Publications

nusa protein is necessary and sufficient in vitro for phage lambda n gene product to suppress a rho-independent terminator placed downstream of nutl.	transcription antitermination by phage lambda n protein is reproduced in vitro solely with purified components. we have placed a strong rho-independent terminator, lambda tr', in the pl operon about 200 base pairs downstream from the n-recognition site, nutl, and have monitored terminated and run-off transcripts produced by single-round transcription of linear plasmids. in the presence of nusa, one of several host factors implicated in antitermination, n is found to virtually abolish termination ...	1988	2965813
three-dimensional reconstruction of maltoporin from electron microscopy and image processing.	two dimensional crystals of maltoporin (or phage lambda receptor) were obtained by reconstitution of purified maltoporin trimers and escherichia coli phospholipids by detergent dialysis. two different trimer packing forms were observed. one was hexagonal (a = 7.8 nm) and one rectangular (a = 7.8 nm, b = 13.6 nm). in this paper we describe the three-dimensional structure of maltoporin, deduced from the study of the rectangular form by electron microscopy and image processing. at a resolution of a ...	1988	2966066
identification of the dna binding domain of the phage lambda cii transcriptional activator and the direct correlation of cii protein stability with its oligomeric forms.	the bacteriophage lambda transcriptional activator protein cii is a dna-binding protein that coordinately regulates transcription from phage promoters important for lysogenic growth. we have genetically and structurally characterized more than 80 different single amino acid substitutions in this 97-amino-acid protein. a subset of 25 of these variant proteins was utilized for detailed biochemical analysis, which allows us to define specific domains critical for sequence-selective dna recognition, ...	1988	2966093
modulation of escherichia coli recbcd activity by the bacteriophage lambda gam and p22 abc functions.	plasmids that express the bacteriophage lambda gam gene or the p22 abc2 gene (with and without abc1) at controllable levels were placed in escherichia coli and tested for effects on the activity of recbcd. like gam, abc2 inhibited the atp-dependent exonuclease activity of recbcd, apparently not by binding to dna. however, abc2-mediated inhibition was partial, while gam-mediated inhibition was complete. both abc2 and gam inhibited host system-mediated homologous recombination in a chi-containing ...	1988	2966143
changes in dna base sequence induced by gamma-ray mutagenesis of lambda phage and prophage.	mutations in the ci (repressor) gene were induced by gamma-ray irradiation of lambda phage and of prophage, and 121 mutations were sequenced. two-thirds of the mutations in irradiated phage assayed in reca host cells (no induction of the sos response) were g:c to a:t transitions; it is hypothesized that these may arise during dna replication from adenine mispairing with a cytosine product deaminated by irradiation. for irradiated phage assayed in host cells in which the sos response had been ind ...	1988	2966755
lambda transducing phage and clones carrying genes of the cysjihdc gene cluster of escherichia coli k12.	dna from each of two specialized transducing lambda phage, lambda dcysjihd and lambda cysj, has been analysed by heteroduplex mapping. the segment of the escherichia coli chromosome carried by lambda dcysjihd was shown to be large, approximately 18 kb in length, and to replace a large length of lambda dna, approximately 11 kb, which includes the genes for integration and recombination. thus lambda dcysjihd is a bio-type transducing phage. lambda cysj was shown to have lost very little lambda dna ...	1987	2966849
retroregulation of bacteriophage lambda int gene expression.		1988	2967158
the nu1 subunit of bacteriophage lambda terminase.	the maturation and packaging of bacteriophage lambda dna are catalyzed by the phage terminase enzyme. terminase is composed of two protein subunits, gpnu1 and gpa. the holoenzyme is multifunctional in vitro; it binds to and cleaves lambda dna at the cos site (where cos represents cohesive-end site), packages dna into lambda proheads, and is also a dna-dependent atpase. the genes of the two subunits have been cloned separately into powerful expression vectors which allow for very high levels of p ...	1988	2967295
bacteriophage lambda dna packaging: a mutant terminase that is independent of integration host factor.	lambda+ is able to grow in escherichia coli cells lacking integration host factor (ihf), producing a burst of approximately 25% that produced in ihf+ cells. in vitro, however, we find that the lambda dna packaging enzyme terminase is strongly dependent on ihf in both cos cleavage reactions and dna packaging reactions. the cos59 mutation renders lambda dependent on ihf in vivo. the cos59 mutation is a deletion of 3 base pairs at the xmni site in the cohesive end site (cos) of lambda. variants of ...	1988	2967421
recognition of ill-defined signals in nucleic acid sequences.	a set of programs has been developed for the definition and handling of nucleic acid sequence consensus information. the sequences of known genetic control signals are combined in a matrix. the origins and positions of the signals are recorded. old matrices can be updated dynamically: new signals are included and obsolete ones deleted. matrices of several different types are computed optionally. several of these matrices can be combined to find possible new signals. the use of matrices allows th ...	1988	2968135
late stages in bacteriophage lambda head morphogenesis: in vitro studies on the action of the bacteriophage lambda d-gene and w-gene products.	the in vitro maturation of bacteriophage lambda can be divided into discrete steps. concatemers of lambda dna bind terminase to form complex i. this dna-terminase complex then binds a prohead to form a ternary complex (ii). complex ii in turn can be converted to infectious phage by the addition of extracts containing the products of the phage genes d, w, fii, as well as phage tails. by using in vitro complementation assays gpd and gpw have been partially purified and their interactions with comp ...	1988	2968711
tissue-specific expression and cdna cloning of small nuclear ribonucleoprotein-associated polypeptide n.	sera from some patients with systemic lupus erythematosus and other autoimmune diseases have antibodies against nuclear antigens. an example is anti-sm sera, which recognize proteins associated with small nuclear rna molecules [small nuclear ribonucleoprotein (snrnp) particles]. in this paper anti-sm sera were used to probe immunoblots of various rat tissues. a previously unidentified mr 28,000 polypeptide was recognized by these anti-sm sera. this polypeptide, referred to as "n," is expressed i ...	1988	2969109
smart2, a cosmid vector with a phage lambda origin for both systematic chromosome walking and p-element-mediated gene transfer in drosophila.	we describe a new phage-lambda-replicon-based cosmid vector suitable for both chromosome walking and p-element-mediated transformation in drosophila. its unique bamhi cloning site is flanked by the promoters for the sp6 and t7-encoded rna polymerases, permitting the synthesis of probes complementary to the ends of the cloned inserts for library screening. the selectable marker is tet for bacterial cell transformation and neo for drosophila transformation expressed under the control of the drosop ...	1988	2969350
structure of an unusual sea urchin u1 rna gene cluster.	genomic clones containing multiple copies of the lytechinus variegatus u1 gene have been isolated from a gene library in the phage lambda embl3. these clones contain both types of u1 rna gene repeats interspersed in the same 15-kb fragment. in addition, about 1/3 of the repeat units contain a 260-bp insert 460 bp prior to the first nucleotide of the u1 rna sequence. the inserted sequence is abundant in the sea urchin genome as judged by southern blots of genomic dna. there are no repeated sequen ...	1988	2969351
cloning of a complementary deoxyribonucleic acid coding for human thyroxine-binding globulin (tbg): existence of two tbg messenger ribonucleic acid species possessing different 3'-untranslated regions.	an adult human liver cdna library constructed in expression vector, bacteriophage lambda gt11, was screened with polyclonal antibody directed against human t4-binding globulin (tbg). tbg cdna cloned in the present study was 944 nucleotides in length. it contained approximately 70% of the coding region and complete 3'-untranslated region. when the sequence was compared with that of tbg cdna recently cloned by i. l. flint, t. j. bailey, t. a., gustafson, b. e. markham, and e. morkin, the 3'-untran ...	1988	2969453
translation initiation controls the relative rates of expression of the bacteriophage lambda late genes.	the late operon of bacteriophage lambda contains the genes encoding the morphogenetic proteins of the phage. these genes are transcribed equally from the single late promoter. although the functional half-lives of the mrna for the various genes of this operon vary less than 2-fold, their relative rates of expression have been shown to vary by nearly 1000-fold. this variation could result from differing rates of translation initiation, from overlapping upstream translation, or from differential e ...	1988	2969591
domains for protein-protein interactions at the n and c termini of the large subunit of bacteriophage lambda terminase.	the large subunit of phage lambda terminase, gpa, the gene product of the phage a gene, interacts with the small subunit, gpnul, to form functional terminase. terminase binds to lambda dna at cosb to form a binary complex. the terminase:dna complex binds a prohead to form a ternary complex. ternary complex formation involves an interaction of the prohead with gpa. the amino terminus of gpa contains a functional domain for interaction with gpnul, and the carboxy-terminal 38 amino acids of gpa con ...	1988	2969839
an intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in dna.	it has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a holliday-structure which is then converted into complete recombinant products by the second strand exchange. if this hypothesis is correct, one should be able to trap the putative holliday intermediate by preventing the second strand exchange. in this paper, we show that substitution of phosphorothioate for phosphate in one strand of a recombination site ...	1988	2970060
mechanism of cos dna cleavage by bacteriophage lambda terminase: multiple roles of atp.	in the terminus-generating (ter) reaction of phage lambda, the phage enzyme terminase catalyzes the production of staggered nicks within the cohesive-end nicking site (cosn). although the two nicks are related by a rotational symmetry axis that bisects cosn, the in vitro ter reaction is strikingly asymmetric at the nucleotide level. nicking of the lambda r strand precedes nicking of the i strand. furthermore, when the two nicking reactions are uncoupled, they have different nucleotide cofactor r ...	1988	2970303
the endpoints of an inversion in wheat chloroplast dna are associated with short repeated sequences containing homology to att-lambda.	the endpoints of an inversion in wheat chloroplast dna are shown to be associated with copies of a short repeated sequence. recombination across the repeats in an inverted configuration may have been responsible for the inversion, although they are currently in a direct orientation owing to a second inversion. the repeated sequence contains an element homologous to the core of the bacteriophage lambda att-site, which can function as such in vivo.	1985	2970310
characterization of a doubly mutant derivative of the lambda prm promoter. effects of mutations on activation of prm.	the mutation, prme37, located at -14 in the prm promoter of bacteriophage lambda, reduces prm function dramatically both in vitro and in vivo. in a search for second-site revertants of prme37, we isolated a double mutant that exhibits a partially restored prm+ phenotype. the second-site mutation (at -31) is identical to the mutation prmup-1. the activity of the doubly mutant (pseudo-revertant) promoter, prme37prmup-1, was investigated in vivo using a prm-lacz fusion phage and found to be interme ...	1988	2970552
lambda zap: a bacteriophage lambda expression vector with in vivo excision properties.	a lambda insertion type cdna cloning vector, lambda zap, has been constructed. in e. coli a phagemid, pbluescript sk(-), contained within the vector, can be excised by f1 or m13 helper phage. the excision process eliminates the need to subclone dna inserts from the lambda phage into a plasmid by restriction digestion and ligation. this is possible because lambda zap incorporates the signals for both initiation and termination of dna synthesis from the f1 bacteriophage origin of replication (1). ...	1988	2970625
role of the escherichia coli dnak and dnaj heat shock proteins in the initiation of bacteriophage lambda dna replication.	we examined the role of two escherichia coli heat shock proteins, the dnak and dnaj gene products, during the initiation of lambda dv dna replication in vitro. using 14c-labeled lambda p protein we showed that the dnak and dnaj heat shock proteins function together to release lambda p protein from the preprimosomal complex consisting of lambda origin of replication-lambda o-lambda p-dnab protein. hydrolysis of atp, catalyzed presumably by dnak, is required during this reaction. substitution of d ...	1988	2970643
[protein metabolism during the growth of hybridoma cells].	protein metabolism during the growth of mouse hybridoma, producing monoclonal antibodies to phage lambda has been studied. the rate of protein accumulation va at any time of growth was equal to that of protein synthesis vs minus the degradative rate vd and protein secretion rate vsecr (vn = vs--vd--vsecr). cellular protein metabolism was described in terms of the relationship 6.3% hr = 8.1%/hr--1%/hr for the middle of exponential growth phase, and in terms of the relationship 1.4%/hr = 2.9%/hr = ...	1988	2970703
maltose transport and starch binding in phage-resistant point mutants of maltoporin. functional and topological implications.	the relationships between the bacteriophage lambda binding site, the starch binding site and the pore formed by maltoporin (lamb protein, lambda receptor protein) were investigated. bacteria with single amino acid substitutions in the maltoporin sequence, which were previously shown to be strongly reduced in phage lambda sensitivity, were assayed for maltose- (and maltodextrin) selective pore functions. maltose transport assays was performed at low substrate concentrations, under conditions wher ...	1988	2971116
charon bs(+) and (-), versatile lambda phage vectors for constructing directional cdna libraries and their efficient transfer to plasmids.		1988	2971160
new cloning vectors and techniques for easy and rapid restriction mapping.	we have modified plasmid, phage lambda and cosmid cloning vectors to be of general use for easily and unambiguously determining restriction maps of recombinant dna molecules. each vector is constructed so that it contains the rarely found noti restriction site joined to a short synthetic linker sequence that is followed by a multiple cloning site. dna cloned into these vectors may be restriction-mapped by either of two methods. in one technique, the cloned dna is completely digested with noti, f ...	1988	2971593
characterization and cloning of gene 5 of bacillus subtilis phage phi 29.	sequencing of the phi 29 dna region [open reading frames (orfs) 12, 11 and 10] between genes 6 and 4 of the mutant ts5(219) showed that a g in the wild-type phage had been changed to an a in the mutant at position 218 of orf 10 indicating that this orf corresponds to gene 5. orf 10 was cloned in plasmid pplc28 under the control of the pl promoter of phage lambda and, after heat induction of the escherichia coli cells carrying the recombinant plasmid pgm26, a 12-kda protein was overproduced, acco ...	1988	2971594
effect of photoreactivation on mutagenesis of lambda phage by ultraviolet light.	there is disagreement in the literature as to whether the major mutagenic photoproduct induced in dna by ultraviolet light is the cyclobutane dipyrimidine dimer, the most common product, or the [6-4] photoproduct, the next most frequent. in the experiments reported here, cyclobutane dimers were removed from irradiated lambda phage dna by enzymatic photoreactivation, a process thought to affect no other photoproduct. photoreactivation of lambda phage in host cells and of lambda dna in solution re ...	1988	2971813
rapid minipreparations of bacteriophage lambda dna.		1988	2971928
[monoclonal antibody metabolism during the growth of hybridoma cells].	metabolism of monoclonal antibodies (mab) during the growth of mouse hybridoma, producing mab to phage lambda, has been studied. it was shown that the specific production of mab decreased by 25-35% in the stationary phase of growth in comparison with the middle of the exponential growth phase, which was associated with the decrease in the rate of mab synthesis. the secretion kinetics of mab did not change during the growth of hybridoma cells. mab did not degrade inside the cells and in the cultu ...	1988	2972097
pl of coliphage lambda: an alternative solution for an efficient promoter.	promoter pl of coliphage lambda is highly active in vivo although it is recognized 15-30 times less efficiently by rna polymerase when compared with promoters of similar strength. moreover, it differs significantly from the consensus sequence for escherichia coli promoters. sequence variants of pl which are more homologous to consensus promoters bind rna polymerase with increased efficiency. they are nevertheless significantly reduced in their in vivo strength. high activity can be restored by a ...	1988	2972539
analysis of transcription termination signals in the nin region of bacteriophage lambda: the roc deletion.	deletions in the region, nin, between the p and q genes of phage lambda remove a portion of the phage genome that includes signals for termination of transcription. these deletions were selected because they permit growth of lambda derivatives defective in the n-mediated transcription antitermination system; i.e., the deletions confer n independence (nin). thus nin phages (e.g., lambda nin5) grow in most escherichia coli nus mutants. the nus genes encode functions necessary for n action. we repo ...	1988	2972695
nature of the sos mutator activity: genetic characterization of untargeted mutagenesis in escherichia coli.	in escherichia coli, induction of the sos functions by uv irradiation or by mutation in the reca gene promotes an sos mutator activity which generates mutations in undamaged dna. activation of reca protein by the reca730 mutation increases the level of spontaneous mutation in the bacterial dna. the number of reca730-induced mutations is greatly increased in mismatch repair deficient strains in which replication errors are not corrected. this suggests that the majority of reca730-induced mutation ...	1988	2972909
cleavage of the cii protein of phage lambda by purified hfla protease: control of the switch between lysis and lysogeny.	the activity of the cii protein of phage lambda is probably the critical controlling factor in the choice of the lytic or lysogenic pathway by an infecting virus. previous work has established that cii activity is regulated through the turnover of cii protein; the products of the hfla and hflb loci of escherichia coli are needed for a degradative reaction, and lambda ciii functions in stabilizing cii. by using the cloned hfla locus, we have purified a cii-cleaving enzyme that we term hfla. purif ...	1988	2973057
microinjected dna from the x chromosome affects sex determination in caenorhabditis elegans.	the signal for sex determination in the nematode caenorhabditis elegans is the ratio of the number of x chromosomes to the number of sets of autosomes (x/a ratio). by previous genetic tests, elements that feminized chromosomal males appeared to be widespread on the x chromosome, but the nature of these elements was not determined. in experiments to define a feminizing element molecularly, cloned sequences were added to chromosomally male embryos by microinjection into the mother. three different ...	1988	2973125
[a library of genes of plasmid pss120 of shigella sonnei].	the gene library of s. sonnei plasmid pss120 was constructed with the use of plasmid psl5 as vector. the complete restriction of the vector dna and the partial restriction of the dna of plasmid pss120 were carried out by means of the enzyme ecori. the restricted dna was ligated and packed in vitro into the capsid of phage lambda. the titer of negative colonies obtained after packing was 0.8 x 10(3) clones per 1 microgram of s. sonnei dna. the total number of detected clones was 250. on the basis ...	1988	2973196
small-scale purification of bacteriophage lambda dna by an airfuge centrifugation step in cesium chloride gradients.	a rapid and efficient procedure for purifying bacteriophage lambda dna is described. this small-scale purification involves isolation of bacteriophage particles on cesium chloride gradients. using an airfuge ultracentrifuge, the centrifugation step can be readily achieved in 90 minutes. the method allows a 1-day purification of up to 12 independent lambda dna (20-40 micrograms each). the recovered dna, essentially devoid of rna and dna contaminants, is efficiently cut by restriction endonuclease ...	1988	2973426
[transactivation of p'r promoter of phage lambda].	the host-vector system for efficient expression of the cloned genes under the control of transactivated promoter p'r of bacteriophage lambda has been elaborated. the q protein activating p'r promoter is coded by the defective prophage constructed in vitro by means of excision of the late phage genes between the distant sites of the restriction endonuclease mlui and change of the central sali fragment carrying the kill gene for the kanamycin resistance gene. the general recombination system is im ...	1988	2973562
structural bases of a long-stretched deletion: completing the lambda plac5 dna primary structure.	in studying molecular mechanisms of specialised transduction, the laci (e. coli)-ea47 (lambda) dna junction in transducing bacteriophage lambda plac 5 has been structurally elucidated, thus yielding the complete sequence of lambda plac 5 dna including the lac5 substitution, a well-known segment of lambdoid vectors. the lambda plac5 dna is shown to consist of 19368 bp (lambda left arm) + 3924 bp (lac5 substitution) + 25353 bp (lambda right arm), totally amounting to 48645 bp. the presence of the ...	1988	2973573
regulation of two nested proteins from gene 49 (recombination endonuclease vii) and of a lambda rexa-like protein of bacteriophage t4.	phage t4 gene 49, encoding recombination endonuclease vii, specifies, by initiation from an aug and an internal gug codon, two in-frame overlapping peptides (of 18 and 12 kd). the gene is transcribed early and late, albeit from different promoters. the sequence predicts that in long early transcripts, initiated far upstream of the coding sequence, the shine-dalgarno sequence of the first ribosome binding site can be sequestered in a hairpin and/or cleaved. these processes might reduce initiation ...	1988	2974005
organization of the euplotes crassus micronuclear genome.	euplotes crassus, like other hypotrichous ciliated protozoa, eliminates most of its micronuclear chromosomal dna in the process of forming the small linear dna molecules that comprise the macronuclear genome. by characterizing randomly selected lambda phage clones of e. crassus micronuclear dna, we have determined the distribution of repetitive and unique sequences and the arrangement of macronuclear genes relative to eliminated dna. this allows us to compare the e. crassus micronuclear genome o ...	1988	2974078
some mismatch repair activities in escherichia coli.	heterozygous bacteriophage lambda dna molecules, whose replication requires mismatch correction of a mutant nucleotide in the transcribed strand, provide an assay for localized mismatch repair in escherichia coli. we describe two systems: one removes the a in c.a or g.a mismatches and the other removes one or the other c in a c.c mismatch. mutations disabling the first system result in a mutator phenotype that may be identical to muty.	1988	2974159
rapid isolation of lambda phage dna in micro- and macro-variants.		1988	2974539
fluorescence measurement of the kinetics of dna injection by bacteriophage lambda into liposomes.	bacteriophage lambda attaches to gram-negative bacteria using the outer membrane protein lamb as its receptor. subsequently, dna is injected by the bacteriophage into the host cell for replication and expression. the mechanism of dna injection, however, is poorly understood. in order to begin to characterize dna injection, a quantitative kinetic assay to detect injection into reconstituted lamb liposomes is described. the technique involves monitoring the increase in fluorescence of liposome-enc ...	1988	2974726
duplicated region of the mouse genome containing a cytoplasmic gamma-actin processed pseudogene associated with long interspersed repetitive elements.	the structures of two cloned recombinants of bacteriophage lambda and mouse genomic dna (lambda ma14 and lambda ma36) were compared by electron microscopic analysis of various heteroduplex dnas, restriction endonuclease mapping and nucleotide sequence determination. each clone was shown to be derived from a distinct region of the mouse genome, but the two exhibited structural similarity over a region of at least 11,000 bases which included a cytoskeletal gamma-actin processed pseudogene of appro ...	1988	2974886
step-arrest mutants of flp recombinase: implications for the catalytic mechanism of dna recombination.	the site-specific recombinase (flp) encoded by the yeast plasmid 2 micron circle belongs to the integrase (of phage lambda) family of recombinases. the sparse homology within the members of this family contrasts with the invariance of three residues, his-396, arg-399, and tyr-433 (the numbers correspond to the family alignment positions), among them. we report here results on substrate recognition and catalysis by flp proteins altered at these residues. mutations of the conserved his and tyr tha ...	1988	2974924
bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges.	previous work has established that integration of the genome of bacteriophage lambda into the chromosome of its bacterial host proceeds via two independent strand exchanges, which make and then resolve a holliday-structure intermediate. we find that a phosphorothioate substitution at the site of exchange in one strand of a recombination site depresses the yield of holliday structures much more than a similar substitution in the other strand. furthermore, we show that the holliday structures that ...	1988	2975338
translational signals of a major head protein gene of bacteriophage lambda.	the d gene of bacteriophage lambda which codes for a major head protein is expressed at a high level during lytic growth. we have constructed a set of d-lacz gene fusions in order to examine the factors determining the high efficiency of the d translational initiation signals. it was found that an integral sequence, 300 bp long and upstream of the atg initiation codon, is required for maximal protein synthesis.	1988	2975351
chain-bias of escherichia coli rec-mediated lambda patch recombinants is independent of the orientation of lambda cos.	chi is a hotspot for homologous recombination mediated by the recbcd (rec) pathway of escherichia coli. for rec-mediated recombination of phage lambda, the orientation of lambda cos in the lambda chromosome dictates the direction of travel of recbcd enzyme through dna and dictates which orientation of chi or chi-like sequences will be active in stimulating recombination. i previously found that rec-mediated lambda patch heteroduplexes, stimulated by chi or not, are chain-biased; at the lambda p ...	1988	2975616
alleviation of type i restriction in adenine methylase (dam) mutants of escherichia coli.	the host-controlled ecok-restriction of unmodified phage lambda.o is alleviated in dam mutants of escherichia coli by 100- to 300-fold. in addition, the ecok modification activity is substantially decreased in dam- strains. we show that type i restriction (ecob, ecod and ecok) is detectably alleviated in dam mutants. however, no relief of ecori restriction (type ii) occurs in dam- strains and only a slight effect of dam mutation on ecop1 restriction (type iii) is observed. we interpret the allev ...	1988	2976881
2-aminopurine and 5-bromouracil induce alleviation of type i restriction in escherichia coli: mismatches function as inducing signals?	the ecok restriction of unmodified phage lambda is 1000-fold alleviated in escherichia coli grown in the presence of base analogs 2-aminopurine (2ap) and 5-bromouracil (5bu). 2ap treatment of bacteria affects specifically the type i restriction systems (ecoa, ecob, ecod and ecok) and does not influence type ii (ecori) and type iii (ecop1) restriction. 2ap-induced alleviation of restriction occurs in bacteria which are deficient in the sos response (reca and lexa) and mismatch repair (muth, mutl ...	1988	2976882
plaque-lift testing of expression vector lambda gt11 with gold-labeled immunoglobulins.	colloidal gold particles were coated with affinity-purified antibodies against the human plasma protein, c1 inhibitor, and used to probe for fusion proteins of c1 inhibitor with beta-galactosidase encoded by recombinant bacteriophage lambda gt11 dna. plaque-lift tests were done with recombinant proteins immobilized on nitrocellulose applying anti-c1 inhibitor gold particles followed by the silver enhancement treatment. this procedure resulted in a sensitive and specific staining of the recombina ...	1988	2977068
dna double-chain breaks in recombination of phage lambda and of yeast.		1988	2977087
coliphage lambda to terminator lowers the stability of messenger rna in escherichia coli hosts.	the effects of the transcription terminators to and tfd on the overall high-level expression of a human interferon-beta gene (ifn-beta) in escherichia coli hosts were compared. deletion mapping shows that mrna lability is caused by sequences at or near the lambda terminator to stem-loop structure. extensive rna secondary structure in this region indicates a potential rnase iii cleavage/binding site. in rnase iii- e. coli hosts, ifn-beta synthesis is indeed considerably enhanced. the bacteriophag ...	1988	2977353
filter-supported preparation of lambda phage dna.	a rapid and simple method is described for the isolation of dna from phage lambda which requires neither special equipment nor expensive material such as cesium chloride for ultracentrifugation nor extractions with organic solvents or ethanol precipitation. microgram quantities of lambda dna are obtained in less than 2 h from 90-mm plate lysates or 5-ml liquid cultures. the method allows the simultaneous isolation of large numbers of probes, e.g., clones from phage libraries. lambda phages are p ...	1988	2977528
preparation of bacteriophage lambda dna using the tl-100 ultracentrifuge.	a procedure for the preparation of dna from bacteriophage lambda is described, using the beckman tl-100 bench-top ultracentrifuge. the procedure involves growth of phage in agar plates, precipitation with polyethylene glycol, and a single centrifugation in cesium chloride under conditions that disrupt the phage coat. the method avoids the use of enzymes, ion exchange resins, and phenol. it can be completed in less than a day. the resulting dna is of good purity and is easily cuttable by restrict ...	1988	2977529
expression of the escherichia coli lamb gene in vibrio cholerae.	a phage lambda mediated transduction system was devised to facilitate molecular analysis of vibrio cholerae. a lamb expression plasmid, pamh62 was introduced into vibrio cholerae by conjugation. the resulting v. cholerae derivatives harboring pamh62 produced substantial amounts of the lamb protein. this protein was properly inserted into the outer membrane, as suggested by (i) its localization into the cell envelope, (ii) its association with the peptidoglycan layer of the cell wall, and (iii) i ...	1986	2977630
[structural characteristics of alkylated dna in phage lambda].		1987	2977812
[the use of phage lambda promotors for expressing genes of secreted proteins in bacillus subtilis cells].	at was shown with the help of promoterless alpha-amylase and staphylokinase genes that lambda pr and lambda pl promoters could be used in bacillus subtilis. promoters strength was compared to promoter of alpha-amylase gene, this enabled to order the promoters in a row: paa greater than lambda pr greater than lambda pl. the lambda pr promoter region was controlled by temperature in e. coli cells only, but not in b. subtilis, therefore, the active lambda c1857 gene product was not produced in b. s ...	1988	2978050
peculiarities of the b to a transition of the lambda phage regulatory site or3 and of its fragment.	conformations of the synthetic deoxyoligonucleotide 17 base pairs long, which is an or3 operator of lambda phage, and of its 9-b.p. fragment were studied by the circular dichroism method (cd). the regions of stability of the double-stranded state were determined for these duplexes. a comparison of the cd spectra for these oligonucleotides with the cd for a lengthy dna showed the conformation of these short dna pieces to belong to the b-family. a cooperative change in the cd spectra is observed i ...	1985	2978718
the absence of non-local conformational changes in or3 operator dna on complexing with the cro repressor.	the interaction of the cro protein of lambda phage with a synthetic or3 operator having 17 base pairs in length and with its 9 bp fragment has been studied using the circular dichroism (cd) method. in both cases, a considerable change in the cd of the samples was found in the region 260-300 nm upon the addition of the cro protein. the stoichiometry obtained by the cd titration was identical for or3 and its 9 bp fragment: one duplex per dimeric cro. nacl addition makes the complexes dissociate so ...	1985	2978719
nmr studies of dna recognition sequences and their interaction with proteins. the phage lambda or1 operator, a symmetric lac operator and their specific complexes with cro protein and lac repressor "headpiece".	the phage lambda operator or1 and a 18 base pair symmetric lac operator have been studied by high resolution nmr. the imino proton resonances and the resonances of the unexchangeable protons (except the 5' and 5" sugar proton resonances) have been assigned by one- and two-dimensional noe techniques. the imino proton resonances of or1 and the symmetric lac operator have been used to monitor changes induced in the operator structure by the formation of a specific complex with the phage lambda cro ...	1986	2978732
bacteriophage lambda int protein may recognize structural features of the attachment sites.	the bacteriophage lambda int protein binds to and promotes polynucleotide strand exchange within specific dna segments called attachment sites. previous work strongly suggests that the specificity of int protein action is based, at least in part, on its ability to recognize nucleotide sequences in the attachment sites. we suggest that int protein also recognizes structural features of the attachment sites such as the twist and roll angles between adjacent base pairs. this proposal is based on st ...	1986	2978733
quaternary structure and function in phage lambda repressor: 1h-nmr studies of genetically altered proteins.	the quaternary structure and dynamics of phage lambda repressor are investigated in solution by 1h-nmr methods. lambda repressor contains two domains separable by proteolysis: an n-terminal domain that mediates sequence-specific dna-a binding, and a c-terminal domain that contains strong dimer and higher-order contacts. the active species in operator recognition is a dimer. although the crystal structure of an n-terminal fragment has been determined, the intact protein has not been crystallized, ...	1987	2978735
cloning of the gene for the common pathogenic neisseria h.8 antigen from neisseria gonorrhoeae.	neisseria gonorrhoeae dna that encodes the pathogenic neisseria h.8 common antigen was cloned in the lambda phage sep6. the recombinant phage, designated s6h.8, was detected immunologically with a monoclonal antibody that binds to the h.8 antigen. the gonococcal and s6h.8 forms of the antigen yielded identical partial proteolysis epitope maps. neisseria species that did not manifest the h.8 antigen showed little or no dna homology with s6h.8. this clone should facilitate investigation into the c ...	1985	2981198
rho-dependent transcription termination at lambda r1 requires upstream sequences.	in order to define the dna sequence requirements for rho-dependent transcription termination, we have constructed and analyzed two classes of mutants affecting the cro-tr1 region of phage lambda: one class contains progressively larger deletions in the region upstream of the rho-dependent terminator tr1, and the other consists of small insertions or deletions generated by the linker scanning procedure. we show that rho-dependent termination at lambda tr1 in vitro requires contribution from seque ...	1985	2981220
the four c-terminal amino acids of the v-erba polypeptide are encoded by an intronic sequence of the v-erbb oncogene.	the genome of avian erythroblastosis virus (aev), a defective acute leukemia retrovirus, carries two distinct cell-derived oncogenes in the structure 5' delta gag-erba-erbb-delta env3'. the nucleotide sequence of the v-erba gene was recently reported. in order to determine the boundary between the two adjacent oncogenes, the sequence of the v-erba/v-erbb junction of aev was compared to that of a recombinant lambda phage containing a chicken cellular sequence representing the 5' part of c-erbb. t ...	1985	2981452
recombination site selection by tn3 resolvase: topological tests of a tracking mechanism.	in vitro recombination by tn3 resolvase of plasmids containing two directly repeated recombination (res) sites generates two singly interlinked catenated rings. this simple product catenane structure was maintained over a wide range of substrate supercoil densities and in a reaction mixture in which phage lambda int-mediated recombination generated its characteristic multiply interlinked forms. using substrates containing four res sites, we found that resolvase recombined neighboring res sites w ...	1985	2981625
molecular cloning of the phenylalanine ammonia lyase gene from rhodosporidium toruloides in escherichia coli k-12.	a genomic library of rhodosporidium toruloides dna was constructed in bacteriophage lambda 1059. recombinant phage containing phenylalanine ammonia lyase (pal) gene sequences were identified by using 32p-labeled cdna to partially purified pal mrna. the pal gene was subcloned on an 8.5-kilobase psti dna restriction fragment into puc8 to generate the recombinant plasmid phg2. a restriction map of the pal gene, together with its flanking regions, was constructed. northern hybridization analysis of ...	1985	2981805
cloning of the a gene of bacteriophage mu and purification of its product, the mu transposase.	the bacteriophage mu transposase (the mu a gene product), which is absolutely required for both integration of mu and replicative transposition during the lytic cycle, has been overproduced by cloning the gene on a plasmid under the control of the phage lambda pl promoter. the protein has been purified to near homogeneity from the lysate of heat-induced cells of a strain carrying the plasmid. the purified protein is active as judged by its ability to complement mu a- cell extracts for supporting ...	1985	2981873
amplification and purification of the bacteriophage mu encoded b transposition protein.	the a and b proteins encoded by the temperate bacteriophage mu are involved in the high efficiency dna transposition reaction which is the distinguishing feature of this phage. the genes encoding these early proteins were cloned in an expression vector under the control of the bacteriophage lambda leftward promoter. under optimal conditions gpb was overproduced to account for 15% of the total cellular protein. the protein was purified to near homogeneity as determined by silver staining. sequenc ...	1985	2982832
detection and physical map of a omega tox+-related defective prophage in corynebacterium diphtheriae belfanti 1030(-)tox-.	a library of chromosomal dna from corynebacterium diphtheriae belfanti 1030(-)tox- was cloned in the lambda phage vector embl4 and screened for sequences homologous to corynephage omega tox+ and the attb1-attb2 region of the c7(-)tox- chromosome. two portions of the 1030(-)tox- chromosome, 35 and 30.5 kilobases long which contain, respectively, the entire region homologous to corynephage omega tox+ and the attb1-attb2 sites, were mapped with the restriction endonucleases bamhi and ecori. chromos ...	1985	2983113
nucleotide sequence and structure of integrated bovine leukemia virus long terminal repeats.	bovine leukemia virus (blv) proviruses, harbored by the productively infected fetal lamb kidney (flk-blv) cell line, were cloned in bacteriophage lambda l47. the nucleotide sequence of the proviral long terminal repeats (ltr) with flanking cell and virus dna have been determined. the blv ltr is 531 bp in length and is bounded by the dinucleotides 5'-tg...ca-3', which are part of a 3-bp inverted repeat. the integrated provirus is flanked by 6-bp direct repeats of cellular dna. a trnapro primer bi ...	1985	2983496
evidence that the outer membrane protein gene nmpc of escherichia coli k-12 lies within the defective qsr' prophage.	recombinants between phage lambda and the defective qsr' prophage of escherichia coli k-12 were made in an nmpc (p+) mutant strain and in the nmpc+ parent. the outer membrane of strains lysogenic for recombinant qsr' phage derived from the nmpc (p+) strain contained a new protein identical in electrophoretic mobility to the nmpc porin and to the lc porin encoded by phage pa-2. lysogens of qsr' recombinants from the nmpc+ strain and lysogens of lambda p4, which carries the qsr' region, did not pr ...	1985	2984173
the phi 80 and p22 attachment sites. primary structure and interaction with escherichia coli integration host factor.	although the lambdoid bacteriophage phi 80 and p22 possess site-specific recombination systems analogous to bacteriophage lambda, they have different attachment (att) site specificities. we have identified and determined the nucleotide sequences of the att sites of phi 80 and p22 and have examined the interaction of these sites with purified escherichia coli integration host factor (ihf). the sizes of the homologous core regions of the att sites vary greatly: p22 has a 46-base pair core, while p ...	1985	2984205
germline vh genes in an a3 rabbit not typical of any one vha allotype.	we have undertaken investigations in the rabbit of vh genes that may be responsible for the observations of vha allotypes unexpected from an animal's pedigree (latent allotypes). a short cdna probe was prepared and shown to be specific for vha2 mrna. southern analyses with short and large probes were unrevealing but screening of a lambda phage library from a vha3-expressing animal identified a number of unusual genes. these vh genes are remarkable in that they are far closer to one another in th ...	1985	2984292
recognition sequences of restriction endonucleases and methylases--a review.	the properties and sources of all known endonucleases and methylases acting site-specifically on dna are listed. the enzymes are crossindexed (table i), classified according to homologies within their recognition sequences (table ii), and characterized within table ii by the cleavage and methylation positions, the number of recognition sites on the dna of the bacteriophages lambda, phi x174 and m13mp7, the viruses ad2 and sv40, the plasmids pbr322 and pbr328 and the microorganisms from which the ...	1985	2985469
phasmid vectors for identification of genes by complementation of escherichia coli mutants.	a bacteriophage lambda cloning vector was designed to facilitate the isolation of genes from procaryotic organisms by complementation of escherichia coli mutants. this vector, lambda se4, was constructed by attaching a very-low-copy-number replication system (from the plasmid nr1) and a spectinomycin resistance gene to the left arm of lambda 1059 (karn et al., proc. natl. acad. sci. u.s.a. 77:5172-5176, 1980). this phasmid cloning vector is capable of growing lytically as a phage in a nonimmune ...	1985	2985547
the dna restriction endonuclease of escherichia coli b. ii. further studies of the structure of dna intermediates and products.	the dna intermediates and final products formed by the type i restriction endonuclease, ecob, were further characterized. dna cleaved on only one strand (hemi-restricted dna) contains gaps of approximately 70-100 nucleotides, while the fully restricted products contain 3'-single-stranded tails averaging approximately 70-100 nucleotides for each strand cleaved. the gaps and tails are formed with the release of an equal number of nucleotides as small oligonucleotides that are soluble in acid. afte ...	1985	2985610
molecular cloning of a full-length cdna for human alcohol dehydrogenase.	we have cloned a full-length cdna coding for human alcohol dehydrogenase (adh; alcohol:nad+ oxidoreductase, ec 1.1.1.1) from a human liver cdna library constructed in phage lambda gt11. the library was screened by using a rabbit antibody against human adh as a first probe, by the modified method of young and davis [young, r. a. & davis, r. w. (1983) proc. natl. acad. sci. usa 80, 1194-1198]. mixed 14-mer synthetic oligonucleotides encoding asp-asp-his-val-val and gln-cys-gly-lys-cys were used as ...	1985	2986130
a small mobilizable incp group plasmid vector packageable into bacteriophage lambda capsids in vitro.	a mobilizable cosmid derivative of an incp group plasmid was constructed by cloning the orit region of rk2, a wide host-range plasmid, and the minimal dna sequence of bacteriophage lambda required for efficient packaging in vitro. this cosmid is 13 kb in size and has unique restriction sites for ecori, xhoi, hindiii, and sali. the xhoi and hindiii sites are within the kanamycin-resistance gene and the sali site is in the tetracycline-resistance gene. this plasmid was mobilizable from an escheric ...	1985	2986189
[production of immobilized sali and pvuii restrictase preparations].	conditions for the immobilization of specific endonucleases sal i and pvu ii on brcn-activated sepharose 4b have been selected. some physico-chemical properties of the preparations of immobilized restrictases sal i and pvu ii have been characterized. the specific and general activity values of the preparations thus obtained have been established. the immobilized enzymes have been used for the multiple restriction of the dna of phage lambda and the dna of neisseria meningitidis.	1985	2986391
transposable lambda placmu bacteriophages for creating lacz operon fusions and kanamycin resistance insertions in escherichia coli.	we have constructed several derivatives of bacteriophage lambda that translocate by using the transposition machinery of phage mu (lambda placmu phages). each phage carries the c end of mu, containing the mu cits62, ner (cii), and a genes, and the terminal sequences from the mu s end (beta end). these sequences contain the mu attachment sites, and their orientation allows the lambda genome to be inserted into other chromosomes, resulting in a lambda prophage flanked by the mu c and s sequences. ...	1985	2987183
molecular structures of mitochondrial-dna-like sequences in human nuclear dna.	two lambda phage clones carrying mitochondrial-dna-like (mtdna-like) sequences isolated from a human gene library were named lm e-1 and lm c-2, and their dna structures were characterized. lm e-1 contains about 0.4 kb dna homologous to the 5' portion of the mitochondrial 16s ribosomal rna (rrna) gene and lm c-2, a 1.6 kb dna homologous to the 3' portion of the 12s rrna gene and to almost all of the 16s rrna gene. comparisons of their nucleotide sequences with those of the corresponding regions o ...	1985	2987834
cleavage within an rnase iii site can control mrna stability and protein synthesis in vivo.	we report that processing at a cloned bacteriophage t7 rnase iii site results in strong stabilization of the mrna relative to the full-length transcript. in contrast, processing by rnase iii of the bacteriophage lambda int transcript leads to rapid degradation of the messenger. it is proposed that the mode of cleavage within the rnase iii site determines mrna stability. single cleavage leaves part of the phage t7 rnase iii site in a folded structure at the generated 3' end and stabilizes the ups ...	1985	2987846
a cosmid vector that facilitates restriction enzyme mapping.	we describe the construction and use of a cosmid vector, loric, which is derived from the phage lambda origin of replication and appears to be more stable than cole1-derived cosmids. loric recombinants can be efficiently packaged in vivo to yield 100-300 micrograms of dna per liter that is linear and has single-stranded cos ends. we call such molecules "phosmids." phosmid restriction maps can be rapidly generated by labeling either the left or right cos site by annealing on a 32p-labeled oligonu ...	1985	2987911
cloning of cdnas for human aldehyde dehydrogenases 1 and 2.	partial cdna clones encoding human cytosolic aldehyde dehydrogenase (aldh1) and mitochondrial aldehyde dehydrogenase (aldh2) were isolated from a human liver cdna library constructed in phage lambda gt11. the expression library was screened by using rabbit antibodies against aldh1 and aldh2. positive clones thus obtained were subsequently screened with mixed synthetic oligonucleotides compatible with peptide sequences of aldh1 and aldh2. one of the positive clones for aldh1 contained an insertio ...	1985	2987944
evidence that ribosomal protein s10 itself is a cellular component necessary for transcription antitermination by phage lambda n protein.	bacteriophage lambda n gene product acts to modify host rna polymerase allowing the formation of a termination-resistant transcription apparatus. previous studies have demonstrated that the nuse71 mutation that has altered the ribosomal protein s10 prevents n action in vivo. using a coupled transcription-translation system, we demonstrate here that purified s10 protein as well as the 30s ribosomal subunit is sufficient to restore n activity in the nuse mutant extract, allowing antitermination of ...	1985	2987961
[a plasmid vector with temperature-controlled gene expression].	a 169 b.p. fragment including the bla gene promoter p3 has been removed from pbr327 plasmid, and the deleted plasmid used for cloning the taqi/bglii-fragment of the lambda c1857ind- dna containing promoter pr and gene ci to obtain plasmid pce119. cells containing pce119 produced a high level of beta-lactamase at 42 degrees c, the yield at 42 degrees c being 100 times higher than at 32 degrees c. for cloning and functional assays a pcez12 plasmid was constructed, in which promoter pr and represso ...	1985	2988570
sb subregion of the human major histocompatibility complex: gene organization, allelic polymorphism and expression in transformed cells.	the sb region of the human major histocompatibility complex (mhc) has been cloned from cosmid and lambda phage libraries made from the human b-lymphoblastoid cell line priess (dr4/4, dc4/4, sb3/4). two alpha genes and two beta genes are encoded in the 100 kb long sb region in the order sb alpha-sb beta-sx alpha-sx beta. the sb alpha and sb beta genes encode the alpha and beta subunits of the sb subset of class ii mhc molecules. both the sx alpha and the sx beta genes are pseudogenes in the haplo ...	1985	2988934
construction of a human x-chromosome-enriched phage library which facilitates analysis of specific loci.	a human x-chromosome-enriched mboi-partial-digest recombinant library in phage lambda charon30 has been constructed. twelve out of the thirteen x-chromosome dna sequences that were tested were present in the library. most regions were covered in overlapping phage inserts; mean insert size was 13.7 kb. one phage from the library allowed detection of a 225-bp insertion of dna into a region near the duchenne muscular dystrophy (dmd) locus. another recombinant phage represents an expansion of a regi ...	1985	2989089
nucleotide sequence and transcription of a gene encoding human trnaglyccc.	a phage lambda clone containing a 13.1-kb human dna fragment was isolated and found to contain a trna gene encoding a glycine trna. the nucleotide sequence of the gene and its flanking regions has been determined. the gene does not have an intervening sequence nor does it encode the 3'-terminal cca sequence found in mature trnas. although this trna gene has an anticodon sequence of ccc, it has a striking homology (96%) with a human glycine trna which has an anticodon of gcc. as in other eukaryot ...	1985	2989090
a plasmid cloning system utilizing replication and packaging functions of the filamentous bacteriophage fd.	dna cloning vectors were developed which utilize the replication origin (ori) of bacteriophage fd for their propagation. these vectors depend on the expression of viral gene 2 that was inserted into phage lambda, which in turn was integrated into the host genome. the constitutive expression of gene 2 in the host cells is sufficient for the propagation of at least 100 pfd plasmids per cell. in addition to the fd ori, the pfd vectors carry various antibiotic-resistance genes and unique restriction ...	1985	2989095
the dna between rz and cosr in bacteriophage lambda is nonessential.	near the right end of phage lambda dna, between gene rz and the cos site, are 2050 bp of apparently non-coding dna. we have cloned a lambda dna fragment containing this dna into a plasmid and constructed a deletion, omega l, extending from a site within the rz gene to a site about 560 bp from cos. this deletion could be recombined into viable lambda phage at a frequency equal to that observed for the undeleted sequence. recombinant phage lambda carrying the omega l deletion were demonstrated to ...	1985	2989098
cloning of cdnas coding for rat hepatic microsomal udp-glucuronyltransferases.	radioiodinated, affinity-purified, anti-udp-glucuronyltransferase (udpgt) antibodies have been used to isolate cdnas coding for udpgt(s) from a rat liver cdna library cloned in the expression vector bacteriophage lambda gt11. the sizes of ten cloned cdnas range from 0.3-2.1 kb. the identity of the cdnas was confirmed by the hybrid-select translation and immunochemical analyses. restriction mapping indicates that two classes of cdna coding for different udpgt mrnas have been cloned.	1985	2989105
purification of pt181-encoded repc protein required for the initiation of plasmid replication.	the plasmid pt181 of staphylococcus aureus consists of 4437 base pairs and encodes resistance to tetracycline. initiation of pt181 replication specifically requires the plasmid-encoded repc protein. an in vitro system has been shown to carry out semiconservative replication of pt181 and its derivative plasmids (khan, s a., carleton, s. m., and novick, r. p. (1981) proc. natl. acad. sci. u. s. a. 78, 4902-4906). we have used this replication assay to isolate repc protein, which was purified to ne ...	1985	2989292
the terminase of bacteriophage lambda. functional domains for cosb binding and multimer assembly.	terminase is a protein complex involved in lambda dna packaging. the subunits of terminase, gpnul and gpa, are the products of genes nul and a. the actions of terminase include dna binding, prohead binding and dna nicking. phage 21 is a lambdoid phage that also makes a terminase, encoded by genes 1 and 2. the terminases of 21 and lambda are not interchangeable. this specificity involves two actions of terminase; dna binding and prohead binding. in addition, the subunits of lambda terminase will ...	1985	2989542
the novel gene(s) ard of plasmid pkm101: alleviation of ecok restriction.	the host-controlled k restriction of unmodified phage lambda was 10-100-fold alleviated in the wild-type strain e. coli k12, carrying plasmid pkm101 of incompability group n. pkm101-mediated release of k restriction was also observed in lexa-, reca-, and recb- strains of e. coli k12. by restriction mapping tn5 insertions in pkm101, which reduced pkm101-mediated alleviation of restriction, were shown to be located within the bgliib fragment approximately 11 kb anticlockwise from the ri site of pk ...	1985	2989658
umudc and mucab operons whose products are required for uv light- and chemical-induced mutagenesis: umud, muca, and lexa proteins share homology.	the products of the escherichia coli umudc operon and its plasmid-borne analog, mucab, are required for mutagenesis caused by uv light and by many chemicals. we have determined the nucleotide sequences of umudc and mucab and present comparisons of these sequences. the two operons are 52% homologous at the nucleotide level. open reading frames corresponding in position and size to the umu and muc genes have been identified. the reading frames of umud and umuc overlap by 1 base pair, and the readi ...	1985	2989816