DNA . Instead, gene transfer required development of competence and entry of the host DNA by the endonuclease-dependent pathway used for transforming and transfecting DNA . This process often occurred on the assay plate hours after adsorption of the particles to the cells, and the transfer was DNase sensitive if challenged at this time . Phenotypic expression was therefore also delayed . The product of entry was like that in transformation, a single strand of DNA that integrates by formation of a hex-sensitive donor-recipient heteroduplex . Whether this gene transfer process is unique to this system or is only the first one described is not clear . The term "pseudotransduction" may be useful in calling attention to its unexpected features . The DNA of PG24 phage has anomalous physical properties reflecting unusual bases. Biochemistry, 1978 Dec 26, 17(26), 5695 - 705 Transcription of histone-covered T7 DNA by Escherichia coli RNA polymerase; Williamson P et al.; Purified core histones (H2A, H2B, H3, and H4) and bacteriophage T7 DNA have been reconstituted to form a nucleoprotein complex, and the properties of this complex as a template for transcription by Escherichia coli RNA polymerase have been studied . At low ionic strength, RNA chain elongation rates are slow, and the chains produced even after long incubation are short . At higher salt concentrations, chain-elongation rates approach those on naked DNA . Since the salt concentrations used are not in themselves sufficient to dissociate the histones from the DNA, some mechanism must exist that permits passage of the polymerase through histone-covered regions. J Biol Chem, 1978 Dec 25, 253(24), 8941 - 8 A steady state assay for the RNA polymerase initiation reaction; McClure WR et al.; A new assay yielding mechanistic information on the initiation reaction of Escherichia coli RNA polymerase has been developed . It was found to be useful in characterizing the promoters of bacteriophage DNA templates . The binding of the first two triphosphates in an RNA sequence was determined to be equilibrium ordered with ATP binding first followed by UTP on the lambda promoters PL . and PR . The products resulting from phosphodiester bond formation, pppApU and PPi, dissociated rapidly in the absence of the other triphosphates required for RNA synthesis . The resulting steady state conversion of ATP and UTP into pppApU was the basis for the new assay . The rate-limiting step in the initiation reaction was not precisely determined, but it was argued not to be entirely the release of product . The Zn2+ chelator, 1,10-phenanthroline, was partially characterized and found to be an uncompetitive inhibitor of ATP in the reaction (Ki = 100 micrometer) . The unique advantage of this steady state assay is that several steps in the RNA initiation process are amplified kinetically and thus can be examined separately with techniques applicable to any other two-substrate, two-product enzyme reaction. Science, 1978 Dec 22, 202(4374), 1284 - 9 Cloning human fetal gamma globin and mouse alpha-type globin DNA: characterization and partial sequencing; Smithies O et al.; Two globin-related clones isolated from collections of bacteriophages containing unfractionated Eco RI fragments of human and mouse DNA were characterized . Charon3AHs51.1Hbgamma includes 2.7 kilobase pairs of human DNA containing a large part of a fetal gamma globin chain structural gene; Charon 3AMm30.5 includes 4.7 kilobase pairs of mouse DNA related to alpha globin . The human fetal gamma globin gene has within its coding region two intervening sequences of noncoding DNA, IVS 1 and IVS 2, of approximately 1-0 and 900 base pairs . Sequence IVS 1 is located at the position of one of the two intervening sequences occurring in adult globin genes; IVS 2 is located at the position of the other. Science, 1978 Dec 22, 202(4374), 1279 - 84 Cloning human fetal gamma globin and mouse alpha-type globin DNA: preparation and screening of shotgun collections; Blattner FR et al.; Shotgun collections of Charon 3A bacteriophages containing Eco RI fragments of human and mouse DNA were constructed with the use of in vitro packaging . Plaques were screened by hybridization, and globin-specific clones were isolated from both human (Charon 3AHs51.1) and mouse (Charon 3AMm30.5) . The fragments cloned were detected in unfractionated genomic DNA by the Southern method of hybridization. J Biol Chem, 1978 Dec 10, 253(23), 8390 - 9 Determination of the first half of the coat protein cistron of bacteriophage Qbeta as an application of a mapping procedure for RNA fragments; Escarmis C et al.; A method is described to classify, in regard to their location within the genome, fragments obtained by partial cleavage of 32P-labeled bacteriophage Qbeta RNA . The location of many fragments suitable for sequence analysis could be established using as markers 29 large RNase T1-resistant oligonucleotides with known map positions . Applying this method four fragments originating from the coat protein cistron were isolated and analyzed . The sequence of a segment of 239 nucleotides located immediately adjacent to the initiation triplet was determined to be G-C-A-A-A-A-U-U-A-G-A-G-A-C-U-G-U-U-A-C-U-U-U-A-G-G-U-A-A-C-A-U-C-G-G-G-A-A-A-G-A-U-G-G-A-A-A-A-C-A-A-A-C-U-C-U-G-G-U-C-C-U-C-A-A-U-C-C-G-C-G-U-G-G-G-G-U-A-A-A-U-C-C-C-A-C-U-A-A-C-G-G-C-G-U-U-G-C-C-U-C-G-C-U-U-U-C-A-C-A-A-G-C-G-G-G-U-G-C-A-G-U-U-C-C-U-G-C-G-C-U-G-G-A-G-A-A-G-C-G-U-G-U-U-A-C-C-G-U-U-U-C-G-G-U-A-U-C-U-C-A-G-C-C-U-U-C-U-C-G-C-A-A-U-C-G-U-A-A-G-A-A-C-U-A-C-A-A-G-G-U-C-C-A-G-G-U-U-A-A-G-A-U-C-C-A-G-A-A-C-C-C-G-A-C-C-G-C-U-U-G-C-A-C-U-G-C-A-A-A-C-G-G-U-U-C-U-U-Gp . The primary structure and the secondary structure model derived from it did not provide any evidence of homology with the corresponding RNA region of bacteriophage MS2. J Biol Chem, 1978 Dec 10, 253(23), 8400 - 5 A hybridization procedure for the isolation of specific RNA segments applied to the analysis of bacteriophage Qbeta RNA; Shapira A et al.; A method for the isolation of RNA fragments originating from defined regions of bacteriophage Qbeta RNA minus strands is described . Large RNase T1 oligonucleotides were isolated on a preparative scale from Qbeta RNA . The nucleotide sequences (13 to 26 nucleotides) and map positions of these oligonucleotides were known from previous work (Billeter, M . A . (1978) J . Biol . Chem . 253, 8381-8389) . After addition of AMP residues (50 in the average) using terminal adenylate transferase, these pure oligonucleotides were hybridized to 32P-labeled Qbeta RNA minus strands synthesized in vitro . Fragments in the size range of 100 to 500 nucleotides were then generated by partial digestion with RNase T1 . Fragments hybridized to such oligonucleotides were recovered by chromatography on poly(U)-Sephadex and then resolved according to their size by polyacrylamide gel electrophoresis . The specificity and reproducibility of the method as well as its suitability for the sequence analysis of Qbeta RNA was verified by using in particular a linker oligonucleotide derived from a Qbeta RNA region near the 3' end . The sequence catalogues of the RNase T1 and RNase A oligonucleotides of two fragments isolated in this way, 202 and 310 nucleotides in length, were established and all fragments isolated were shown to contain a sequence complementary to the linker oligonucleotide. J Biol Chem, 1978 Dec 10, 253(23), 8381 - 9 Sequence and location of large RNase T1 oligonucleotides in bacteriophage Qbeta RNA; Billeter MA; Twenty-nine oligonucleotides, 11 to 26 nucleotides in length, arising by complete RNase T1 digestion of bacteriophage Qbeta RNA and isolated by two-dimensional polyacrylamide gel electrophoresis, were sequenced . Their location within the genome was established with two methods . (a) In vitro synthesis of Qbeta RNA plus strands was started synchronously, using minus strands as template and nucleoside {alpha-32P}triphosphates as substrate; after various times, the reaction was stopped and the length of the products formed was correlated with their content of T1 oligonucleotides . (b) Qbeta {32P}RNA was elongated with poly(A) using terminal riboadenylate transferase; after mild treatment with alkali the fragments were fractionated by size and the poly(A)-containing molecules of each size class were isolated by chromatography on poly(U)-Sephadex and assayed for T1 oligonucleotides . The oligonucleotides in the 5' region were localized more precisely with method a, those near the 3' end with method b; in the middle region, the results of the two sets of analyses confirmed each other . The use of these oligonucleotides in the sequence determination of Qbeta RNA is discussed. Nucleic Acids Res, 1978 Dec, 5(12), 4495 - 503 Nucleotide sequence of bacteriophage fd DNA; Beck E et al.; The sequence of the 6,408 nucleotides of bacteriophage fd DNA has been determined . This allows to deduce the exact organisation of the filamentous phage genome and provides easy access to DNA segments of known structure and function. Eur J Biochem, 1978 Dec, 92(2), 589 - 96 Structure and synthesis of a lipid-containing bacteriophage . Total reconstitution of bacteriophage PM2 in vitro; Schafer R et al.; The lipid-containing bacteriophage PM2 was reconstituted stepwise from its purified denatured subunits . In the first step the nucleocapsid was reconstituted from the DNA and the two nucleocapsid proteins . Slight biochemical differences between reconstituted nucleocapsids and those isolated from native virus were seen . Combination of reconstituted nucleocapsid or nucleocapsid from virions with the coat and spike proteins in the presence of the viral lipids resulted in the formation of infectious virus in both cases . The reconstituted particles contained amounts of viral components similar to those in native virus, except for the lipid content . The amount of lipids present in the reconstituted particles was twice as high as the lipid content of native bacteriophage. Eur J Biochem, 1978 Dec, 92(2), 579 - 88 Structure and synthesis of a lipid-containing bacteriophage . Dissociation of bacteriophage PM2 into its morphological subunits; Schafer R et al.; The lipid-containing bacteriophage PM2 was dissociated stepwise in 1 M NcCl (pH 7.2)with increasing urea concentrations . In 2 M urea the following substructures could be identified: (a) a nucleocapsid containing all of the viral lipid, the DNA, proteins III and IV, plus a fraction of protein II, and (b) a second substructure respresenting particles which contained all viral elements except protein I, the spike protein . In 4 M urea the viral nucleocapsid containing all of proteins III and IV, the DNA, plus a fraction of protein II, was isolated . Upon increasing the urea concentration further, this nucleocapsid is stable up to 8.5 M urea; in 9 M urea protein III was partly dissociated from the nucleocapsid . The nucleocapsid in 4--8.5 M urea is stabilized by the addition of 0.1--3 M NaCl but dissociates if the NaCl concentration is less than 0.1 M . The nucleocapsid was also dissociated in 4--8.5 M urea at pH 4.5 . The nucleocapsid structures and some intermediate morphological subunits have been analysed by physical methods, enabling us to draw some conclusions about the structure and hydration of the virus. J Virol, 1978 Dec, 28(3), 917 - 28 Electrophoresis of bacteriophage T7 and T7 capsids in agarose gels; Serwer P et al.; Agarose gel electrophoresis of the following was performed in 0.05 M sodium phosphate-0.001 M MgCl2 (pH 7.4): (i) bacteriophage T7; (ii) a T7 precursor capsid (capsid I), isolated from T7-infected Escherichia coli, which has a thicker and less angular envelope than bacteriophage T7; (iii) a second capsid (capsid II), isolated from T7-infected E . coli, which has a bacteriophage-like envelope; and (iv) capsids (capsid IV) produced by temperature shock of bacteriophage T7 . Bacteriophage T7 and all of the above capsids migrated towards the anode . In a 0.9% agarose gel, capsid I had an electrophoretic mobility of 9.1 +/- 0.4 X 10(-5) cm2/V.s; bacteriophage T7 migrated 0.31 +/- 0.02 times as fast as capsid I . The mobilities of different preparations of capsid II varied in such gels: the fastest-migrating capsid II preparation was 0.51 +/- 0.03 times as fast as capsid I and the slowest was 0.37 +/- 0.02 times as fast as capsid I . Capsid IV with and without the phage tail migrated 0.29 +/- 0.02 and 0.42 +/- 0.02 times as fast as capsid I . The results of the extrapolation of bacteriophage and capsid mobilities to 0% agarose concentration indicated that the above differences in mobility are caused by differences in average surface charge density . To increase the accuracy of mobility comparisons and to increase the number of samples that could be simultaneously analyzed, multisample horizontal slab gels were used . Treatment with the ionic detergent sodium dodecyl sulfate converted capsid I to a capsid that migated in the capsid II region during electrophoresis through agarose gels . In the electron microscope, most of the envelopes of these latter capsids resembled the capsid II envelope, but some envelope regions were thicker than the capsid II envelope. J Virol, 1978 Dec, 28(3), 895 - 904 Bacteriophage phi29 terminal protein: its association with the 5' termini of the phi29 genome; Ito J; The location of the protein bound to bacteriophage phi29 DNA has been studied with restriction endonucleases, exonucleases, and polynucleotide kinase . The protein is invariably associated with the two terminal DNA fragments generated by restriction endonucleases . The phi29 DNA prepared with or without proteinase K treatment is resistant to the action of the 5'-terminal-specific exonucleases, lambda-exonuclease and T7 exonuclease . The phi29 DNA is also inaccessible to phosphorylation by polynucleotide kinase even after treatment with alkaline phosphatase . On the other hand, phi29 DNA is sensitive to exonuclease III, and the 3' termini of the DNA can be labeled by incubating with alpha-{32P}ATP and terminal deoxynucleotidyl transferase . The protein remains associated with the phi29 DNA after treatment with various chaotropic agents, including 8 M urea, 6 M guanidine-hydrochloride, 4 M sodium perchlorate, 2 M sodium thiocyanate, and 2 M LiCl . These results are consistent with the notion that the protein is linked covalently to the 5' termini of the phi29 DNA. J Virol, 1978 Dec, 28(3), 877 - 84 Bacteriophage lambda mutants (lambdatp) that overproduce repressor; Truitt CL et al.; Lambda tp mutants, selected for their ability to form turbid plaques on lon hosts, overproduce repressor . The tp1 and tp2 mutations have been located within (or adjacent to) the cIII gene . The tp1 mutation reduced late gene expression, as measured by endolysin synthesis (in the absence of functional cI repressor) and progeny phage yield . The tp4 mutation was mapped in the cY-cII region, and complementation tests indicated that tp4 affects the diffusible product of the cII gene . The tp4 mutation also reduced progeny production, but did not markedly affect endolysin synthesis. J Virol, 1978 Dec, 28(3), 835 - 42 Transcription of bacteriophage M13 DNA: existence of promoters directly preceding genes III, VI, and I; Edens L et al.; In vitro transcription and coupled transcription-translation studies have been performed with restriction fragments of bacteriophage M13 replicative-form DNA which contain either gene III, gene VI, or gene I . It could be demonstrated that DNA fragments which contain gene III were able to direct the synthesis of gene III protein . Fragments which encompassed genes VI and I gave rise to the synthesis of gene I protein only, whereas gene I-containing fragments were able to direct the synthesis of gene I protein . None of the fragments studied gave rise to a detectable level of gene VI protein, although an RNA transcript of gene VI could readily be obtained during in vitro transcription of the relevant gene VI-containing DNA fragments . From these results we have concluded that the promoters A0.44 and A0.49 are located in front of genes VI and I, respectively, and that gene III is also equipped with a promoter (X0.25) . Introduction of a single cleavage within the gene III region does not abolish the expression of genes VI and I in vitro . Hence, the expression of these genes is not solely dependent on the initiation of RNA synthesis at the gene III promoter or on leakage of transcription through the central termination site (T0.25), but is also determined by the initiation frequency of RNA synthesis at their individual promoters. Nucleic Acids Res, 1978 Dec, 5(12), 4725 - 36 Detection of yeast ribosomal RNA sequences in E . coli infected with hybrid bacteriophage; Kramer RA et al.; Yeast ribosomal DNA was inserted into Escherichia coli on a bacteriophage vector and the host cell RNA was then extracted and analyzed for the presence of yeast ribosomal RNA sequences . RNA complementary to yeast rDNA was detected by hybridization . The transcription of yeast rDNA was found to be independent of phage RNA synthesis and to occur on the same DNA strand as rRNA transcription in yeast . However, hybridization to restriction fragments of yeast rDNA suggested that the RNA species detected in E . coli differ somewhat from authentic yeast rRNA. Nucleic Acids Res, 1978 Dec, 5(12), 4677 - 98 Nucleotide sequence of gene VII and of a hypothetical gene (IX) in bacteriophage M13; Hulsebos T et al.; A DNA fragment containing gene VII of bacteriophage M13 has been transcribed and the nucleotide sequence of this 169-nucleotides long transcript was determined by RNA sequencing methods . Additionally, the nucleotide sequence of this gene and parts of its neighbouring genes V and VIII has been determined by the dimethylsulphate-hydrazine technique . The reading frame of gene VII has been established by determining the nucleotide changes occurring in the transcripts of two amber mutants of this gene . From these combined data it is apparent that gene VII is only 99 nucleotides long and is immediately followed by the termination codon UGA . Its initiation codon AUG is separated from gene V by only a single nucleotide . It was noted that between the UGA termination codon of gene VII and the initiation codon of the next gene (gene VIII) there is space for another, hitherto unknown gene . This gene (IX) most probably codes for the small polypeptide ("C-protein") present in mature M13 phage particles. Nucleic Acids Res, 1978 Dec, 5(12), 4479 - 94 Bacteriophage lambda and plasmid vectors, allowing fusion of cloned genes in each of the three translational phases; Charnay P et al.; We have constructed vectors from bacteriophage lambda and from plasmid pBR322 having a single EcoRI restriction site which is immediately downstream from the lac UV5 promotor . Each vector allows the fusion of a cloned gene to the lac Z gene in a different phase relative to the translation initiation codon of the lac Z gene . These vectors were constructed through modification of the initial EcoRI restriction site by S1 endonuclease treatment and then addition of octadeoxyribonucleotides (EcoRI linkers), which shifted the restriction site by 2 or 4 nucleotides . Used in combination these vectors should allow translation of a cloned gene in any one of the three coding phases . The bacteriophages vectors are certified as B2 (EK2) safety level vectors by the French "recombinaison genetique in vitro" committee (D.G.R.S.T.). J Gen Virol, 1978 Dec, 41(3), 609 - 22 Formation of concatemeric DNA as an intermediate in the replication of bacteriophage T1 DNA molecules; Ritchie DA et al.; The structure of intracellular DNA extracted from phage T1 infected cells was analysed by sedimentation through sucrose gradients . DNA labelled with 3H-dThd during a short pulse given at any time during T1 DNA synthesis sedimented in neutral gradients as a broad heterogeneous band with a large fraction of the label sedimenting more rapidly than mature T1 DNA molecules . Rapidly-sedimenting label was also observed when pulse-labelled DNA was denatured and analysed on alkaline sucrose gradients . Electron microscopy of intracellular T1 DNA revealed linear molecules of variable length the longest of which were three to four times the mature genome length . The distribution of lengths derived from electron microscopy are consistent with the molecular length distributions calculated from the sedimentation coefficients . We conclude that the rapidly-sedimenting DNA is in the form of concatemers consisting of linear tandem repeats of the T1 genome . The concatemeric form of replicating T1 DNA is a precursor of progeny T1 genomes since in pulse-chase experiments it was converted efficiently into mature, infectious T1 phage particles . The identification of this concatemeric form of T1 DNA provides supporting evidence for the model proposed by Gill & MacHattie (1976) to account for the formation of the very limited number of cyclic permutations of gene sequence found for mature T1 DNA molecules. J Gen Microbiol, 1978 Dec, 109(2), 329 - 33 Chromosomal location of the mop (groE) gene necessary for bacteriophage morphogenesis in escherichia coli; Guest JR et al.; The chromosomal location of a host gene, mop (groE), which is essential for the morphogenesis of several bacteriophages in Escherichia coli, was determined by two- and three-factor transductional crosses using phage P1 . Cotransduction frequencies beteen mop and other markers were: aspA, 90%; ampA, 77%; frdA, 73%; mel, 24% . The sequence of markers in the corresponding segment (mel to purA; 91.5 to 93.5 min) of the E . coli linkage map was shown to be mel--aspA--mop(groE)--ampA--frdA--pur A. Proc Natl Acad Sci U S A, 1978 Dec, 75(12), 5827 - 30 Three-dimensional structure of thioredoxin induced by bacteriophage T4; Soderberg BO et al.; The three-dimensional structure of thioredoxin from bacteriophage T4 has been determined from a 2.8-angstrom resolution electron density map . Phase angles for this map were determined from one heavy atom derivative and anomalous differences from cadmium in the native crystals . The molecule of 87 amino acid residues is built up from two simple folding units; a betaalphabeta unit from the amino end of the chain and a betabetaalpha unit from the carboxyl end . This structure is similar to that of thioredoxin from Escherichia coli in spite of their completely different amino acid sequences . The redox-active S--S bridge is part of a protrusion of the molecule as in E . coli thioredoxin, but with quite different surroundings . The structural differences in this region have been correlated to differences in specificity towards the enzyme ribonucleotide reductase from different species. J Virol, 1978 Dec, 28(3), 717 - 24 Replication of RNA bacteriophages in the presence of rifamycin; Bauman V et al.; Replication of RNA bacteriophages in the presence of rifamycin was studied in different Escherichia coli strains that vary in RNase content but are not isogenic: AB259 RNase+, Q13 RNase I- PNPase-, AB105 RNase I- RNase III- . It was found that rifamycin did not affect characteristics of phage replication such as the general pattern of viral RNA synthesis and intracellular development of the phage . These characteristics are strain specific and independent of the cell growth rate, which defines only phage release . The inhibition of cell division by rifamycin interfered with the release of the phage and thus produced an apparent effect of rifamycin on phage replication. J Virol, 1978 Dec, 28(3), 679 - 85 Replication of bacteriophage M13 . XIV . Differential inhibition of the replication of M13 and M13 miniphage in a mutant of Escherichia coli defective in the 5' leads to 3' exonuclease associated with DNA polymerase I; Chen TC et al.; Previous studies have shown that M13 single-strand synthesis is inhibited at nonpermissive temperature in Escherichia coli polAexl, a temperature-sensitive mutant defective in the 5' leads to 3' exonuclease activity of polymerase I (T.-C . Chen and D . S . Ray, J . Mol . Biol . 106:589-604, 1976) . Under these conditions the formation of covalently closed replicative form (RF) molecules is greatly reduced, and miniature forms of RF accumulate . We show here that the accumulation of mini-RFs is the consequence of a differential inhibition of the replication of unit-length phage and preexisting miniphage rather than a de novo production of miniphage . Mini-RFs do not accumulate even after as many as nine cycles of growth in the mutant host infected only with unit-length phage . Mixed infections of the mutant host with plaque-purified unit-length phage and a single cloned miniphage show that discontinuities in the mini-RFs are joined with higher efficiency than are those contained in unit-length RFs . After a shift to nonpermissive temperature during single-strand synthesis in cells infected with plaque-purified phage alone, M13 RFs are found largely as RFII molecules (RF form having one or more single-strand discontinuities) containing only a single discontinuity in the viral strand . The inability of the accumulated unit-length RFII molecules to actively replicate may reflect the presence of either a bound protein or RNA primer on the 5' terminus of the viral strand and provides further support for the existence of distinct initiation and termination events in the synthesis of the viral strand. J Gen Microbiol, 1978 Dec, 109(2), 329 - 33 Chromosomal location of the mop (groE) gene necessary for bacteriophage morphogenesis in Escherichia coli; Guest JR et al.; The chromosomal location of a host gene, mop (groE), which is essential for the morphogenesis of several bacteriophages in Escherichia coli, was determined by two- and three-factor transductional crosses using phage P1 . Cotransduction frequencies between mop and other markers were: aspA, 90%; ampA, 77%; frdA, 73%; mel, 24% . The sequence of markers in the corresponding segment (mel to pur A; 91.5 to 93.5 min) of the E . coli linkage map was shown to be mel-aspA-mop(groE)-ampA-frdA-purA. Cell, 1978 Dec, 15(4), 1187 - 97 Nonsense and insertion mutants in the relA gene of E . coli: cloning relA; Friesen JD et al.; We have made use of lysogens of a specialized transducing bacteriophage, lambdapyrG+ relA+, to select nonsense (relAnon) and insertion (relAins) mutations in the relA gene . Three independent relAnon mutants were isolated on the phage . In all three, the relaxed phenotype was suppressed by supD, supE, supF or sup6 . Three independent relAins mutants were isolated, all containing an insertion element (probably IS2) in an apparently identical location in the relA gene . Polyacrylamide gel electrophoretic analysis of peptides synthesized by the phages in ultraviolet lightkilled host cells revealed that no stringent factor was coded for by either the relAins or relAnon phages (the latter in a sup+ cell); stringent factor was detected when the relAnon phages were used in a similar experiment with supD or supE host cells . The relAnon and relAins mutations could be crossed in haploid form in the E . coli chromosome . These recombinants grew with a normal doubling time, had a ppGpp pool which was between 70 and 100% compared with the classical relA strain, and underwent a normal carbon source shift-down . A restriction endonuclease map of the pyrG relA region of the specialized transducing phage is presented in which the position of the insertion element (recognized by a novel Hind III-cut site) defines the position of the relA gene . This position was verified by an analysis of the structure of five plasmids formed by cloning portions of the region in the pBR322 cloning vehicle . Our results indicate that the relA gene is not an essential cellular function, that there might be a second mechanism for the synthesis of basal level ppGpp in the cell and that the sole function of the relA gene is apparently the high level ppGpp synthesis triggered in response to deacylated tRNA. Mutat Res, 1978 Dec, 52(3), 313 - 22 Non-essential UV-sensitive bacteriophage T4 mutants affecting early DNA synthesis: a third pathway of DNA repair; Minderhout L et al.; Non-essential bacteriophage T4 mutants uvs58 and uvs79 showed a lower UV sensitivity than either the excision-repair mutant v am5 or the replication-dependent recombination-repair mutant y10 . The UV sensitivity of double and triple mutants carrying one of the mutations uvs58 or uvs79, and v am 5 or (and) y10 was higher than the sum of the sensitivities of the single mutants . The uvs58 mutation was mapped to the early gene region, close to amN81 (gene 41) . The unirradiated mutants uvs58 and uvs79 accumulated newly synthesized DNA at a slower rate than wild-type T4 . Double mutants uvs58:am59 and uvs79:am59 showed DNA synthesis in E . coli B su- to be arrested at a 3--5 times lower level than that in am59-infected cells . Chloramphenicol, added 9--12 min after infection, suppressed arrests of DNA synthesis, the double mutants showing a lag of 8 min as compared with am59 . Results from analysis of sucrose gradients of parental uvs58 and uvs79 DNA were in agreement with the suggestion of a mutation in an early function . The mutants uvs58 and uvs79 are suggested to be defective in a component of the DNA replication apparatus with a function in the adaptation to irregularities in the DNA structure . The third pathway of UV repair is tentatively designated as non-catalytic replication repair. J Bacteriol, 1978 Dec, 136(3), 1192 - 6 Construction of a hybrid bacteriophage-plasmid recombinant DNA vector; Donoghue DJ et al.; A phage-plasmid hybrid was constructed for use as a recombinant DNA vector, allowing the propagation of cloned EcoRI restriction endonuclease fragments of about 2 X 10(6) to 11 X 10(6) daltons . The colicin E1 plasmid replicon was fused to the left arm of a lambdagt generalized transducing phage with a thermolabile repressor, yielding a genome which could be replicated either by phage lambda functions or via the colicin E1 plasmid replicon . At the nonpermissive temperature, phage functions were derepressed and phage growth occurred lytically . Alternatively, at the permissive temperature, lambda functions were repressed and the vector replicated as a covalently closed circular plasmid . The phage-plasmid hybrid vector could be maintained at a copy number determined by the colicin E1 plasmid replicon and was also sensitive to amplification after chloramphenicol treatment . An EcoRI fragment of Escherichia coli DNA encoding genes of the arabinose operon also was inserted into the central portion of the vector. J Bacteriol, 1978 Dec, 136(3), 1109 - 19 malB region in Escherichia coli K-12: specialized transducing bacteriophages and first restriction map; Marchal C et al.; By starting from an Escherichia coli K-12 strain with a lambda phage integrated in the malB region, series of transducing phages carrying part or all of the malB region have been isolated . Genetic mapping of the transduced malB fragments was accomplished by complementation and recombination with known mutations in the region . By using the DNA of these phages, it was found that the malB region is cleaved by the restriction enzymes BglII, EcoRI, HaeII, HincII, SalI, and SstI, but not BamHI, HindIII, KpnI, PstI, XbaI, or XhoI . A physical map was constructed and tentatively correlated with the genetic map. J Bacteriol, 1978 Dec, 136(3), 1084 - 93 Properties of lambda transducing bacteriophages carrying R100 plasmid DNA: mercury resistance genes; Dempsey WB et al.; Three lambdamer (resistance to Hg2+ and mercurials) transducing phages were prepared from three independent cointegrate isolates of bacteriophage lambda and plasmid R100 . DNA heteroduplex and restriction nuclease analyses of the lambdamer DNA showed that all three phages had resulted from lambda insertion at kilobase coordinate 8.6 of plasmid R100, followed by loss of different lengths of lambda DNA and replacement with different lengths of R100 DNA . Two of the lambdamer phages were defective, containing deletions from lambdaatt through the lambdaN gene and into the lambdarex gene; the third, VAlambda14, was an N+ Spi- plaque-forming phage . With VAlambda14, N-dependent transcription of R100 mer from the lambdapL promoter suggested that transcription of mer proceeded in the direction from IS1b toward the sulfonamide resistance determinant (i.e., from a plasmid promoter in restriction nuclease fragment EcoRI-H toward fragment EcoRI-I) . Phage-directed protein synthesis in a UV-irradiated lambdaind- lysogen showed the Hg2+-inducible synthesis of three major polypeptides of molecular weights 68,000, 11,500, and 8,500 and three minor ones of molecular weights 54,000, 33,000, and 13,500 . The largest of the major polypeptides is identified as the subunit of the mercuric reductase enzyme . The functions of the smaller polypeptides are not known . Hg2+ reductase enzyme assays confirmed the regulation of mer synthesis during phage infection. Proc Natl Acad Sci U S A, 1978 Dec, 75(12), 6182 - 6 A single base-pair change creates a Chi recombinational hotspot in bacteriophage lambda; Sprague KU et al.; X4+ mutations, responsible for the Chi phenotype in phage lambda, locally increase the rate of recombination promoted by the Escherichia coli recombination system (Rec) . X+ mutations in the cII gene, one of a few sites in lambda at which such mutations arise, were located genetically and physically with overlapping deletions . DNA sequence analysis of the deletion segment containing the X+ C mutations showed that two independent X+ C mutations arose by the same A-T to T-A transversion . Presumably, this change creates a nucleotide sequence recognized by a protein involved in a rate-limiting step of recombination. Proc Natl Acad Sci U S A, 1978 Dec, 75(12), 6144 - 8 Marker rescue and partial replication of bacteriophage T7 DNA; Burck KB et al.; Experiments reported here show that some UV-irradiated wild-type T7 phage markers can be rescued efficiently by coinfection with T7 amber mutant phage in a permissive host . Other results show that the segments of a UV-irradiated genome that replicate efficiently are those that also are rescued efficiently during a marker rescue experiment . At higher doses, fewer markers are rescued efficiently and fewer segments of the genome replicate efficiently . The results clearly indicate that the probability of marker rescue is correlated with the ability of the DNA containing the marker to replicate . Sucrose density gradient analysis shows that UV irradiation does not produce double-strand scissions in T7 DNA at doses used here . Therefore, the partial replication and rescue of markers from the left end of the genome is not due simply to injection of only the left end of the T7 DNA. Proc Natl Acad Sci U S A, 1978 Dec, 75(12), 5817 - 21 Interaction of bacteriophage lambda repressor with nonoperator DNA containing single-strand gaps; Sussman R et al.; In direct binding assays, purified lambdaind+ repressor displayed high affinity for nonoperator DNA containing single-strand gaps . Its affinity for this same DNA but completely double-stranded, nicked, or denatured was considerably lower . In contrast, purified lambdaind- repressor had 1/10th the affinity for the gapped DNA, a level comparable to that of purified lac repressor . In the presence of limiting amounts of ind+ repressor, nonoperator DNA containing gaps could be shown to compete effectively with lambda DNA for binding of repressor . A previous model of lambda induction {Sussman, R . & Ben-Zeev, H . (1975) Proc . Natl . Acad . Sci . USA 72, 1973--1976}, based on the assumption that this phenomenon involves the binding of repressor to lesions in the host DNA, is reevaluated in the light of the data reported here. C R Acad Sci Hebd Seances Acad Sci D, 1978 Dec, 287(16), 1453 - 6 {Cloning of the hepatitis B virus genome in Escherichia coli}; Fritsch A et al.; The whole genome of the hepatitis B virus (Dane particles) was inserted in vitro in the genome of the bacteriophage lambda gtWES . LAMBDA B . The recombinant DNA molecule was cloned in E . coli . Amplification of the hybrid bacteriophage enables the preparation of large amounts of hepatitis B virus DNA . The possibilities offered by the utilization of this recombinant bacteriophage are discussed. Mol Gen Genet, 1978 Nov 29, 167(2), 197 - 207 Recombinational repair of alkylation lesions in phage T4 . II . Ethyl methanesulfonate; Johns V et al.; Treatment of bacteriophage T4 by ethyl methanesulfonate (EMS) caused more than a doubling in recombination between two rII markers . The functions of genes 47, 46, 32, 30, uvsX and y are known to be required for genetic recombination, and mutants defective in these genes were found to be more sensitive to inactivation by EMS than wild-type phage . This suggests that a recombinational pathway involving the products of these genes may be employed in repairing EMS induced lethal lesions . Genes 45 and denV are apparently not involved in recombination, and mutants defective in these genes were not EMS-sensitive . Gene 47, 46 and y mutants which were defective in the repair of EMS induced lethal lesions had no detectable deficiency in their ability to undergo EMS-induced mutation . This implies that recombinational repair of EMS lesions does not contribute substantially to EMS mutagenesis . The results obtained here with EMS are general similar to the results reported in the preceding paper with MNNG, suggesting that the lesions caused by both of these monofunctional alkylating agents may be eliminated by similar recombinational repair processes. Biochim Biophys Acta, 1978 Nov 21, 521(1), 27 - 44 Expression of bacteriophage M13 dna in vivo . I . Synthesis of phage-specific RNA and protein in minicells; Smits MA et al.; It is demonstrated that after infection of the appropriate minicell-producing strain of Escherichia coli with the filamentous bacteriophage M13, its replicative form DNA is segregated into minicells . Consequently these minicells have acquired the capability to direct the synthesis of phage-specific RNA and protein . Comparision of the electrophoretic mobilities of phage-specific RNA species made in vitro with those made in M13 replicative form DNA harbouring minicells, have indicated that almost all in vitro synthesized G-start RNAs have an equivalent among the in vivo synthesized RNA products . Furthermore it could be demonstrated that in M13 replicative form DNA harbouring minicells the phage-specific proteins encoded by genes III, IV, V and VIII are made . In addition the synthesis of a phage-specific polypeptide (molecular weight approx . 3000) co-migrating with the recently discovered capsid protein (designated C-protein) could be demonstrated . The meaning of these results for the resolution of the regulatory mechanisms operative during the life cycle of this phage will be discussed. Mol Gen Genet, 1978 Nov 16, 167(1), 105 - 12 Evidence for a near UV-induced photoproduct of 5-hydroxymethylcytosine in bacteriophage T4 that can be recognized by endonuclease V; Childs JD et al.; Non-photoreactivable endonuclease V-sensitive sites have been detected in the DNA of wild type bacteriophage T4 irradiated with near UV light (320 nm) . Such sites were not detected in the DNA of (a) wild type T4 irradiated with far UV (254 nm) or (B) in T4 mutants in which non-glucosylated 5-hydroxy-methylcytosine (5HMC) or cytosine replaces glucosylated 5HMC normally present in T4, irradiated with 320 nm or 254 nm light . Although the non-photoreactivable sites accounted for approximately 50% of the endonuclease V-sensitive sites in the DNA of glucosylated T4 irradiated with near UV, there was very little difference in the sensitivities of T4 containing glucosylated 5HMC, non-glucosylated 5HMC and cytosine to near UV (313 nm) . We propose that the photoproduct responsible for the non-photoreactivable, but endonuclease V-sensitive, sites in glucosylated DNA is formed from glucosylated 5HMC and that a similar photoproduct is formed from non-glucosylated 5HMC or cytosine in the appropriate phage strains . We further propose that the glucosylated 5HMC photoproduct is non-photoreactivable whereas the cytosine and non-glucosylated 5HMC photoproducts are photoreactivable and are therefore possibly cyclobutane dimers. Nature, 1978 Nov 16, 276(5685), 236 - 47 Nucleotide sequence of bacteriophage G4 DNA; Godson GN et al.; The 5,577 nucleotide long sequence of bacteriophage G4 DNA has been determined using the 'plus and minus' and chain termination methods of DNA sequencing . This sequence has been compared with that of the closely related bacteriophage phiX174 (refs 1, 55) . In the coding regions there is an average of 33.1% nucleotide sequence differences between the two genomes, but the distribution of these changes is not random and the sequence of some genes is more conserved than others . There is less sequence similarity between the untranslated intergenic regions of G4 and phiX174, but despite this the sequences of the J/F, F/G and H/A untranslated spaces in both genomes have similar sized hairpin loops, which may be related to their function. Eur J Biochem, 1978 Nov 15, 91(2), 465 - 73 The effects of tiamulin, a semisynthetic pleuromutilin derivative, on bacterial polypeptide chain initiation; Dornhelm P et al.; Tiamulin, a water-soluble and highly effective semisynthetic derivative of pleuromutilin leads to the formation of physiologically inactive polypeptide chain initiation complexes which readily decompose and do not enter the phase of peptide chain elongation . Once elongation has begun it continues even in the presence of tiamulin as has been shown by measuring the formation of N-acetylphenylalanine-poly(phenylalanine) . The formation of abortive initiation complexes was observed regardless of whether AcPhe-tRNA of fMet-tRNA was used as an initiator or whether artificial messengers or a natural messenger, like R17 bacteriophage RNA, was used . When this drug was acting on whole cells, it led to the disappearance of polysomes . The only structures which could be detected were of the monosome size . Therefore, polysomes seem to elongate the polypeptide chains in whole cells in the presence of this antibiotic, but since effective reinitiation is blocked, the polysome pool of the cell soon becomes depleted. Mol Gen Genet, 1978 Nov 9, 166(3), 277 - 85 Specific labelling of replicating SPP1 DNA: analysis of viral DNA synthesis and identification of phage DNA-genes; Burger KJ et al.; Specific labelling of replicating bacteriophage SPP1 DNA can be achieved by infection at nonpermissive temperature of a B . subtilis strain carrying the initation mutation dnaB ts134 . Under these conditions host DNA synthesis is reduced by 90 to 95% . This technique was used to identify cistrons of SPP1 involved in phage DNA synthesis and to define intermediates in SPP1 replication. Mol Biol (Mosk), 1978 Nov-Dec, 12(6), 1329 - 40 {Structural organization of the genome of bacteriophage T5 by specific endonucleases}; Chernov AP et al.; The DNA of Bacteriophage T5+ has been treated with restriction endonucleases EcoRI, HindIII, BamI, SmaI, PstI, SalI, KpnI and the electrophorectic pattern obtained in agarose gel has been analyzed in order to localize the specific cleavage sites on the T5 DNA . The localization of cleavage sites has been resolved from the electrophoretic pattern of double and partial digests, the digests of isolated restriction fragments and the digests of deletion mutant T5 st(O) DNA . Four BamI cleavage sites have been found and localized on the physical map of T5 DNA at 0.225; 0.68; 0.715 and 0.725 fractional lenght . Endonuclease PstI cuts T5 DNA at 11 sites: 0.095; 0.215; 0.320; 0.510; 0.635; 0.675; 0.710; 0.770; 0.810; 0.840; 0.875 fractional length . Six KpnI cleavage sites have been mapped at 0.140; 0.160; 0.530; 0.720; 0.760; 0.840 fractional length . 14 out of 17 HindIII cleavage sites have been localized at 0.10; 0.24; 0.255; 0.345; 0.40; 0.52; 0.54; 0.57; 0.70; 0.76; 0.80; 0.84; 0.87; 0.89, fractional length of T5 DNA . Complete cleavage map of the phage genome is presented for seven restriction enzymes. Cell, 1978 Nov, 15(3), 1045 - 53 Nucleotide sequence of the J gene and surrounding untranslated regions of phage G4 DNA: comparison with phage phiX174; Fiddes JC et al.; A 290 nucleotide long region of the bacteriophage G4 genome including the end of the overlapping genes D and E, the entire gene J and the untranslated region between genes J and F has been sequenced and compared with the same region in bacteriophage phiX174 . Deletions, insertions, duplications and single base changes in G4 relative to phiX174 have resulted in the following changes: the loss of the phiX174 overlapping gene Dtermination and gene J initiation codons, resulting in their separation by 32 untranslated nucleotides; the deletion of one third of the gene J coding region, so that the G4 protein is only 24 amino acids long compared with 37 amino acids in phiX174; and the establishment of a long untranslated region between G4 genes J and F, which despite many nucleotide changes retains the ability to form a stable hairpin loop in the same place and with the same geometry as in phiX174 . The G4 overlapping gene E is longer than in phiX174 and extends beyond gene D . Sixteen nucleotides at the end of genes D and E in phiX174 are duplicated in G4 before gene J. In Vitro, 1978 Nov, 14(11), 935 - 8 Decontamination of bacterial infection of monolayer cultures with a specific bacteriophage; Riche PH et al.; A few cell lines and primary monolayer cultures were accidentally infected by bacteria . These cultures were successfully decontaminated by means of the specific bacteriophage virus after quick identification of the responsible bacteria . This method presents a practical interest for preservation of valuable cultures. Proc Natl Acad Sci U S A, 1978 Nov, 75(11), 5594 - 8 Analysis of bacteriophage P1 immunity by using lambda-P1 recombinants constructed in vitro; Sternberg N et al.; We describe the dissection and reconstruction of a complex control circuit, the P1 immunity system, by a method that involves inserting EcoRI-generated fragments of P1 DNA into lambda vectors that can then be sequentially inserted into a bacterial cell . Using these techniques we have isolated lambda-P1 hybrid phages that express the products of P1 genes c1, c4, ant, and ban and, in appropriately constructed lysogens, confirmed the roles played by the first three of these products in phage immunity . In addition we have localized to particular P1 fragments the sites requisite for expression and repression of these gene products . The analysis leads to the conclusion that gpant acts in trans to antagonize repression mediated by gpc1, in support of one of two proposed models for gpant action . Moreover, two features of the immunity system are revealed: (i) a hitherto unknown component that effects gpc1 repression; and (ii) an unexpected ability of gpc4 to channel a superinfecting c1+ phage into the lysogenic state, which suggests that gpc4 activity regulates the establishment phase of lysogeny. Proc Natl Acad Sci U S A, 1978 Nov, 75(11), 5437 - 41 Structure of the lambda att sites generated by int-dependent deletions; Hoess RH et al.; Bacteriophage lambda integrates into the chromosome of its Escherichia coli host by means of a site-specific recombination between a locus on the phage chromosome (phage att site) and a locus on the bacterial chromosome (bacterial att site) . The nucleotide sequence of four lambda att sites altered in site-specific recombination has been determined . The int-dependent deletions that generated these att sites have one end point within the phage att site and extend either to the left or to the right . As a result of the new internucleotide bond created by deletion formation, these phage have alterations in the 15-base-pair common core region . The new DNA sequences brought to the att sites by the deletions, designated delta for regions to the left and delta' for regions to the right, do not share any discernible homology with their analogous counterparts in the phage att site arms, P and P', respectively, or with the bacterial att site arms, B and B', respectively . The finding of alterations in the 15-base-pair common core region necessitates a reinterpretation of the genetic properties of these att sites in site-specific recombination . The structure of these sites in relation to their genetic properties can be viewed as being consistent with a model in which the only specificity elements in int-dependent site-specific recombination are the common core region, O, and the phage arms, P and P'. Proc Natl Acad Sci U S A, 1978 Nov, 75(11), 5281 - 5 A photo-CIDNP study of the interaction of oligonucleotides with gene-5 protein of bacteriophage M13; Garssen GJ et al.; It is shown that photo-CIDNP effects (CIDNP, chemically induced dynamic nuclear polarization) can be generated in the 360-MHz proton NMR spectrum of gene-5 protein from bacteriophage M13 . This technique is used to determine the number of tyrosyl residues at the surface of the protein and to assign the resonances from the 3,5-ring protons of these residues . The DNA-binding site of the protein is investigated by formation of complexes with oligonucleotides . Complex formation leads to shifting and/or quenching of the photo-CIDNP emission signals of the surface tyrosines, implying that they are involved in DNA-protein interaction . These experiments are complemented by studying the complex formation of Lys-Tyr-Lys to poly(A). Nucleic Acids Res, 1978 Nov, 5(11), 4129 - 39 An Escherichia coli ribonuclease which removes an extra nucleotide from a biosynthetic intermediate of bacteriophage T4 proline transfer RNA; Schmidt FJ et al.; The biosynthesis of bacteriophage T4 tRNAPro, tRNASer, and tRNAIle requires enzymatic removal of extra nucleotides from the 3' terminus of the respective precursor RNAs . A ribonuclease activity capable of catalyzing such reactions has been partially purified from uninfected Escherichia coli using an artificial precursor RNA as substrate . A number of ribonuclease activities were resolved during purification . Use of E . coli strain BN, a mutant known to be deficient in the relevant ribonuclease activity, permitted us to identify it in wild-type cells . This activity was designated the BN ribonuclease . BN ribonuclease had an apparent molecular weight of 35,000 as measured by Sephadex gel filtration . Mg2+ was required for activity, which was optimal at {Mg2+} of 2mM . Activity did not require monovalent cations K+ or Na+ . BN ribonuclease was less efficient at removing extra residues in the biosynthesis of tRNASer and tRNAIle than in the biosynthesis of tRNAPro. J Virol, 1978 Nov, 28(2), 643 - 55 Model for DNA packaging into bacteriophage T4 heads; Black LW et al.; The mechanism of DNA packaging into bacteriophage T4 heads in vivo was investigated by glucosylation of hydroxymethylcytosine residues in a conditionally glucose-deficient host . Cytoplasmic DNA associated with partially packaged ts49 heads can be fully glucosylated, whereas DNA already packaged into these heads is shown to be resistant to glucosylation . After temperature shift and completion of arrested packaging into the reversible temperature-sensitive ts49 head, the structure of the DNA in the mature ts49 phage was investigated by restriction enzyme digestion, autoradiography, and other techniques . Such mature DNA appears to be fully glucosylated along part of its length and nonglucosylated on the remainder . Its structure suggests that the DNA is run into the head linearly and unidirectionally from one mature end and that there is little sequence specificity in that portion of the T4 DNA which first enters the capsid . This technique should be useful in investigation of the three-dimensional structure of first- and last-packaged DNA within the head; preliminary studies including autoradiography of osmotically shocked phage suggest that the DNA which first enters the head is deposited toward the center of the capsid and that the end of the DNA which first enters the head exits first upon injection . In conjunction with studies of the structure of condensed DNA, the positions and functions of T4 capsid proteins in DNA packaging, and the order of T4 packaging functions {Earnshaw and Harrison, Nature (London) 268:598-602, 1977; Hsiao and Black, Proc . Natl . Acad . Sci . U.S.A . 74:3652-3656, 1977; Muller-Salamin et al., J . Virol . 24:121-134, 1977; Richards et al., J . Mol . Biol . 78:255-259, 1973}, the features described above suggest the following model: the first DNA end is fixed to the proximal apex of the head at p20 and the DNA is then pumped into the head enzymatically by proteins (p20 + p17) which induce torsion in the DNA molecule. Genetika, 1978 Nov, 14(11), 1908 - 12 {Adsorptive capacity of bacteriophage Mu on Escherichia coli K-12 strains with deletions in the attlambda region}; Koretskaia NG et al.; Escherichia coli strains with deletions in att lambda region were obtained . The comparison of the extent of deletions with the sensitivity of the corresponding mutant clones to phage Mu showed that the gene controlling the sensitivity of E . coli K-12 to the phage Mu is located in nad A-gal region of the bacterial chromosome . It is shown that the resistance of E . coli strains which had lost the region of bacterial chromosome between nad A gene and genes of gal-operon have adsorption character . Deletion of the nad A-gal region does not affect the adsorption of other phages (lambda, P1 and T4) . Thus, the gene, located in this region, is responsible for the specific adsorption of the phage Mu. J Bacteriol, 1978 Nov, 136(2), 808 - 11 Plasmids of incompatibility group P code for the capacity to propagate bacteriophage IKe; Grant RB et al.; Seven of eight plasmids of incompatibility group P were found to code for the capacity to propagate bacteriophage IKe in Escherichia coli . Six of the seven plasmids allowed propagation of IKe by one bacterial host (RG172) but not by another (RG176); the other plasmid allowed IKe propagation by both hosts . IKe propagation by a number of E . coli K-12 strains was quite variable . IKeh, an extended host range mutant of IKe, was found to plaque specifically on N+ and P+ strains. J Bacteriol, 1978 Nov, 136(2), 742 - 56 Analysis of sequences transposed by complementation of two classes of transposition-deficient mutants of Tn3; Gill R et al.; The Tn1 and Tn3 elements are closely related transposons which carry the structural gene for ampicillin resistance . Two classes of deletion mutants of the plasmid pMB8::Tn3 (RSF1050) are unable to transpose ampicillin resistance but can be complemented in trans by a coresident Tn1 or Tn3 element . The analysis of the sequences transposed upon complementation of one class of mutants (type I) showed that the mutant element had undergone bona fide transposition . Complementation of the type II mutants led to the transposition of a sequence analogous to bacteriophage mu-promoted integration of non-mu DNA . The transposed sequence consisted of two Tn3 elements which flanked a single copy of the pMB8 portion of the RSF1050 genome . Complementation data indicated that the type II mutants are defective in at least one trans-acting function which must be supplied for transposition to occur . The nature of sequence transposed from the type II mutant is the consequence of a defective cis-acting function (or site) . In addition, the type II mutants were defective in a trans-acting function which regulated the frequency of transposition. J Bacteriol, 1978 Nov, 136(2), 693 - 9 Role of lipopolysaccharide and outer membrane protein of Escherichia coli K-12 in the receptor activity for bacteriophage T4; Mutoh N et al.; Lipopolysaccharide isolated from Escherichia coli K-12 did not inactivate phage T4, although the cell envelopes with 1% sodium deoxycholate resulted in the release of cytoplasmic membrane proteins, 70% of the lipopolysaccharide, and almost all of the phospholipid . The reconstitution of phage receptor activity was achieved from deoxycholate-soluble and -insoluble fractions by dialysis against a solution of magnesium chloride . Lipopolysaccharide was the only essential component in the deoxycholate-soluble fraction . PhageT4-resistant mutants YA21-6 and YA21-82, having defects in the deoxycholate-soluble and -insoluble fractions, respectively, were isolated . The deoxycholate-soluble fraction of YA21-6 possessed heptoseless lipopolysaccharide, and this defect was responsible for the phage resistance . The deoxycholate-insoluble fraction of YA21-82 lacked outer membrane protein O-8 . The addition of O-8 to this fraction together with the wild-type lipopolysaccharide resulted in the appearance of the receptor activity . Furthermore, the reconstitution was successfully achieved with only O-8 and the wild-type lipopolysaccharide, indicating that O-8 was an essential component in the deoxycholate-insoluble fraction. Mol Gen Genet, 1978 Oct 30, 166(2), 229 - 31 Binding of lac repressor to the secondary lac operator in Escherichia coli; Rambach A et al.; In the lac operon, the existence of a secondary repressor binding site, inside Z gene, had been inferred from in vitro binding studies (Reznikoff et al., 1974; Gilbert et al., 1975) . A series of deletions have been constructed from a lac transducing lambda bacteriophage . Some of those deleted bacteriophages have still the property of derepressing a chromosomal lac operon, even though they do not contain any more the lac operator . This phenomenon is an indication that the secondary repressor binding site is also active in vivo. Mol Gen Genet, 1978 Oct 25, 166(1), 61 - 73 Mutational analysis of the operators of bacteriophage lambda; Flashman SM; Oc mutations in the operators of bacteriophage lambda have been used to analyze the functional organization of the operators . In each operator, repressor binding sites 1 and 2, as identified biochemically, were found to be primarily responsible for the repressor affinity of the operators in vitro and for the repression of lytic functions in vivo . In addition, both sites were shown to be involved in the action of cro product at the operators . The data obtained have been used to estimate the repressor affinities of the individual binding sites . These affinities suggest that repressor bound at OR1 and OR2 interacts cooperatively . The results obtained support a model for repression of the early lambda operons where repressor bound at binding sites 1 and 2 interferes with RNA polymerase binding to the promotor sites. J Biol Chem, 1978 Oct 25, 253(20), 7149 - 57 The bacteriophage lambda int gene product . A filter assay for genetic recombination, purification of int, and specific binding to DNA; Kikuchi Y et al.; Bacteriophage lambda int gene is required for the integration of viral DNA into the chromosome of Escherichia coli . We have extensively purified the product of the int gene (Int) from a lysogen of E . coli that constitutively expresses this gene . Int was assayed by its ability to promote integrative recombination of supertwisted substrate DNA in vitro using a new method based on filter trapping of a recombinant product DNA . In order to catalyze integrative recombination, Int must be supplemented by other factors that can be extracted from bacterial host cells . By itself, purified Int does not demonstrate detectable endonuclease, exonuclease, or nicking-closing activities . However, Int does make stable complexes with double-stranded lambda-DNA containing an attachment site, the region at which recombination takes place . No stable complexes are observed between Int and lambda-DNA without an attachment site or between Int and DNA containing the bacterial site of integration . Int, therefore, appears to be a specificity element that relies on additional factor(s) to provide or activate the catalytic functions required for recombination. Biochim Biophys Acta, 1978 Oct 24, 520(3), 505 - 11 Replication of bacteriophage G13 DNA in dna mutants of Escherichia coli; Taketo A et al.; Host functions required for replication of microvirid phage G13 DNA were investigated in vivo, using thermosensitive dna mutants of Escherichia coli . In dna+ bacteria, conversion of viral single-stranded DNA into double-stranded replicative form (stage I synthesis) was resistant to 150 microgram/ml of chloramphenicol or 200 microgram/ml of rifampicin . Although multiplication of G13 phage was severely inhibited at 42--43 degrees C even in dna+ host, considerable amount of parental replicative form was synthesized at 43 degrees C in dna+, dnaA or dnaE bacteria . In dnaB and dnaG mutants, however, synthesis of parental replicative form was severely inhibited at the restrictive temperature . Interestingly enough, stage I replication of G13 DNA was, unlike that of phiX174, dependent on host dnaC(D) function . Moreover, the stage I synthesis of G13 DNA in dnaZ was thermosensitive in nutrient broth but not in Tris/casamino acids/glucose medium . In contrast with the stage I replication, synthesis of G13 progeny replicative form was remarkably thermosensitive even in dna+ or dnA cells. J Biol Chem, 1978 Oct 10, 253(19), 7011 - 6 Inhibition of primase, the dnaG protein of Escherichia coli by 2'-deoxy-2'-azidocytidine triphosphate; Reichard P et al.; 2'-Deoxy-2'-azidocytidine-5'-triphosphate was investigated as an inhibitor in two reconstructed enzyme systems which catalyze the replication of two viral DNAs . During replication of the duplex replicative form of phiX174 DNA, DNA polymerase III holoenzyme was weakly inhibited and inhibition was reversed by dCTP . A more pronounced inhibition, not reversed by either dCTP or CTP, was observed during replication of the single-stranded DNA of the bacteriophage G4, a close relative of phiX174 . This effect depended on the incorporation of 2'-deoxy-2'-azidocytidine-5'-triphosphate by primase (dnaG protein) which synthesizes a 29-residue RNA primer at the unique origin of bacteriophage G4 DNA replication . Extension of the primer strand, terminated by 2'-deoxy-2'-azidocytidine-5'-triphosphate is then severely inhibited . Primase was also inhibited by the 2'-deoxy-2'-azido derivatives of ATP, GTP, and UTP. Nature, 1978 Oct 5, 275(5679), 424 - 8 Bacteriophages inhibit degradation of abnormal proteins in E . coli; Simon LD et al.; On infection of Escherichia coli cells by bacteriophages T4, T5 or T7, the degradation of E . coli protein fragments and abnormal proteins is inhibited . Normal E . coli proteins, however, continue to be degraded at their usual rates . T4 early proteins (s) is needed to inhibit the turnover of abnormal proteins in T4-infected E . coli cells. J Biochem (Tokyo), 1978 Oct, 84(4), 917 - 24 "Thermal stability" maps for several double-stranded DNA fragments of known sequence; Ueno S et al.; The origin of cooperatively melting regions in DNA, which appear as fine structures in the optical melting profile, has been examined for DNA fragments of known base sequences from bacteriophages phiX174 and fd . Thermal stability maps, which indicate the states of base pairs along these DNA strands, were constructed within the established theoretical framework using the parameters which best reproduce the melting profiles obtained by high temperature resolution experiments . By comparing these stability maps with genetic maps, it was found that several cooperatively melting regions which span several hundred bases have some correlation with the gene locations. J Virol, 1978 Oct, 28(1), 408 - 10 Identification of lysis protein E of bacteriophage phiX174; Pollock TJ et al.; The product of gene E, the lysis gene of phiX174, has been identified as a distinct band in a sodium dodecyl sulfate-gel electropherogram . The position of the band is consistent with the molecular weight of 10,589 calculated from the nucleotide sequence of the gene . The band is eliminated by a nonsense mutation in gene E . It is estimated that roughly 100 to 300 molecules of E protein are made in an infected cell; this appears to be less than one-tenth the amount of protein made by gene D, in which gene E is wholly contained. J Virol, 1978 Oct, 28(1), 270 - 8 Anomalous behavior of bacteriophage lambda polypeptides in polyacrylamide gels: resolution, identification, and control of the lambda rex gene product; Belfort M; The resolution of lambia proteins was compared on the two types of sodium dodecyl sulfate-polyacrylamide gels commonly in use . The two kinds of gel differ essentially in the ratio of the cross-linker, N'-N-bismethylene-acrylamide (bisacrylamide), to acrylamide monomer . Several lambda proteins migrate relatively more slowly in gels with high bisacrylamide/acrylamide ratios (HB gels) than in gels with low ratios, although the two types of gel are of roughly equivalent porosity . This effect is illustrated by a change in relative position of both the Rex and Int proteins, with apparent increases in molecular weight of about 8 and 15%, respectively, in the HB gels . This work confirms that like repressor and Int, the 28.5-kilodalton protein, identified as Rex on HB gels, is postively regulated by the lambdacII and cIII products and negatively controlled Cro . An intact y site is required for Rex and repressor expression after infection, whereas their synthesis in a lysogen is dependent upon a functional maintenance promoter, Prm. Ann Microbiol (Paris), 1978 Oct, 129 B(3), 391 - 5 A model for plasmid maintenance of bacteriophage P1; Jaffe-Brachet A; Studies of the stability of P1 plasmid in a P1 cry Escherichia coli lysogen have suggested a model for equipartition of plasmid copies . Equipartition might be controlled by the detachment of P1 copies after replication, followed by their reattachment to membrane sites, in coordination with bacterial division. Proc Natl Acad Sci U S A, 1978 Oct, 75(10), 5099 - 103 Bacteriophage lambda carrying the Escherichia coli chromosomal region of the replication origin; Miki T et al.; A transducing phage lambdaasn was isolated . The late gene region of its genome was found to have been substituted by an Escherichia coli chromosomal segment containing the genes bgIR, bgIC, glmS, uncA, and asn . Restriction endonuclease cleavage mapping and electron microscopic analysis of the lambdaasn DNA revealed that the size of the bacterial segment is approximately 1.75 X 10(7) daltons, corresponding to about 26.4 kilobases . The circular DNA of lambdaasn was digested with restriction endonuclease EcoRI, diluted, and sealed with DNA ligase . When the reaction mixture was used to transform a recipient E . coli strain, a small plasmid of about 1 X 10(7) daltons (named pMCR115) was obtained . Restriction endonuclease cleavage mapping of pMCR115 and other evidence suggested that it contained the replication origin (oriC) of the E . coli chromosome. Gene, 1978 Oct, 4(2), 85 - 107 Plasmids useable as gene-cloning vectors in an in vitro packaging by coliphage lambda: "cosmids"; Collins J et al.; A plasmid which contains a cos site of lambda and can be packaged into lambda bacteriophage particles is termed a "cosmid" . Such plasmids can be used as gene cloning vectors in conjunction with an in vitro packaging system . The properties of a new series of cosmids based on the ColE1 replicon are described, including small temperature-sensitive plasmids which have lost mobilisation functions and carry no IS sequences . Amongst these plasmids are vectors for XmaI, BglII, BamHI, HindIII, PstI, KpnI, SalI and EcoRI . It is demonstrated that by using cosmids in particular size ranges these plasmids provide a high efficiency cloning system which yields essentially only hybrid clones without resort to a second selection or screening step, and without prior modification (e.g . phosphatase) treatment of the DNA . Attempts were made to optimise the cloning properties of the cosmid system . An Escherichia coli "gene bank" was obtained with an efficiency of 5 . 10(5) clones per microgram of E . coli DNA, and in which any particular unselected marker may be found in about one out of every 400 clones . It was demonstrated that deletion of mobilisation functions leads to loss of ability to form relaxation-complex without affecting copy number or segregation properties of the temperature-sensitive derivatives . The vectors are amplifiable in chloramphenicol to make up about 50% of the total cellular DNA. Genetika, 1978 Oct, 14(10), 1706 - 13 {Effect of mutations in Escherichia coli genes PolAm RecA, RecB and RecC on the frequency of genetic recombination in amber-mutants involving the early genes of bacteriophage T4}; Slutskii AM et al.; Effects of mutations in genes PolA, RecA, RecB and RecC of Escherichia coli on the recombination frequencies between rII markers of T4 have been studied in conditions of partial inhibition of some early functions . It was found that the presence of the mutations in genes PolA or RecA decreased significantly the recombination frequency of phage amber mutant in the gene 43 (DNA polymerase), increased it in the case of amber mutation in the gene 46 (exonuclease) and had no effect on the recombination of amber mutants in genes 30, 32, 33, 41, 42, 45, 44, 52 . None of the amber mutants studied changed recombination frequencies in the presence of the mutations in genes RecB or RecC . Possible mechanisms of some of the effects observed are discussed. J Bacteriol, 1978 Oct, 136(1), 423 - 8 Bacteriophage Mu-induced modification of DNA is dependent upon a host function; Khatoon H et al.; The DNA of bacteriophage Mu, extracted from induced lysates, is partially resistant to digestion by the endonuclease BalI . This modification of DNA is controlled by the Mu modification function (mom), which acts in conjunction with the dam (DNA-adenine methylation) function of Escherichia coli . Since the BalI recognition site is apparently different from the dam recognition site, these results imply that either the specificity of the dam function is changed by the mom function or the mom function requires the dam function for its activity. Proc Natl Acad Sci U S A, 1978 Oct, 75(10), 4779 - 83 Symmetry mismatch and DNA packaging in large bacteriophages; Hendrix RW; A model is presented for the mechanism of packaging double-stranded DNA into phage heads . The model is based on, and rationalizes, the mismatch in symmetry between the heads and tails of large bacteriophages . DNA movement is postulated to be mediated by a rotating protein structure at the tail-proximal vertex of the head. J Virol, 1978 Oct, 28(1), 262 - 9 Synthesis of T4 DNA and bacteriophage in the absence of dCMP hydroxymethylase; Morton D et al.; Several lines of research have suggested that the dCMP hydroxymethylase (HMase) coded by bacteriophage T4 is an essential protein in a DNA replication complex, as well as a supplier of hydroxymethyl dCMP for phage DNA synthesis . We show that a mutant {HMase, dCTPase, endonuclease II, endonuclease IV} which lacked this enzyme made cytosine-containing DNA at about two-thirds of the normal rate . When coupled with an alc mutation which permitted synthesis of late proteins, a small burst of phage was produced whose DNA contained no hydroxymethylcytosine . This pentuple mutant made both early and late proteins with abnormal kinetics, whereas the HMase+ parent showed normal kinetics . However, intracellular phage DNA showed no gross abnormalities in alkaline sucrose gradients . We conclude that HMase is not required for DNA synthesis when hydroxymethyl dCMP is not needed as a substrate; however, its absence still impairs both replication and transcription. J Virol, 1978 Oct, 28(1), 95 - 105 Restriction fragment analysis of bacteriophage SPP1 in vitro transcription by host RNA polymerase; Chenciner N et al.; In vitro transcription of SPP1 DNA occurred on only one of the two strands, the same which is predominantly transcribed in SPP1-infected cells . Transcripts were distributed in several size classes . Analysis of elongation kinetics and of size distribution, coupled with hybridization to DNA restriction fragments, showed that some regions of the template have more initiation sites than others; some have none . Some regions were transcribed directly, some were transcribed from initiation sites located in other regions, and one was never transcribed . Several transcription initiation sites on SPP1 DNA are located on EcoRI fragment 1; four to five others are distributed among other fragments . Cutting the DNA with EcoRI did not introduce artifactual initiation sites . In vitro transcription units can be localized and oriented with respect to the EcoRI restriction map of SPP1 DNA. J Biol Chem, 1978 Sep 25, 253(18), 6551 - 60 Mutagenesis at a specific position in a DNA sequence; Hutchison CA 3rd et al.; Predefined changes in a known DNA sequence were introduced by a general method . Oligodeoxyribonucleotides complementary to positions 582 to 593 of the viral DNA strand of the bacteriophage phiX174 am3 mutant (pGTATCCTACAAA), and to the wild type sequence in this region (pGTATCCTACAAA), were synthesized and used as specific mutagens . Each of these oligonucleotides was incorporated into a complete circular complementary strand when used as primer on a genetically heterologous viral strand template, by the combined action of subtilisin-treated Escherichia coli DNA polymerase I and T4 DNA ligase . Incomplete duplexes were removed or were inactivated by nuclease S1 and the products were used to transfect spheroplasts of E . coli . Both oligonucleotides induced specific mutations at high efficiency when used with heterologous template (15% mutants among progeny phage) . The am phages isolated by this procedure are phenotypically gene E mutants, and contain A at position 587 of the viral strand . They thus appear identical with am3 and provide evidence that the change G leads to A at position 587 is sufficient to produce a defective E function . Since the template for the induction of am mutants carried another genetic marker (sB1), the strains carrying the induced mutations have the new genotype am3 sB1 . It should be possible to introduce the am3 mutation into any known mutant strain of phi174 using this same oligonucleotide . Both possible transition mutations were induced in these experiments . In principle, the method could also induce transversions, insertions, and deletions . The method should be applicable to other circular DNAs of similar size, for example recombinant DNA plasmids. J Biol Chem, 1978 Sep 25, 253(18), 6544 - 50 Localization of the arginine tRNA gene to the D segment of T5 bacteriophage DNA . A new procedure for producing duplex DNA fragments; Desai SM et al.; The tRNA genes of bacteriophage T5 are located in four clusters on the continuous heavy DNA strand (Chen, M.-J., Locker, J., and Weiss, S.B . (1976) J . Biol . Chem . 251, 536--547) . Three of the four clusters are within the DNA C segment; the fourth cluster, to which only tRNAArg has been localized, maps in a 3.02 kilobase (kb) region of which 1.99 kb are at the right end of the C segment and 1.03 kb at the left end of the D segment . In order to localize the tRNAArg gene further and to define its relationship to the C-D nick, we devised a suitable method for preparing T5 DNA fragments whose ends correspond to the position of the T5 DNA nicks contained in the light DNA strand . In this method, DNA is denatured, partially renatured, and digested with low concentrations of S1 nuclease . Agarose-gel electrophoresis of these digests gives a pattern of bands which correlate in size with the pattern expected from the nicked structure of T5 DNA . Annealing of individual purified T5 {35P}tRNA species to the T5 DNA fragments transferred to nitrocellulose filters shows that tRNAArg hybridizes exclusively to the D fragment and is therefore localized to 1.03 kb at the 5' (left) end of the heavy strand of the D segment . This finding suggests that the promotor for this early gene is to the right of the C-D nick in T5 DNA; hence, the C-D nick does not coincide with this early promotor. Mol Gen Genet, 1978 Sep 20, 165(1), 39 - 46 Regulation of the int gene of bacteriophage lambda: activation by the cII and cIII gene products and the role of the Pi and Pl promoters; Oppenheim A et al.; The activation of the int gene by the cII and cIII gene products was studied by analysing int expression following infection of UV-irradiated cells by various phage mutants . Residual expression of int, probably from Pl, takes place in the absence of cII/cIII activation . Activation of the int gene, like that of the cI repressor gene, is poor at low multiplicities of infection . The mutation intC, which allows constitutive int expression in the lysogenic state, partially relieves the requirement for cII and cIII activation . The kinetics of Int synthesis after addition of the inhibitor rifampicin suggest that the activation occurs at the transcriptional level. Mol Biol (Mosk), 1978 Sep-Oct, 12(5), 1050 - 6 {Unwinding effect of F1 gene 5 protein on double-stranded polynucleotides and DNA}; Permogorov VI et al.; The effect of gene 5 protein from bacteriophage f1 on melting of double-stranded polynucleotides and DNAs has been investigated using the UV-spectroscopy method . A dependence of the melting temperature of polynucleotide (DNA)-gene 5 protein complexes upon the polynucleotide (DNA) GC-pair content has been detected . Using experimental data and examining some model systems we came to the supposition that the lowering of melting temperature of polynucleotide (DNA) induced by this protein is probably stipulated by intercalation of the protein tyrosyl residues into one of the chains of polynucleotide (DNA) double helix. Biophys Chem, 1978 Sep, 8(4), 281 - 94 Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions . Application to lac repressor-operator interactions; Lohman TM et al.; The effects of monovalent and divalent cations on the bimolecular rate constant of the reaction of a positively charged ligand with a nucleic acid polyanion are analyzed for two possible reaction mechanisms . One mechanism postulates that the association reaction occurs without intermediates, and that ion effects on the rate constant result entirely from the screening of the charged reactants by ionic atmospheres of low molecular weight ions (a screening-controlled mechanism) . This mechanism is analyzed by analogy with the Bronsted-Bjerrum theory for the kinetics of interaction of low molecular weight ions . The second mechanism to be considered here postulates the existence of a ligand-DNA intermediate which is in rapid equilibrium with the reactants (pre-equilibrium mechanism) . Ion concentration effects on the association rate constants for the pre-equilibrium mechanism result mainly from the release of counterions from the DNA upon formation of the intermediate . Both of the above mechanisms predict that the logarithm of the association rate constant, ka, will be a linear function of the logarithm of the monovalent cation concentration, {M+} (in the absence of competition by divalent cations or anions) . Knowledge of the salt dependences of ka and of the observed equilibrium constance Kobs of the ligand-nucleic acid interaction should usually be sufficient to determine whether a screening controlled mechanism or a pre-equilibrium mechanism is suitable to describe the process . If the association reaction can be described by a pre-equilibrium mechanism, the number of ionic interactions involved in the ligand-nucleic acid intermediate can be estimated . This analysis, extended to include the effects of divalent cations on screening or on the pre-equilibrium step, is applied to literature data on the salt dependence of the kinetics of the interaction of lac repressor with lac operator DNA . When the operator is present on bacteriophage lambda DNA, the observed reaction kinetics are consistent with the formation of an intermediate repressor-DNA complex in a pre-equilibrium step . On the other hand, the kinetics of association of lac repressor with synthetic lac operator fragments may be an example of a screening-controlled reaction. Biokhimiia, 1978 Sep, 43(9), 1563 - 77 {Interaction between sodium bisulfite and bacteriophage SD DNA}; Skliadneva VB et al.; The interaction between sodium bisulfite and the cytosine residues within the intraphage DNA of phage SD was studied to elucidate the structure of viral nucleoprotein . Hydrolysis with perchloric acid of bisulfite-modified phage SD results in 18% decrease of cytosine and appearance of products having the properties of cytosyl amino acids (most probably cytosyl lysine) . When the modified phage before hydrolysis was subjected to mild destruction in 0.1--1 M NaCl or Tris-HCl buffer (pH 7.0), neither the decrease of cytosine nor the appearance of cytosyl peptides was observed . However, these results were observed when the phage was heated at 70 degrees C in a medium containing 0.05 M phosphate buffer, pH 7.9--8.5 . The presence of cytosyl amino acids in the modified phage, representing nucleotide-protein covalent cross-links explains the results of viscosometry and centrifugation in CS2SO4 density gradient . It is assumed that the bisulfite reaction with cytosine within phage SD is completed at the stage of intermediate product formation, i.e . C5--C6-dihydro-C6-sulfopyrimidine, in which the amino group is screened by interaction with protein (product VII) . This product may exist only in situ; when the phage nucleoprotein is destroyed in phsophate-free media, product VII is converted into original cytosine . Under acidic hydrolysis or in the presence of phosphate ions under heating, product VII undergoes transamination accompanied by SO3 split-off and reconstitution of C5--C6 double bond to form cytosylamino acids. Nucleic Acids Res, 1978 Sep, 5(9), 3209 - 18 Determination of the endpoints of partial deletion mutants of the attachment site of bacteriophage lambda by DNA sequencing; Davies RW et al.; The deletion mutants b508 and b522 of bacteriophage lambda both end within the attachment site . The formation of such deletions is dependent upon the presence of intact integrase, and thus the deletion endpoints may be related to the normal crossover site in site-specific recombination . We have determined the DNA sequences of the attachment site regions of these deletions . Comparison of the sequences with lambda wildtype shows that both the deletions end within the central common homology region but at different positions . The consequences of these findings for current models of site-specific recombination are discussed. Nucleic Acids Res, 1978 Sep, 5(9), 3141 - 56 Nucleotide sequence of the O gene and of the origin of replication in bacteriophage lambda DNA; Scherer G; The nucleotide sequence of the O gene in bacteriophage lambda DNA is presented . According to two possible initiator codons, the primary structure of the O protein deduced from the DNA sequence consists of 278 or 299 amino acid residues . Structure and function of the O protein--one of the two phage initiator proteins for lambda DNA replication--are discussed in the light of a secondary structure model for the O protein . The central part of the O gene contains a cluster of symmetrical sequences extending over 160 base pairs . The point mutation of the cis-dominant replication mutant ti12 is located in this region. J Virol, 1978 Sep, 27(3), 835 - 7 Absence of phospholipase activity in bacteriophage T4; Thiel T et al.; We assayed phospholipase activity in T4Dt+ and in t mutant phage grown under permissive and restrictive conditions . There was no correlation between the presence of the t+ gene product and phospholipase activity . Phospholipase activity in phage lysates could be attributed to the presence of bacterial debris or to the use of commercial DNase which contains phospholipase. J Virol, 1978 Sep, 27(3), 745 - 53 Evolution of bacteriophage phi C174 . V . Alignment of the phi X174, G4, and St-1 restriction enzyme cleavage maps; Grindley JN et al.; The restriciton enzyme cleavage maps of bacteriophage phiS174, G4, and St-1 were aligned by two-dimensional filter hybridization . These studies show that the basic genome