Publications

isolation and characterization of two repetitive dna fragments located near the centromere of the mouse x chromosome.	two repetitive dna fragments located on the mouse x chromosome are described. the fragments were isolated from a lambda phage library enriched in x-chromosomal sequences by flow sorting. both fragments, which are repeated 20 to 50 times in the genome, were mapped to the mouse x chromosome by southern blot hybridization to dna from hybrid cells retaining the mouse x chromosome, by dosage analysis, and by in situ hybridization to mouse chromosomes. in mouse strain c57bl/10bk, one fragment appeared ...	1985	2932308
endpoint distribution for deletions into imm lambda region forming p lambda cm replicons: phage lambda gene rex affects plasmid establishment.	for the p lambda cm family of lambda-derived self-encapsidating plasmids, the rexb gene product facilitates plasmid establishment following injection into a new host cell. temperature-stable chloramphenicol resistance (cmr at 40 degrees c) conferred by low-multiplicity infection with lambda::tn9 ci857 lysates (tn9 sites tested: 22.60 or 24.08 kb, in the b region, or 28.41 kb, in int) is usually due to a lambda::tn9 plasmid (p lambda cm) formed by a deletion penetrating the lambda immunity region ...	1985	2932369
nucleotide sequence of the gdh gene coding for the nadp-specific glutamate dehydrogenase of saccharomyces cerevisiae.	the isolation of the saccharomyces cerevisiae gene for nadp-dependent glutamate dehydrogenase (nadp-gdh) by cross hybridization to the neurospora crassa am gene, known to encode for nadp-gdh is described. two dna fragments selected from a yeast genomic library in phage lambda gt11 were shown by restriction analysis to share 2.5 kb of common sequence. a yeast shuttle vector (cv13) carrying either to the cloned fragments complements the gdh- strain of s. cerevisiae and directs substantial overprod ...	1985	2932370
identification of a temperature-sensitive mutation in the htpr (rpoh) gene of escherichia coli k-12.	a new mutation in the htpr (rpoh) gene of escherichia coli k-12 was identified. the mutation resulted in a temperature-sensitive phenotype in terms of cell growth and bacteriophage lambda development. as in the case of the classical htpr tsn-165 mutation, synthesis of heat shock polypeptides was not induced in strains carrying the mutation described here.	1985	2932429
the polymerase subunit of dna polymerase iii of escherichia coli. i. amplification of the dnae gene product and polymerase activity of the alpha subunit.	the escherichia coli dnae gene, which encodes the alpha subunit of dna polymerase iii (pol iii) holoenzyme, has been cloned in a plasmid containing the pl promoter of phage lambda and thermally induced to overproduce the alpha subunit. in cells carrying this plasmid (pkh167), the alpha subunit was amplified, after heat induction, to a level of about 0.2% of the total cellular protein. polymerase activity was assayed in three ways: (i) gap-filling by pol iii holoenzyme and subassemblies of it, (i ...	1985	2932432
frameshift mutagenesis in the repressor gene of bacteriophage lambda: influence of a c/g----t/a transition upon the mutability by 9-aminoacridine of an adjacent run of 4 g/c base pairs.		1985	2932635
control of directionality in lambda site specific recombination.	the simple relation between the substrates and products of site-specific recombination raises questions about the control of directionality often observed in this class of dna transactions. for bacteriophage lambda, viral integration and excision proceed by discrete pathways, and dna substrates with the intrinsic property of recombining in only one direction can be constructed. these pathways display an asymmetric reliance on a complex array of protein binding sites, and they respond differently ...	1985	2932798
plating efficiencies of modified lambda bio particles on temperature-sensitive hsd mutants of escherichia coli k12.	two mutants of escherichia coli k12 that are temperature sensitive in cell growth and lambda phage production are shown to contain at least two mutations. one of the mutations in each of the isolates is in the hsd locus, and modification and restriction of lambda exhibits temperature sensitivity. one of the hsd mutations causes plaque formation by modified lambda bio particles that do not contain an intact ral gene to be temperature dependent.	1985	2932844
ribitol dehydrogenase of klebsiella aerogenes. sequence of the structural gene.	the ribitol dehydrogenase gene was cloned from wild-type klebsiella aerogenes and also from a transducing phage lambda prbt which expresses the rbt operon constitutively. the coding sequence for 249 amino acids is separated from the following d-ribulokinase gene by 31 base pairs containing three stop codons, one of which overlaps the ribosome binding site for d-ribulokinase. three residues in the amino acid sequence differ from that predicted from the dna sequence: asp-212 for asn-212 is probabl ...	1985	2933028
1h nmr studies of lambda cro repressor. 2. sequential resonance assignments of the 1h nmr spectrum.	the cro repressor protein from bacteriophage lambda has been studied in solution by two-dimensional nuclear magnetic resonance spectroscopy (2d nmr). following the approach of wüthrich and co-workers [wüthrich, k., wider, g., wagner, g., & braun, w. (1982) j. mol. biol. 155, 311-319], individual spin systems were identified by j-correlated spectroscopy (cosy) supplemented, where necessary, by relayed coherence transfer spectroscopy (relay). nuclear overhauser effect spectroscopy (noesy) was used ...	1985	2933070
improved in vitro packaging of coliphage lambda dna: a one-strain system free from endogenous phage.	in previous systems for in vitro packaging of lambda dna, phages are produced from the packaging components as well as from added dna. we have developed a new genetic strategy for in vitro packaging that bypasses this endogenous phage problem. our system employs a single bacterial strain whose lambda prophage codes for all of the packaging proteins but is deleted for cos, the packaging origin. crude extracts of the single lysogen: (i) are virtually free from endogenous phages, (ii) package added ...	1985	2933300
high-level synthesis of the phage lambda outer-membrane protein from the cloned lom gene.	a 2.7-kb kpni-ecori fragment carrying the lom gene of bacteriophage lambda has been cloned into plasmid ppr42 and recloned into the smai site of puc9. large quantities of lom were seen in outer-membrane (om) preparations of strains carrying the latter clone and its derivatives. the reading frame of lom was identified as orf206a. the protein was not demonstrably associated either covalently or non-covalently with the peptidoglycan layer of the cell envelope.	1985	2933301
toxicity and mutagenicity of plumbagin and the induction of a possible new dna repair pathway in escherichia coli.	actively growing escherichia coli cells exposed to plumbagin, a redox cycling quinone that increases the flux of o2- radicals in the cell, were mutagenized or killed by this treatment. the toxicity of plumbagin was not found to be mediated by membrane damage. cells pretreated with plumbagin could partially reactivate lambda phage damaged by exposure to riboflavin plus light, a treatment that produces active oxygen species. the result suggested the induction of a dna repair response. lambda phage ...	1985	2933393
genetic and dna mapping of the late regulation and lysis genes of salmonella bacteriophage p22 and coliphage lambda.	genetic and dna heteroduplex analyses of lambda imm22 hybrid phages were used to compare the salmonella bacteriophage p22 and coliphage lambda genes which control late gene regulation and lysis. homologous dna sequences were correlated with p22 gene 23 and lambda gene q (late gene regulation) and with p22 gene 13 and lambda gene s (lysis control). nonhomologous dna sequences were correlated with p22 gene 19 and lambda gene r (lysozyme and endolysin) and with the region encoding the p22 alpha and ...	1985	2933531
detection of sub-picogram quantities of specific dna sequences on blot hybridization with biotinylated probes.	a sensitive method for detecting biotinylated dna probes on dot and southern blots is described which is based on the principle outlined by leary et al (1). this system has two main components: detection of biotinylated dna by a two-step procedure with streptavidin and poly(alkaline phosphatase); and blocking background with tween 20. 32fg and 80fg of lambda phage dna was detected on dot and southern blot hybridizations respectively. 150fg of beta-globin was detected on southern blots of genomic ...	1985	2933635
isolation of a functional human interleukin 2 gene from a cosmid library by recombination in vivo.	a method has been developed that allows the isolation of genomic clones from a cosmid library by homologous recombination in vivo. this method was used to isolate a human genomic interleukin 2 (il2) gene. the genomic cosmid library was packaged in vivo into lambda phage particles. a recombination-proficient host strain carrying il2 cdna sequences in a non-homologous plasmid vector was infected by the packaged cosmid library. after in vivo packaging and reinfection, recombinants carrying the anti ...	1985	2934295
translation initiation of bacteriophage lambda gene cii requires integration host factor.	escherichia coli integration host factor (ihf), a dna-binding protein, positively regulates expression of the lambda cii gene. purified ihf stimulates cii protein synthesis in vitro, suggesting a direct role for host factor in cii expression. further evidence for a direct role for ihf was obtained with operon and gene fusions between cii and lacz or cii and gale. analysis of these fusions in vivo demonstrated that ihf is essential for the initiation of cii translation. replacement of the entire ...	1986	2934377
gene organization of plda and pldb, the structural genes for detergent-resistant phospholipase a and lysophospholipase l2 of escherichia coli.	the genes coding for the phospholipid degradation enzymes in e. coli, detergent-resistant (dr-) phospholipase a (plda) and lysophospholipase l2 (pldb), were cloned together on the plasmid pko1 (homma, h., kobayashi, t., ito, y., kudo, i., inoue, k., ikeda, h., sekiguchi, m., & nojima, s. (1983) j. biochem. 94, 2079-2081). to study their gene organization, a transducing lambda phage, lambda pldapldb, carrying both the plda and pldb genes was constructed in vitro from plasmid pko1. viable deletion ...	1985	2934380
phage lambda repressor revertants. amino acid substitutions that restore activity to mutant proteins.	we have isolated same-site and second-site revertants that restore partial activity, wild-type activity, or greater than wild-type activity, to lambda repressor proteins bearing different mutations in the dna binding domain. in some cases the revertant repressors contain same-site substitutions that are similar to the wild-type side-chain (e.g. tyr22----phe, ser77----thr). the activity of these revertants makes it possible to assess the role of specific hydrogen bonds and/or packing interactions ...	1985	2934554
damages induced in lambda phage dna by enzyme-generated triplet acetone.	exposure of lambda phage to triplet acetone, generated via the oxidation of isobutanal by peroxidase, leads to genome lesions. the majority of these lesions are detected as dna single-strand breaks only under alkaline conditions, and so true breaks do not occur. also, no sites sensitive to uv-endonuclease from micrococcus luteus were found in dna from treated phage. the participation of triplet acetone in the generation of such dna damage is discussed.	1986	2934629
cloning an expressed gene shared by the human sex chromosomes.	the existence of genes shared by mammalian sex chromosomes has been predicted on both evolutionary and functional grounds. however, the only experimental evidence for such genes in humans is the cell-surface antigen encoded by loci on the x and y chromosomes (mic2x and mic2y, respectively), which is recognized by the monoclonal antibody 12e7. using the bacteriophage lambda gt11 expression system in escherichia coli and immunoscreening techniques, we have isolated a cdna clone whose primary produ ...	1986	2934738
the overproduction and characterization of the bacteriophage mu regulatory dna-binding protein ner.	the bacteriophage mu ner gene has been cloned under the control of the lacuv5 promoter in the expression vector pop95-15. the gene products of the recombinant plasmid, pud88, visualized by in vitro coupled transcription-translation, are the bacteriophage mu ner protein (8 kda) and a 23 kda protein consisting of the amino terminus of gpa (mu transposase) fused to the carboxy terminus of beta-lactamase. dna-binding activity was measured by the retardation of migration of a 32p-labeled dna restrict ...	1986	2934891
isolation and crystallization of lambda exonuclease.	lambda exonuclease is a deoxyribonuclease induced by bacteriophage lambda. mutations in the structural gene for the protein affect general recombination and indicate a possible function for the enzyme. a large scale isolation procedure was employed to purify enough enzyme from a heat-induced lambda lysogen for x-ray crystallographic analysis. analytical ultracentrifugation and sds-polyacrylamide electrophoresis revealed that lambda exonuclease is a tetramer with molecular mass 107,000 da. crysta ...	1985	2935081
processing of mispaired and unpaired bases in heteroduplex dna in e. coli.	bacteriophage lambda and phi x 174 dnas, carrying sequenced mutations, have been used to construct in vitro defined species of heteroduplex dna. such heteroduplex dnas were introduced by transfection, as single copies, into e. coli host cells. the progeny of individual heteroduplex molecules from each infective center was analyzed. the effect of the presence of gatc sequences (phi x 174 system) and of their methylation (lambda system) was tested. the following conclusions can be drawn: some mism ...	1985	2935198
sequence specificity of mutagenesis in the ci gene of bacteriophage lambda.	studies of dna base sequence alterations have shown that for every agent the mutagenic process is specific with respect to the types of base changes induced and the location of the changes in the dna. analysis of the types of mutations produced by mutagenic agents can provide insight into the mechanism of mutation and can suggest which dna lesions may be involved in the actual mutagenic event. we have developed a system for the analysis of chemically induced base sequence alterations in the ci r ...	1985	2935390
effect of an umuc mutation on phage lambda induction.	a possible role of the umuc gene product in the induction of the sos responses was examined. we compared the expression of a genetic fusion, in which gene lacz, encoding beta-galactosidase in escherichia coli is under the direct control of the ci repressor from prophage lambda, in a umuc+ strain and in an otherwise isogenic umuc- mutant. we found that two times higher uv doses were required to obtain a similar induction in the umuc+ strain as in the umuc mutant. in addition we showed that, at th ...	1985	2935710
weigle reactivation and mutagenesis of bacteriophage lambda in lexa(def) mutants of e. coli k12.	the sos response in uv-irradiated bacteria enhances the survival and mutagenesis of infecting damaged bacteriophage lambda. in a lexa(def) strain, sos bacterial genes are fully derepressed by an inactivating mutation in the lexa repressor gene. we tested several lexa(def) derivative strains for their capacity to constitutively promote high survival and mutagenesis of irradiated lambda. we showed that uv irradiation of the lexa(def) host bacteria is still necessary for optimal efficiency of both ...	1985	2935711
repair and recombination of nonreplicating uv-irradiated phage dna in e. coli ii. stimulation of recf-dependent recombination by excision repair of cyclobutane pyrimidine dimers and of other photoproducts.	three aspects of recombination of uv-irradiated nonreplicating lambda phage dna were addressed: the photoproduct(s) responsible, the role of uvrabc-mediated excision repair, and the dependence on recf function. cyclobutane pyrimidine dimers appeared responsible for some recombination because photoreactivation reduced the frequency of 254-nm-stimulated recombination and because photosensitized 313-nm irradiation stimulated recombination. other photoproducts seemed recombinogenic as well, because ...	1985	2935712
repair and recombination of nonreplicating uv-irradiated phage dna in e. coli iii. enhancement of excision repair in uv-treated bacteria.	the question of whether induction of the sos response in escherichia coli increases the efficiency of excision repair was addressed by measuring repair of uv-damaged nonreplicating lambda phage dna in previously irradiated bacteria. prior uv irradiation of lex+ bacteria enhanced both the rate of regeneration of infective phage dna (about 10-fold) and the rate of cyclobutane dimer removal early in repressed infections. indirect induction of sos-regulated repair activities by the nonreplicating ir ...	1985	2935713
specificity of the interaction between lambda cro repressor protein and operator dna fragments.	cro repressor protein is known to interact with specific sites in the operator dna. the cro protein of lambda phage was isolated and the mode of its interaction with three different dna fragment, lambda-or3 17mer, phi 80-or2 19mer and cap binding site 22-mer, were examined by the use of proton nmr. some of the imino proton resonances of lambda-or3 shifted and were broadened remarkably on addition of lambda-cro protein, which indicated the induction of conformational change with complexation. in ...	1985	2935788
three human alcohol dehydrogenase subunits: cdna structure and molecular and evolutionary divergence.	class i human alcohol dehydrogenase (adh; alcohol:nad+ oxidoreductase, ec 1.1.1.1) consists of several homo- and heterodimers of alpha, beta, and gamma subunits that are governed by the adh1, adh2, and adh3 loci. we previously cloned a full length of cdna for the beta subunit, and the complete sequence of 374 amino acid residues was established. cdnas for the alpha and gamma subunits were cloned and characterized. a human liver cdna library, constructed in phage lambda gt11, was screened by usin ...	1986	2935875
a genomic clone encoding the alpha chain of the okm1, lfa-1, and platelet glycoprotein iib-iiia molecules.	lfa-1, an antigen involved in cytolytic t lymphocyte-mediated killing, and mac-1, the receptor for complement component c3bi, constitute a family of structurally and functionally related cell surface glycoproteins involved in cellular interactions. in both mouse and man, mac-1 (okm1) and lfa-1 share a common 95-kda beta subunit but are distinguished by their alpha chains, which have different cellular distributions, apparent molecular masses (165 and 177 kda, respectively), and peptide maps. we ...	1986	2935876
mutations in bacteriophage lambda that alter phage dependence on the htpr gene product of escherichia coli.	six mutants of lambda having reduced dependence on the htpr function of escherichia coli were isolated from lambda cits857. burst sizes in htprts cells at 40.5 degrees were in the range of 10 to 20 particles per cell. mapping and complementation analysis of one of the mutants suggested that the mutation in this isolate is in gene j. additional evidence that the mutations in most of the isolates are in j was provided by the finding that all but one of the mutants differ from the parental phage in ...	1986	2935990
[nmr study of the or1 operator from phage lambda and its specific complex with cro-repressor].		1986	2936589
binding and bending of the lambda replication origin by the phage o protein.	we have characterized the binding of lambda phage replication initiation protein o to the phage origin of replication. the minimal dna segment required for o binding is the single iteron, a 19-bp sequence of hyphenated dyad symmetry that is repeated with variations four times in the origin. the isolated amino terminus of o protein is also sufficient to bind dna. electrophoretic studies show that the amino terminus of o protein induces bending of a single iteron. the dna-protein interaction was c ...	1985	2936603
use of phage lambda ci857aprtcrn derivative for isolation of prophage-free cells.	a method for obtaining nonlysogenic bacteria from wild-type phage lysogenized strains using phage lambda with aprtcr markers and double amber-mutation in n gene is proposed. when the lysogenic culture is infected with antibiotic-resistant phage, the nonlysogenic cells present in the population are lysogenized and isolated on selective medium with ap and tc. subsequent culturing of lysogenized cells on media without antibiotics leads to phage elimination due to its instability.	1986	2936945
base substitution mutations induced in the ci gene of lambda phage by neocarzinostatin chromophore: correlation with depyrimidination hotspots at the sequence agc.	treatment of intact lambda phage with the nonprotein chromophore of neocarzinostatin resulted in efficient phage inactivation and generation of clear-plaque mutants. both effects required a preincubation at low ph to allow diffusion of chromophore into the phage head. chromophore activation was then effected by addition of a sulfhydryl cofactor, followed by a shift to neutral ph. sequence analysis of mutations mapped to the dna-binding region of the ci gene revealed that nearly all were single b ...	1986	2937016
detection and analysis of uv-induced mutations in mammalian cell dna using a lambda phage shuttle vector.	in order to study mutagenesis in mammalian cells, stable mouse l-cell lines were established with multiple copies of a lambda phage vector that contains the supf gene of escherichia coli as a target for mutagenesis. rescue of viable phage from high molecular weight mouse cell dna using lambda in vitro packaging extracts was efficient (5 phage per microgram of cell dna per copy) and yielded a negligible background of mutant phage (0 out of 54,605). from mouse cells exposed to 254-nm ultraviolet l ...	1986	2937054
isolation of structural genes for yeast rna polymerases by immunological screening.	a lambda gt11 yeast genomic library was screened with antibodies directed against yeast rna polymerases a, b, and c. thirty-five individual recombinant phages that expressed proteins in escherichia coli that were antigenically related to rna polymerases a, b, or c were isolated by using 22 distinct antisera. thus, all 22 genes for the rna polymerase subunits were potentially cloned. in three cases (lambda a-43, lambda a-40, and lambda a-34.5), an antigenic protein was expressed in e. coli with t ...	1986	2937059
a genetic analysis of primary products of bacteriophage lambda recombination.	primary products of bacteriophage lambda recombination that display heterozygosity as a consequence of the presence of regions of heteroduplex dna are rare in standard lambda crosses. phage manifesting heterozygosity at a given allele are evident when recombinants, emerging from a cross, are selected for an exchange in a neighboring interval. we show that the abundance of such heterozygotes can be increased 10- to 20-fold by selection on an e. coli indicator that is defective in methyl-directed ...	1986	2937684
activity of chi recombinational hotspots in salmonella typhimurium.	chi sites have previously been shown to stimulate homologous recombination by the escherichia coli recbc pathway. to test the activity of chi in another organism, bacteriophage lambda crosses were carried out in salmonella typhimurium strains bearing the e. coli lambda receptor protein. chi is active in these crosses in s. typhimurium, but is less active than in the same crosses carried out in e. coli. the lower chi activity in s. typhimurium appears to be intrinsic to the s. typhimurium recbc e ...	1986	2937685
relationship between cellular reca protein concentration and untargeted mutagenesis in escherichia coli.	we measured the production of untargeted mutations in the ci and cii genes of untreated lambda phage undergoing a lytic cycle in uv-irradiated bacterial hosts. as previously shown, treatment with 4 micrograms/ml of rifampicin during post-irradiation incubation inhibited amplification of the reca protein in these cells. in addition, we observed a decreased mutation rate compared to the untreated, irradiated bacteria. treatment with 4 micrograms/ml or 8 micrograms/ml rifampicin did not prevent the ...	1986	2938000
codon usage and gene expression.	the hypothesis that codon usage regulates gene expression at the level of translation is tested. codon usage of escherichia coli and phage lambda is compared by correspondence analysis, and the basis of this hypothesis is examined by connecting codon and trna distributions to polypeptide elongation kinetics. both approaches indicate that if codon usage was random trna limitation would only affect the rarest trna species. general discrimination against their cognate codons indicates that polypept ...	1986	2938078
hflb, a new escherichia coli locus regulating lysogeny and the level of bacteriophage lambda cii protein.	the level of the viral cii protein has been proposed to be the crucial determinant in the lysis-lysogeny decision of bacteriophage lambda. a new escherichia coli locus (hflb) has been identified in which a mutation (hflb29) leads to high frequency of lysogeny by lambda. a double mutant defective in both hflb and the previously identified hfla gene displays a more severe hfl- phenotype than either single mutant. the hflb locus is at 69 minutes on the e. coli map, 85% co-transducible with argg. th ...	1986	2939254
spontaneous lambda or mutations suppress inhibition of bacteriophage growth by nonimmune exclusion phenotype of defective lambda prophage.	survivor clones with defects in gene functions that participate in the replicative killing of thermally induced escherichia coli constructs with integrated lambda n through p or ciii through p gene fragments were selected at a frequency of about 10(-6). among the population of survivors, clones were identified that exhibited normal lambda immunity at 30 degrees c, as shown by their ability to prevent the plating of lambda wild type and to support the plating of a nearly identical heteroimmune ba ...	1986	2939262
methyl-directed repair of frameshift mutations in heteroduplex dna.	dna heteroduplexes with single unpaired bases of the four different kinds were prepared by annealing separated strands of bacteriophage lambda dna and used to transfect escherichia coli. genetic analysis of the progeny phages obtained from transfected bacteria indicates that the e. coli mismatch repair system can recognize and repair heteroduplexes with single unpaired bases--i.e., frameshift/wild-type heteroduplexes. the repair of a particular strand of the heteroduplex is inhibited by full met ...	1986	2939450
mismatch-stimulated killing.	dna duplexes with or without mismatches and with or without adenine-methylated gatc sequences were prepared from separated strands of bacteriophage lambda dna and used to transfect escherichia coli. unmethylated heteroduplexes containing one or more repairable mismatches transfect cells with a functioning mismatch repair system less efficiently than they transfect cells deficient in mismatch repair. no difference is observed when the duplexes contain no mismatch or a poorly repaired mismatch or ...	1986	2939453
[mapping of interactions of bacteriophage lambda cro-repressor with nonspecific dna using a method of dna-protein chemical cross-linking].		1986	2940078
dna synthesis at the site of a red-mediated exchange in phage lambda.	in phage lambda, progeny particles bearing unreplicated chromosomes are recombinant by action of lambda's red system only near the right end of the chromosome. these recombinants are frequently heterozygous (heteroduplex) for markers located there. in replication-blocked crosses involving two heavy-labeled parents we find that particles in the solitary peak, containing progeny with fully conserved dna, vary in density. those on the heavy side of this peak are more apt to be heterozygous than are ...	1986	2940146
deletion of the spf (spot 42 rna) gene of escherichia coli.	to investigate the function of spot 42 rna, a small rna of escherichia coli, we constructed a strain in which spf, the structural gene for this rna, is deleted. we achieved this by using a delta att phage lambda carrying a dna fragment spanning the spf region but with a precise deletion of spf. by integration of this phage at the spf locus and by its subsequent excision, we were able to cross the spf deletion onto the bacterial chromosome. the fact that such a deletion could be obtained indicate ...	1986	2940230
the homologous recombination system of phage lambda. pairing activities of beta protein.	the red genes of phage lambda specify two proteins, exonuclease and beta protein, which are essential for its general genetic recombination in reca- cells. these proteins seem to occur in vivo as an equimolar complex. in addition, beta protein forms a complex with another polypeptide, probably of phage origin, of mr 70,000. the 70-kda protein appears to be neither a precursor nor an aggregated form of either exonuclease or beta protein, since antibodies directed against the latter two proteins f ...	1986	2940241
role of reca protein in untargeted uv mutagenesis of bacteriophage lambda: evidence for the requirement for the dinb gene.	untargeted uv mutagenesis of bacteriophage lambda--i.e., the increased recovery of lambda mutants when unirradiated lambda infects uv-irradiated escherichia coli--is thought to be mediated by a transient decrease in dna replication fidelity, generating mutations in the newly synthesized strands. using the bacteriophage lambda ci857----lambda c mutation system, we provide evidence that the reca protein, shown previously to be required for this mutagenic pathway, is no longer needed when the lexa ...	1986	2940594
plasmid expression vector using the lambda late promoter.	a plasmid expression vector called pqte1 based on the late promoter, pr', and positive control gene q of bacteriophage lambda has been constructed. this vector has unique cloning sites for placing exogenous dna under control of pr'. induction of expression of genes cloned into the pqte1 plasmid leads to massive overproduction of the gene products. also, transcription from the pr' promoter on pqte1 appears to be insensitive to polarity effects.	1986	2940611
transcriptional antitermination activity of the synthetic nut elements of coliphage lambda. i. assembly of the nutr recognition site from boxa and nut core elements.	an active nutr antiterminator was reconstructed from two synthetic modules, one containing the 8-bp boxa (5'-cgctctta) and the other the 17-bp nutr core (5'-agccctgaaaaagggca) sequence. the modules were synthesized with hindiii cohesive ends, which upon annealing and ligation created an 8-bp spacer (5'-caaagctt) between the boxa and nutr core. the 8-bp length was the same as in the native nutr (5'-cacattcc), but the sequence showed less than 38% homology. the antitermination mediated by the synt ...	1986	2941338
translational regulatory signals within the coding region of the bacteriophage lambda ciii gene.	six independent mutations which enhance the lysogenic response were analyzed. the mutations cause single-base substitutions at three sites within the ciii coding sequence, one of which does not change the amino acid code. the mutations allow for elevated translation of the ciii gene, possibly via changes in the mrna secondary structure.	1986	2941413
conformations of signal peptides induced by lipids suggest initial steps in protein export.	despite the requirement for a functional signal sequence in protein export, little is known of the conformational properties and membrane interactions of these highly hydrophobic amino terminal extensions on nearly all exported proteins. the escherichia coli lambda phage receptor signal sequence was studied in phospholipid monolayers by circular dichroism and fourier transform infrared spectroscopy; the signal peptide was shown to prefer an alpha-helical conformation when inserted into the lipid ...	1986	2941862
multiply branched dna molecules from bacteriophage lambda: putative post-replicational repair dna intermediates.	previous studies have shown that thymidine deprivation causes the formation of multiply branched molecules among bacteriophage lambda dna replicative intermediates. in the present report, we present supporting evidence indicating that the induction of the sos response is involved in this process. moreover, close inspection of the dna replicatives intermediates present in a reca deficient strain, shows an accumulation of gapped replicative intermediates. from these observations we postulate a mod ...	1986	2942142
formation of nucleus-like structure in the cytoplasm of lambda-dna-injected fertilized eggs and its partition into blastomeres during early embryogenesis in xenopus laevis.	the fate of bacteriophage lambda-dna was examined after injection into the fertilized eggs of xenopus laevis. injection of a large amount of lambda-dna (ca. 24 ng) into a fertilized xenopus egg induced the formation around the injected dna of a giant nucleus-like structure which was surrounded by an apparently normal bilayered nuclear membrane with nuclear pore complexes. southern blot analysis revealed the persistence of injected lambda-dna until the blastula stage. the nucleus-like structure w ...	1986	2942430
promoter recognition by escherichia coli rna polymerase. effects of substitutions in the spacer dna separating the -10 and -35 regions.	a family of variants of the prm promoter of lambda phage was constructed, bearing nine base pair substitutions in a stretch of the spacer dna separating the contacted -10 and -35 regions. the substituted sequences were chosen for their potential to adopt structures different from those of average b-form dna and thus to affect the interaction of rna polymerase with the two contacted regions. characterization of the promoters in vitro and in vivo provides additional support for the lack of specifi ...	1986	2942546
multiple dna-protein interactions governing high-precision dna transactions.	the precise association of dna-binding proteins with localized regions of dna is crucial for regulated replication and expression of the genome. for certain dna transactions, the requirement for precision in localization and control is extremely high. high-precision events amenable to detailed biochemical analysis are the initiation of dna replication and site-specific recombination by bacteriophage lambda and escherichia coli. recent experiments indicate that site-localization and control in th ...	1986	2943018
[expression of hepatitis b virus core antigen gene in e. coli controlled by the pl promoter of coliphage lambda].		1985	2943083
selective inhibition of escherichia coli recbc activities by plasmid-encoded gams function of phage lambda.	the gam locus of bacteriophage lambda encompasses two coding sequences with the same reading frame and translational stop, one corresponding to an mr 11646 polypeptide (gams gene), the other to an mr 16349 polypeptide (gaml gene). a dna segment encoding gams but not gaml was placed under lambda pr promoter control (regulated by the cits857-coded repressor) on a multicopy plasmid, and an insertion mutation (gams201) was constructed. expression of gams+, but not gams201, inhibited escherichia coli ...	1986	2943636
mutational analysis of bacteriophage lambda lysis gene s.	a plasmid carrying the bacteriophage lambda lysis genes under lac control was subjected to hydroxylamine mutagenesis, and mutations eliminating the host lethality of the s gene were selected. dna sequence analysis revealed 48 single-base mutations which resulted in alterations within the coding sequence of the s gene. thirty-three different missense alleles were generated. most of the missense changes clustered in the first two-thirds of the molecule from the n terminus. a simple model for the d ...	1986	2943725
role of homology and pathway specificity for recombination between plasmids and bacteriophage lambda.	to determine the minimum amount of homology required for efficient recombination in escherichia coli, we measured recombination frequencies between bacteriophage lambda and pbr322 derivatives containing lambda dna fragments of various sizes by assaying for phages that could transduce the bla and ori genes of pbr322. efficient recombination required about 40 bp of homology; increases in homology above 40 bp resulted in proportionate increases in recombination, while decreases below 40 bp resulted ...	1986	2943972
isolation and sequence of the cdna for human protein s, a regulator of blood coagulation.	protein s is a cofactor of activated protein c; together they function as a regulator of blood coagulation. a human liver cdna library constructed in bacteriophage lambda gt11 was screened with dna fragments from a full-length bovine cdna clone encoding protein s. several cdna clones were isolated and sequenced. the combined cdna sequences encoded the mature protein and 15 residues of the leader sequence when compared to bovine protein s. human protein s is a single-chain protein consisting of 6 ...	1986	2944113
in vivo loss of supercoiled dna carrying a palindromic sequence.	interest in the fate of long palindromic dna sequences in e. coli has been kindled by the observation that their inviability is overcome in recbc sbcb strains and that these hosts permit the construction of dna libraries containing long palindromic sequences present in the human genome. in this paper we show that a reduction in the level of intracellular supercoiled dna occurs as the result of the presence of a 530 bp palindrome in bacteriophage lambda. this reduction occurs in rec+ and reca str ...	1986	2945078
[spatial structure of the cro-repressor in a solution. i. identification of interaction in a hydrophobic cluster using the nuclear overhauser effect].	the structure of a bacteriophage lambda cro repressor hydrophobic globule was studied by the technique of 1h nmr spectroscopy at 500 mhz. the analysis of noe difference spectra and building of the molecular models for the most probable fragments of the secondary structure allowed us to assign many signals in the protein spectrum and to identify the intramolecular interactions which stabilized the hydrophobic globule and the tertiary structure of the molecule. the results suggest that the structu ...	1986	2945092
[cloning and gene expression of the surface protein gene of the htlv-iii virus in e. coli].	a system has been developed for expression of surface protein (sp) of the virus of acquired immune deficiency syndrome (aids) in e. coli. for this purpose, cloning and substitution of a fragment of sp gene of htlv-iii virus under control of pl-promoter of phage lambda was carried out using pre-modified plasmid vector ppl-lambda. in the constructed plasmid pl2 1950 paranucleotides, the pvuii fragment of htlv-iii virus dna is built-in in such a way that the frames of transcription of phage lambda ...	1986	2945326
isolation and expression of cdna clones for a rat liver asialoglycoprotein receptor.	cdna clones for the major rat liver asialoglycoprotein (asgp) receptor were isolated from a phage lambda gt11 library using synthetic oligonucleotide probes corresponding to two regions of the protein sequence. the longest clone obtained encoded all but the first 11 codons of the receptor. the cdna was completed with synthetic oligonucleotides and was used to direct the synthesis of mrna for the receptor in vitro. subsequent translation in a wheat germ lysate produced authentic asgp receptor whi ...	1986	2945599
a remarkable amino acid sequence homology between a phage t4 tail fibre protein and orf314 of phage lambda located in the tail operon.	we have found that the amino acid (aa) sequence of the tip of phage t4 tail fibre (gene 37) shows more than 50% homology with the aa sequence predicted from an open reading frame (orf314) in the phage lambda genome. orf314 is near the 3' end of the late morphogenetic operon, beyond gene j coding for the lambda tail fibre. the homologous sequences are for the most part composed of repeated aa, the most remarkable of which is a gly-x-his-y-his motif where x and y are small, uncharged aa, found six ...	1986	2945762
molecular cloning and sequencing of a gene encoding biologically active porcine alpha-interferon.	nine distinct genomic clones containing human alpha 1-interferon (ifn-alpha 1) related sequences were isolated from a porcine genomic library constructed in phage lambda. restriction mapping and southern blot analysis revealed that these clones contained a total of 10 potential porcine ifn-alpha genes or pseudogenes belonging to a multigene family of at least 12 members. one of these genes was subcloned in plasmid puc8 and the recombinant plasmid obtained was shown to direct the synthesis of a l ...	1986	2945869
ion etching of bacteriophage lambda: evidence that the right end of the dna is located at the outside of the phage dna mass.	bacteriophage lambda was etched in an ar+ plasma under conditions in which the capsid and some of the dna were eroded (by sputtering) from the particle surface. analysis of the dna remaining in etched phage demonstrated an enrichment in sequences derived from the left end and middle of the genome; sequences from the right end were selectively lost. the results suggest that the dna in the mature phage is arranged with its left end toward the center and its right end toward the exterior of the ove ...	1986	2945932
[a model for demonstrating the accumulation and elimination of phage lambda in mytilus chilensis].		1986	2946128
cloning of the lambda resistant genes from brevibacterium albidum and proteus vulgaris into escherichia coli.	genes from proteus vulgaris atcc13315 and brevibacterium albidum atcc15831 were introduced into escherichia coli, which rendered the host resistant to coliphage lambda. the clones transformed by any one of the two recombinant plasmids, prmg101 or prmg216, were totally resistant against the infection of virulent lambda and n4, but sensitive to ø80, t4 and t7. however, when maltose transport systems of the clones were induced by maltose, the clones were no more resistant to the phage: thus, this p ...	1986	2946296
rna structural elements for expression in escherichia coli. alpha 1-antitrypsin synthesis using translation control elements based on the cii ribosome-binding site of phage lambda.	analysis of a series of lambda cii::alpha 1-antitrypsin (alpha 1at) gene fusions of different sizes showed that increased alpha 1at expression correlated with the stabilisation of a particular computer-predicted rna secondary structure. moreover, significant synthesis of unfused alpha 1at was achieved by reconstruction of this conformation to permit interaction between the upstream region of the ribosome-binding site and the first part of the alpha 1at coding sequence. this high-level expression ...	1986	2946602
phage lambda and plasmid expression vectors with multiple cloning sites and lacz alpha-complementation.	two new lambda vectors were constructed which permit cloning of genes that are potentially lethal if cloned in analogous plasmid vectors. lambda dl10 and lambda dl11 contain the alpha-complementing fragment of lacz and multiple cloning sites found in the polylinker region of m13mp10 and m13mp11, respectively. dna cloned into the unique cloning sites of these vectors can be detected by inactivation of alpha-complementation. these lambda vectors provide a lac promoter for expression of foreign gen ...	1986	2946626
roles of reca protease and recombinase activities of escherichia coli in spontaneous and uv-induced mutagenesis and in weigle repair.	the reca protein has a second, direct role in the mutagenesis of escherichia coli and bacteriophage lambda in addition to its first, indirect role of inducing the sos system by enhancing the proteolytic cleavage of the lexa repressor protein. the need for reca protease and recombinase functions in the direct role was examined in cells containing split-phenotype reca mutations, in the absence of lexa protein. spontaneous mutation of e. coli (his----his+) required both the protease and recombinase ...	1986	2946663
expression of the x gene of hepatitis b virus.	the hepatitis b virus (hbv) genome carries an open reading frame of 462 bases, the x region, but the corresponding protein has yet to be identified as a natural product. in rodent cells cotransformed with the thymidine kinase gene of herpes simplex virus and hbv dna, however, gough [1983] identified a mrna that hybridises uniquely with the x region of the hbv genome. a large fragment of the x region was inserted into plasmid pcl19 delta y-t in order to produce, in escherichia coli, the x gene pr ...	1986	2946812
structure and inherent properties of the bacteriophage lambda head shell. v. amber mutants in gene e.	a total of 940 amber mutants in gene e of bacteriophage lambda was isolated to study the structure-function relationship of the gene product, the major capsid protein. the mutants were mapped to 43 mutation sites, most of which have been located, albeit tentatively, at exact points in the known base sequence, by deletion mapping and by the specificity of mutagenesis and the patterns of suppression. the patterns of suppression were interpreted in terms of both the efficiency of insertion of amino ...	1986	2946872
a unique four-stranded model of a homologous recombination intermediate.	this paper proposes a model of four-stranded dna synapsis during recombination between homologous segments of two dna duplexes. the proposed intermediate is one of only two known models having relative chain orientations about the synaptic junction that are consistent with recent topological results on the integrative recombination of bacteriophage lambda. this model has the advantage of providing a mechanism for recognition of sequence homology between duplexes through specific hydrogen-bond fo ...	1986	2946898
efficient homologous recombination of linear dna substrates after injection into xenopus laevis oocytes.	when dna molecules are injected into xenopus oocyte nuclei, they can recombine with each other. with bacteriophage lambda dnas, it was shown that this recombination is stimulated greatly by introduction of double-strand breaks into the substrates and is dependent on homologous overlaps in the recombination interval. with plasmid dnas it was shown that little or no recombination occurs between circular molecules but both intra- and intermolecular events take place very efficiently with linear mol ...	1986	2946937
interaction of peptide antigens and class ii major histocompatibility complex antigens.	t lymphocytes require a foreign antigen to be presented on a cell surface in association with a self-transplantation antigen before they can recognize it effectively. this phenomenon is known as major histocompatibility complex (mhc) restriction. it is not clear how an incalculably large number of foreign proteins form unique complexes with a very limited number of mhc molecules. we studied the recognition properties of t cells specific for a peptide derived from bacteriophage lambda ci protein. ...	1986	2946957
an improved method for the isolation of high yields of bacteriophage lambda dna.		1986	2947045
bacteriophage lambda cro mutations: effects on activity and intracellular degradation.	following random mutagenesis of the bacteriophage lambda cro gene, we have isolated missense mutations that affect approximately half of the 66 residue positions of cro. about two-thirds of the mutations change residues involved in the maintenance of cro structure and stability. the corresponding mutant proteins are severely degraded in the cell but often have specific activities near that of wild-type cro. the remaining mutations affect residues involved in dna binding. these mutant proteins ar ...	1986	2947238
the sigma subunit of rna polymerase contacts the leading ends of transcripts 9-13 bases long on the lambda pr promoter but not on t7 a1.	the sigma subunit of rna polymerase is responsible for specific initiation of rna synthesis at promoter sites on dna. sigma dissociates shortly after initiation. photoaffinity-labeling experiments performed on transcription complexes with two different dna promoters, which have highly homologous control sequences upstream from the transcribed regions, have revealed that the sigma subunit of rna polymerase is contacted by the 5' ends of quite different lengths of nascent rna in each transcription ...	1986	2947623
lambdoid coliphages conferring a novel pattern of phage sensitivity on escherichia coli k12.	seven temperate coliphages recovered from naturally occurring lysogenic strains of escherichia coli were found to lyse e. coli c but not k12. four of these c-specific phages produced mutants (hrk) able to grow on k cells. the k cells harbouring hk253hrk and hk183hrk were converted so that they could adsorb and be lysed by three other non-mutant c-specific phages. hk253, hk183 and two other phages were shown to recombine with phage lambda.	1986	2947971
lambda phage protein nu 1 contains the conserved dna binding fold of repressors.	analysis of 64 lambda phage proteins revealed the presence of four strong variants of the conserved dna binding fold of repressors. three of them have been known from previous studies but the nu 1 gene product is a new member of the family of proteins that may bind strongly to dna in the repressor-like fashion. it is peculiar that the motif occurs in the very n terminus of nu 1 just between two possible starts of its gene.	1986	2948020
mutations of bacteriophage lambda that define independent but overlapping rna processing and transcription termination sites.	bacteriophage lambda int gene expression is regulated differentially from transcripts originated at the pl and pi promoters. transcripts initiated at pi terminate at the site ti and express int gene product efficiently. polymerases starting at pl do not terminate at ti, due to the antiterminating activity of lambda n protein. the pl transcripts are unable to express int protein efficiently because sib, a control site overlapping ti in the unterminated rna, is processed by host rnase iii. we have ...	1986	2948021
[the use of the mutant phage lambda ci857 aprtcrn- for isolation of cells lacking the prophage lambda].		1985	2948118
[expression of the chloramphenicol acetyltransferase gene is under control of various promoters of e. coli and phage lambda].	plasmids have been constructed with the structural region of the cat gene being under the control of the lactose (lacuv5), tryptophane (trpop), operons of escherichia coli, the hybrid trp-lac (tac) promoter and early bacteriophage lambda promoters (pl, pr and plit). the expression of chloramphenicolacetyltransferase gene in escherichia coli cells harbouring such recombinant plasmids and pbr325 as well has been examined by determining the chloramphenicol resistance and studying the enzyme activit ...	1986	2948120
[mutagenic effect of o-methylhydroxylamine on the prophage and extracellular phage lambda].	induction of c-mutations in extracellular bacteriophage and prophage lambda ci857 ind-treated with 1 m o-methylhydroxylamine (omha) at 32 degrees and ph 5.6 has been studied. the frequency of c-mutations increases proportionally to the time of treatment of extracellular phage and does not depend on cellular reca+ or pola+ functions and on induction of sos-repair system caused by uv-irradiation of host cells. prophage is inactivated and mutagenized approximately 10-fold faster than extracellular ...	1985	2948121
n-terminal domain of the bacteriophage lambda repressor: investigation of secondary structure and tyrosine hydrogen bonding in wild-type and mutant sequences by raman spectroscopy.	laser raman spectroscopy has been employed to investigate structures of the lambda repressor n-terminal fragment, which recognizes operator dna. examination of repressor fragments containing deuterated amide groups and specifically labeled deuteriotyrosines has enabled the assignment of many of the conformation-sensitive raman bands. by use of fourier deconvolution and signal averaging techniques, the spectra of both wild-type and mutant sequences have been obtained as a function of the total pr ...	1986	2948552
intramolecular cleavage of lexa and phage lambda repressors: dependence of kinetics on repressor concentration, ph, temperature, and solvent.	lexa repressor of escherichia coli and phage lambda repressor are inactivated in vivo and in vitro by specific cleavage of an ala-gly peptide bond in reactions requiring reca protein. at mildly alkaline ph, the in vitro cleavage reaction also proceeds spontaneously, suggesting that peptide bond hydrolysis is an activity of the repressors rather than of reca. the spontaneous cleavage reaction, termed "autodigestion", has been characterized for the lexa and lambda repressors. the results show that ...	1986	2948553
[relative effectiveness of various promoters from escherichia coli and phage lambda].		1986	2948811
very short patch mismatch repair in phage lambda: repair sites and length of repair tracts.	five amber mutations in the repressor (ci) gene of bacteriophage lambda recombine anomalously with nearby ci mutations. when any of these markers is used in four-factor crosses, ci+ recombinants that are expected to require three cross-overs occur at high frequencies. these recombinants are attributable to very-short-patch (vsp) repair of specific mismatches in dna heteroduplexes formed during recombination between the markers flanking ci. the sites of the repair-prone mutations and the lengths ...	1986	2948873
repression of a mutant derivative of the pre promoter of bacteriophage lambda by its activator, cii.	a 2-bp insertion between the -10 and -35 regions of the pre promoter of bacteriophage lambda reverses the effect of the activator protein, cii, on transcription from pre in vitro. the mutant promoter is weakly constitutive in the absence of cii protein and repressed in its presence. this is in sharp contrast to wild-type pre which is inactive in the absence of cii protein and stimulated at least 1000-fold in its presence (shih and gussin, 1984a; mcclure and hoopes, 1985). these effects are expla ...	1986	2948878
role of escherichia coli ihf protein in lambda site-specific recombination. a mutational analysis of binding sites.	the phage lambda attachment site, attp, contains three binding sites for an escherichia coli protein, ihf, that is needed for efficient integrative recombination. we have used synthetic oligodeoxyribonucleotides to direct multiple base changes at each of these three sites. alteration by two base-pairs of the consensus sequence for the leftmost binding site specifically interferes with ihf binding to that site and modestly depresses recombination in vitro. for each of the three binding sites, alt ...	1986	2949082
mitochondrial gene urfn of neurospora crassa codes for a long polypeptide with highly repetitive structure.	the mitochondrial dna of neurospora crassa contains a long potential gene, designated urfn, which is located immediately downstream from the co1 gene. these two genes are encoded in different reading frames and overlap by 13 codons. urfn is 633 triplets long and terminates at a uag stop codon. its codon usage is atypical for n. crassa mitochondrial exons and introns, and resembles that of the long open reading frame (orf) of the mitochondrial plasmid present in n. crassa strain mauriceville. mul ...	1986	2949084
[1h-nmr study of the or1 operon in bacteriophage lambda. i. assignment of signals from imino protons and adenine c2 protons].	an oligodeoxyribonucleotide composed of 17 residues, d(tatcaccgccagaggta), and a complementary chain were synthesized. their duplex was identical with the operator or1, the binding site for bacteriophage lambda cro and c1 repressors. the 1h nmr spectra (500 mhz) of the duplex imino and aromatic protons were studied at 10, 20 and 25 degrees c. signals from the imino protons of complementary base pairs and from the c2 protons of adenine (with the exception of the duplex terminal nucleotides) were ...	1986	2949139
wavelength dependence for the induction of bacteriophage lambda by antitumor agent gilvocarcin v.		1986	2949330