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a nuclear gene encoding beta-amylase of sweet potato.a nuclear amyb gene from sweet potato encoding beta-amylase (beta amy) that is abundant in tuberous roots and inducible in other organs by an exogenous supply of sucrose or polygalacturonic acid, was isolated and characterized. genomic southern blot hybridization, restriction maps of independently isolated phage lambda genomic clones, and the nucleotide sequence of amyb compared with that of the cdna, all suggested that beta amy of sweet potato is encoded by a gene that is present in a single co ...19921383095
molecular cloning of murine monoclonal anti-idiotypic fab.anti-idiotypic antibodies (ab2) binding to idiotopes on antibodies with various antigen binding specificities (ab1) are potential regulators of immunity in a variety of diseases, such as autoimmunity, cancer, and viral, bacterial, or parasitic infections. furthermore, ab2 are useful probes for the characterization of receptor/ligand interactions. thus far, ab2 production has been limited to the isolation of polyclonal ab2 from immune sera or monoclonal ab2 from hybridoma supernatants. however, b ...19921383347
role of the metr regulatory system in vitamin b12-mediated repression of the salmonella typhimurium mete gene.the vitamin b12 (b12)-mediated repression of the mete gene in escherichia coli and salmonella typhimurium requires the b12-dependent transmethylase, the meth gene product. it has been proposed that the meth-b12 holoenzyme complex is involved directly in the repression mechanism. using escherichia coli strains lysogenized with a lambda phage carrying a mete-lacz gene fusion, we examined b12-mediated repression of the mete-lacz gene fusion. although b12 supplementation results in a 10-fold repress ...19921385596
meiotic recombination on artificial chromosomes in yeast.we have examined the meiotic recombination characteristics of artificial chromosomes in saccharomyces cerevisiae. our experiments were carried out using minichromosome derivatives of yeast chromosome iii and yeast artificial chromosomes composed primarily of bacteriophage lambda dna. tetrad analysis revealed that the artificial chromosomes exhibit very low levels of meiotic recombination. however, when a 12.5-kbp fragment from yeast chromosome viii was inserted into the right arm of the artifici ...19921385793
characterization of the transcription activator protein c1 of bacteriophage p22.we cloned, expressed, and purified the positive regulatory protein c1 of the temperate phage p22 of salmonella typhimurium. the purified protein was characterized as to its amino acid composition, protein sequence, molecular weight, and antigenicity. p22 c1 was shown to be a tetrameric protein composed of four identical subunits with m(r) = 10,000. moreover, we identified and characterized two p22 c1-dependent phage promoters, p(re) and pa23, whose function was completely dependent on c1 both in ...19921385814
cloning, expression, and crystallization of recoverin, a calcium sensor in vision.recoverin, a recently discovered 23-kda calcium-binding protein, activates retinal rod guanylate cyclase when the calcium level is lowered in the submicromolar range. we report here the cloning and sequencing of a cdna for recoverin from a bovine retinal expression library. the recoverin coding sequence was inserted into a pet-11a expression vector under control of the t7 phage promoter. a second expression system, in which the coding sequence was placed under control of the lambda phage pr prom ...19921385864
bacteriophage cloning and escherichia coli expression of a human igm fab.we have combined the molecular biology methods of the polymerase chain reaction and recombinant dna cloning in bacteriophage lambda to express a human igm fab in escherichia coli using genes derived from an epstein-barr virus transformed cell line. this method comprises three cdna amplifications and a single cloning step, culminating in the stable overexpression of mammalian heterodimeric recombinant protein in a prokaryotic host.19921385989
partial loss of function mutations in dnak, the escherichia coli homologue of the 70-kda heat shock proteins, affect highly conserved amino acids implicated in atp binding and hydrolysis.a set of 37 mutations in dnak, the escherichia coli homologue of the 70-kda heat shock proteins, was isolated using a selection for high constitutive expression of heat shock proteins. of these, 11 mutants were able to carry out some but not all functions of dnak. these partial function mutants were divided into two classes. class i mutants are recessive and permit replication of bacteriophage lambda and growth of cells up to 40 degrees c. class ii mutants are dominant, do not permit growth of l ...19921386674
dnabind: an interactive microcomputer program searching for nucleotide sequences that may code for conserved dna-binding protein motifs.this paper presents a simple program for interactive searching for nucleotide sequences that may code for the helix-turn-helix, zinc finger or leucine zipper motifs in proteins. the helix-turn-helix motifs are predicted using the recently published method of dodd and egan, while zinc fingers and leucine zippers are searched for by our original methods. dnabind is shown to detect all four known helix-turn-helix motifs in bacteriophage lambda genes and both zinc fingers of the adr1 gene of yeast.19921386773
bacteriophage lambda dna fragments replicate in the paramecium macronucleus: absence of active copy number control.we show that bacteriophage lambda dna fragments microinjected into the macronucleus of the ciliated protozoan paramecium can replicate as unit-length linear molecules. these linear dna molecules are substrates for the addition of paramecium telomeres by an endogenous telomerase. the linear dna pieces can exist at copy numbers much higher than that of typical endogenous macronuclear chromosomes. we show that the copy number of injected dna many fissions after microinjection reflects that of the o ...19921386793
stability of coliphage lambda dna replication initiator, the lambda o protein.the initiator of coliphage lambda dna replication, lambda o protein, may be detected among other 35s-labeled phage and bacterial proteins by a method based on immunoprecipitation. this method makes it possible to study lambda o proteolytic degradation in lambda plasmid-harboring or lambda phage-infected cells; it avoids ultraviolet (u.v.)-irradiation of bacteria, used for depression of host protein synthesis, prior to lambda phage infection. we confirm the rapid decay of lambda o protein (half-t ...19921387170
new cloning vectors for integration in the lambda attachment site attb of the escherichia coli chromosome.a set of plasmid cloning vectors has been constructed, allowing the integration of any dna fragment into the bacteriophage lambda attachment site attb of the escherichia coli chromosome. the system is based upon two components: (i) a number of cloning vectors containing the lambda attachment site attp and (ii) a helper plasmid, bearing the lambda int gene, transcribed from the lambda pr promoter under the control of the temperature-sensitive repressor ci857. the dna fragment of interest is clone ...19921387714
a large decrease in heat-shock-induced proteolysis after tryptophan starvation leads to increased expression of phage lambda lysozyme cloned in escherichia coli.the r gene coding for phage lambda lysozyme (lambda l), cloned under the control of the pl promoter on a multicopy vector, is expressed in an escherichia coli strain auxotrophic for tryptophan. induction by a thermal shift after tryptophan supplementation in a culture initially brought into stationary phase by tryptophan starvation leads to highly increased expression. a thermally unstable mutant protein, difficult to obtain under standard conditions, can be easily produced by post-stationary-ph ...19921387788
refined 1.8 a crystal structure of the lambda repressor-operator complex.the crystal structure of the lambda repressor-operator complex has been refined to an r-factor of 18.9% at 1.8 a resolution. this refinement, using data collected at low temperature, has revealed the structure of the n-terminal arm and shows that the interactions of repressor with the two halves of the pseudo-symmetric operator site are significantly different. the two halves of the complex are most similar near the outer edge of the operator site (in a region where the lambda and 434 repressors ...19921387915
host factor requirements for processive antitermination of transcription and suppression of pausing by the n protein of bacteriophage lambda.the n protein of phage lambda prevents termination of transcription by escherichia coli rna polymerase at rho-dependent and -independent terminators in the lambda early operons. the modification of rna polymerase by n requires an n-utilization (nut) site, present in each lambda early operon, and involves the e. coli factors nusa, nusb, nusg, and ribosomal protein s10. we show that, in the presence of nusa, n inhibits pausing by rna polymerase and rho-dependent termination in vitro at three sites ...19921388170
detection of individual human chromosomes by chromosome in situ suppression hybridization using pcr-amplified bacteriophage library probes.we used the polymerase chain reaction (pcr) to prepare chromosome-specific probes from the bacteriophage lambda library lao1ns01, prepared at the los alamos national laboratory from flow sorted human chromosome 1. by using oligonucleotide primers flanking the ecori insertion site of the charon 21a vector, we were able to amplify the human sequences preferentially in the library up to 9.1 kb (maximum insert size). the product of the pcr reaction was nick translated with incorporation of biotinyla ...19921389339
the spoiin279(ts) mutation affects the ftsa protein of bacillus subtilis.the spo-279(ts) mutation, originally thought to be located in the spoiig operon of bacillus subtilis, has been mapped in close proximity but outside of the spoiig locus. this mutation defines a new gene, spoiin, located midway between the spoiig and the spove loci, and whose product is required for successful completion of the asymmetric septation step. the spoiin locus was cloned using a combination of 'walking steps' upstream from the spoiig region and hybridization screening of a bacteriophag ...19921391048
a satellite iii sequence shared by human chromosomes 13, 14, and 21 that is contiguous with alpha satellite dna.we report the isolation of a clone (ptr9) from a human chromosome 21 lambda phage library, which was found to contain two distinct components: (1) a previously unreported subfamily of human satellite iii (ptr9-s3; 1,485 bp) and (2) an alpha satellite sequence (ptr9-alpha; 250 bp) containing 1.5 copies of a 171-bp alphoid unit that shows 88.4% homology to a previously reported alpha satellite consensus sequence. the two components are separated by two direct repeats of 9 bp. use of the polymerase ...19921395730
characterization of the bacteriophage lambda excisionase (xis) protein: the c-terminus is required for xis-integrase cooperativity but not for dna binding.we have performed a mutational analysis of the xis gene of bacteriophage lambda. the xis protein is 72 amino acids in length and required for excisive recombination. twenty-six mutants of xis were isolated that were impaired or deficient in lambda excision. mutant proteins that contained amino acid substitutions in the n-terminal 49 amino acids of xis were defective in excisive recombination and were unable to bind dna. in contrast, one mutant protein containing a leucine to proline substitution ...19921396573
chicken vigilin gene organization and expression pattern. the domain structure of the protein is reflected by the exon structure.chicken vigilin was identified as a member of an evolutionary-conserved protein family with a unique repetitive domain structure. 14 tandemly repeated domains are found in chicken vigilin, all of which consist of a conserved sequence motif (subdomain a) and a potential alpha-helical region (subdomain b) [1]. we have established the physical structure of the chicken vigilin gene by restriction-fragment analysis and dna sequencing of overlapping clones isolated from a phage lambda genomic dna libr ...19921396708
mak10, a glucose-repressible gene necessary for replication of a dsrna virus of saccharomyces cerevisiae, has t cell receptor alpha-subunit motifs.the mak10 gene is necessary for the propagation of the l-a dsrna virus of the yeast saccharomyces cerevisiae. we have isolated mak10 from selected phage lambda genomic dna clones that map near mak10. this gene encodes a 733-amino acid protein with several regions of similarity to t cell receptor alpha-subunit v (variable) regions. we show that mak10 is essential for optimal growth on nonfermentable carbon sources independent of its effect on l-a. although loss of l-a by mak10-1 mutants is partia ...19921398065
construction of lambda gt103, a derivative of phage lambda gt10 that has unique ecori, noti, saci and spei sites and retains positive selection for recombinants.a phage vector, lambda gt103, that has unique ecori, noti, saci and spei sites within the imm434 ci repressor gene, was constructed by pcr-aided site-directed mutagenesis of lambda gt10 [huynh et al., dna cloning techniques: a practical approach, 1985, pp. 49-78]. this vector allows directional cloning and retains positive selection for recombinants on escherichia coli c600hfl strains (since only phages with disrupted ci genes plate on this host). libraries made with this phage vector can be eff ...19921398127
cloning of aklavinone biosynthesis genes from streptomyces galilaeus.aklavinone is an aglycone of aclacinomycin a which is an important antitumor drug. genes for the biosynthesis of aklavinone were cloned from streptomyces galilaeus 3ar-33, an aklavinone-producing mutant, by use of the acti and actiii polyketide synthase gene probes. restriction mapping and southern analysis of the dna cloned in a lambda phage vector established that the dna represented three different regions of the s. galilaeus 3ar-33 genome that contained 3.4, 2.5, and 4.1 kb bamhi fragments w ...19921399850
how the phage lambda n gene product suppresses transcription termination: communication of rna polymerase with regulatory proteins mediated by signals in nascent rna. 19921400223
guinea pigs possess a highly mutated gene for l-gulono-gamma-lactone oxidase, the key enzyme for l-ascorbic acid biosynthesis missing in this species.guinea pigs cannot synthesize l-ascorbic acid because of their deficiency in l-gulono-gamma-lactone oxidase, a key enzyme for the biosynthesis of this vitamin in higher animals. in this study we isolated the l-gulono-gamma-lactone oxidase gene of the rat and the homologue of this gene of the guinea pig by screening rat and guinea pig genomic dna libraries in lambda phage vectors, respectively, using a rat l-gulono-gamma-lactone oxidase cdna as a probe. sequencing analysis showed that the amino a ...19921400507
specific and complex interactions of murine p53 with dna.biologically active mutant p53 from balb/c mouse tumor cells (meth a) was analysed for its specific interaction with dna. restricted phage lambda dna, representing dna of high complexity with regard to sequence and secondary structure, was used to probe for such an activity in a target-bound dna-binding assay, using doubly immunopurified p53. a single lambda dna fragment was specifically retained with very high affinity (kd = 10(-10) m). specific dna binding was shown to be an intrinsic property ...19921408133
construction and use of lambda pl promoter vectors for direct cloning and high level expression of pcr amplified dna coding sequences.a set of plasmid vectors which allow single-step cloning and expression of pcr-amplified dna coding sequences has been constructed. the vectors contain the phage lambda pl promoter, a synthetic translation initiation region (tir), and convenient cloning sites. the cloning sites provide all or part of an aug translation initiation codon and facilitate the precise fusion of target dna sequences to vector transcriptional and translational signals. the vectors were constructed with synthetic tirs be ...19921408761
symmetry in the mechanism of bacteriophage lambda integrative recombination.during the strand-exchange events of bacteriophage lambda integration, pairs of phosphodiester bonds are broken and then rejoined to form novel dna linkages. the reaction proceeds in vitro in the absence of an external energy source; the bond energy needed to rejoin broken strands of dna must therefore be conserved during cleavage. although some of this conservation involves a covalent intermediate between dna and the recombinase int, it is possible that such an intermediate is formed with only ...19921409677
construction of coliphage lambda charon vectors with bamh1 cloning sites. 1980. 19921422018
generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. 1989. 19921422064
overproduction and purification of bacillus subtilis dna polymerase iii.the objectives of this work were to engineer the cloned polc gene encoding bacillus subtilis dna polymerase iii for controlled overexpression in escherichia coli and to devise a facile purification scheme permitting the large-scale production of pure recombinant polymerase. the translational signals of polc were restructured by expression cassette pcr (macferrin et al., 1990, proc. natl. acad. sci. usa 87, 1937-1941), and the modified gene was inserted into the expression plasmid, pkc30 (rosenbe ...19921422209
a modified vector for the controlled high-level overproduction of staphylococcal protein a fusion proteins in the periplasm of escherichia coli.a vector encoding the staphylococcal protein a was modified by cloning the spa gene, including its signal peptide-encoding sequence, downstream of the translation initiation sites of the phage lambda cro gene and under the control of the temperature-inducible phage lambda pr promoter. the expression from this construct was studied using the escherichia coli phoa gene as a reporter gene after fusion to the spa gene. determination of alkaline phosphatase activity, 1 h after temperature induction o ...19921422213
rabbit single domain antibodies specific to protein c expressed in prokaryotes.vdj genes were amplified by the polymerase chain reaction from mrna isolated from peripheral blood b cells of rabbits immunized with protein c. the amplified genes were cloned into a lambda phage expression vector and packaged. a library of 6 x 10(5) recombinant phages was screened with labelled protein c and 30 positive clones were found. three of them were plaque purified and the affinity of the single domain antibodies to the antigen determined to be 10(6)-10(7) l m-1. the data indicate the f ...19921427991
phenol hydroxylase from trichosporon cutaneum: gene cloning, sequence analysis, and functional expression in escherichia coli.a cdna clone encoding phenol hydroxylase from the soil yeast trichosporon cutaneum was isolated and characterized. the clone was identified by hybridization screening of a bacteriophage lambda zap-based cdna library with an oligonucleotide probe which corresponded to the n-terminal amino acid sequence of the purified enzyme. the cdna encodes a protein consisting of 664 amino acids. amino acid sequences of a number of peptides obtained by edman degradation of various cleavage products of the puri ...19921429434
an internal region of rpob is required for autogenous translational regulation of the beta subunit of escherichia coli rna polymerase.in order to delineate the region involved in feedback regulation of the rna polymerase beta subunit (encoded by rpob), a collection of rpob-lacz translational fusions with different endpoints both upstream and downstream of the rpob start site was assembled on lambda phage vectors. the extent of translational repression of beta was monitored by measuring beta-galactosidase levels in monolysogens of the fusions under conditions of increased intracellular concentrations of beta and beta' achieved ...19921429440
inhibition of bacteriophage lambda development by the klaa gene of broad-host-range plasmid rk2.the kil-kor regulon of broad-host-range plasmid rk2 is an unusual array of eight co-regulated operons that express at least 21 genes, including the plasmid replication initiator gene. some of the operons were first identified as kil loci because uncontrolled expression in the absence of certain kor regulatory genes leads to death of the host cells. the functions of kila, c and e are unknown, although co-regulation with the replication initiator gene suggests that they may have importance in the ...19921433286
stimulation of the phage lambda pl promoter by integration host factor requires the carboxy terminus of the alpha-subunit of rna polymerase.escherichia coli integration host factor (ihf) binds with high affinity to two tandem ihf consensus sequences located upstream from the pl promoter of bacteriophage lambda. ihf was shown to stimulate transcription initiation from the pl promoter by increasing close complex formation (kb). we show here, by the use of reconstituted mutant rna polymerases, that the c-terminal portion of the alpha subunit of rna polymerase plays an essential role in the stimulation of transcription by ihf. our resul ...19921433303
the translation initiation site of recombinant trypanosoma brucei ornithine decarboxylase varies with different promoters.expression of the trypanosoma brucei ornithine decarboxylase (odc) gene in escherichia coli behind the lambda phage pr promoter led to the production of a recombinant enzyme having the same subunit molecular weight as the native enzyme [4]. however, when the same gene is expressed behind the tac promoter or the phoa promoter, the odcs produced by the transformed e. coli have subunit molecular weights approximately 2 kda higher than that of the native enzyme. amino terminal sequencing of the reco ...19921435879
[replication and gene expression of lambda phage]. 19921438832
bacteriophage lambda papa: not the mother of all lambda phages.the common laboratory strain of bacteriophage lambda--lambda wild type or lambda papa--carries a frameshift mutation relative to ur-lambda, the original isolate. the ur-lambda virions have thin, jointed tail fibers that are absent from lambda wild type. two novel proteins of ur-lambda constitute the fibers: the product of stf, the gene that is disrupted in lambda wild type by the frameshift mutation, and the product of gene tfa, a protein that is implicated in facilitating tail fiber assembly. r ...19921439823
determination of mutagenicity in tissues of transgenic mice following exposure to 1,3-butadiene and n-ethyl-n-nitrosourea.1,3-butadiene (bd) is carcinogenic in the b6c3f1 mouse in multiple organs, including lung and liver. we conducted a study to measure the frequency of bd mutations in mouse tissues using a transgenic mouse (muta mouse; mm). mm is a balb/c x dba/2 (cd2f1) mouse that has a bacteriophage lambda shuttle vector with the target gene lacz integrated into the mouse genome. mice were exposed by inhalation to 625 ppm bd (6 hr/day) for 5 days and the lacz- mutant frequency (mf) was determined in lung, bone ...19921440614
mechanisms for gene conversion and homologous recombination: the double-strand break repair model and the successive half crossing-over model.two mechanisms for gene conversion and homologous recombination were discussed. (1) the double-strand break repair model. a double-strand break is expanded to a gap, which is then repaired by copying a homologous sequence. the gene conversion is often accompanied by crossing-over of the flanking sequences. we obtained evidence for this model in red pathway of bacteriophage lambda and rece pathway of e. coli. (2) the successive half crossing-over model. half crossing-over leaves one recombinant d ...19921442245
nucleotide sequence of bovine interleukin-6 cdna.we report the cloning of bovine interleukin-6 (il-6) cdna. the clone was isolated from a bovine-leukemia virus (blv)-induced b cell-lymphosarcoma cdna library cloned in the bacteriophage lambda gt11. the cdna encodes a full length il-6 protein made of 208 amino acids with 65, 53, 42 and 42% homology to published sequences of porcine, human, mouse and rat il-6, respectively. the significance of il-6 expression in a blv-induced tumor is briefly discussed.19921446077
genetic analysis of cosb, the binding site for terminase, the dna packaging enzyme of bacteriophage lambda.cosb, the binding site for terminase, the dna packaging enzyme of bacteriophage lambda, consists of three binding sites (called r3, r2 and r1) for gpnu1, the small subunit of terminase; and i1, a binding site for integration host factor (ihf), the dna bending protein of escherichia coli. cosb is located between cosn, the site where terminase introduces staggered nicks to generate cohesive ends, and the nu1 gene; the order of sites is: cosn-r3-i1-r2-r1-nu1. a series of lambda mutants have been co ...19921447794
genetic analysis of mutations affecting terminase, the bacteriophage lambda dna packaging enzyme, that suppress mutations in cosb, the terminase binding site.terminase, the dna packaging enzyme of phage lambda, binds to lambda dna at a site called cosb, and introduces staggered nicks at an adjacent site, cosn, to generate the cohesive ends of virion lambda dna molecules. terminase also is involved in separation of the cohesive ends and in binding the prohead, the empty protein shell into which lambda dna is packaged. terminase is a dna-dependent atpase, and both subunits, gpnu1 and gpa, have atpase activity. cosb contains a series of gpnu1 binding si ...19921447796
the role of integration host factor in gene expression in escherichia coli.integration host factor is a sequence-specific, histone-like, multifunctional dna-binding and -bending protein of escherichia coli. the characterization and functional analysis of this protein has been done mainly in bacteriophage lambda and other mobile genetic elements. less is known concerning the role of integration host factor (ihf) in e. coli, although it has been implicated in a number of processes in this organism including dna replication, site-specific recombination, and gene expressio ...19921447969
analysis of the region in between two closely linked patatin genes: class ii promoter activity in tuber, root and leaf.from a potato genomic library a phage lambda clone was isolated that carried nucleotide sequences of two patatin genes, thus demonstrating a close physical linkage between these two members of the patatin gene family. sequence and restriction analysis showed the genes to be oriented in tandem. the more upstream gene was a pseudogene truncated at the 3' end, whereas the downstream gene was a class ii patatin gene. in addition to a 208 bp fragment also present in patatin class i promoters, the reg ...19921450383
involvement of the escherichia coli rna polymerase alpha subunit in transcriptional activation by the bacteriophage lambda ci and cii proteins.escherichia coli cells harbouring the rpoa341 mutation produce an rna polymerase which transcribes inefficiently certain operons subject to positive control. here, we demonstrate that the rpoa341 allele also prevents lysogenization of the host strain by bacteriophage lambda, a process dependent upon the action of two phage-encoded activators. this phenomenon was shown to arise from an inability to establish an integrated prophage rather than a failure to maintain the lysogenic state. the inabili ...19921452017
cloning and sequence analysis of the gene encoding l-lactate dehydrogenase from lactococcus lactis: evolutionary relationships between 21 different ldh enzymes.lactate dehydrogenase (ldh; ec1.1.1.27) is a key enzyme in the fermentation of milk by lactic acid bacteria used in the dairy industry. an 800-bp dna fragment containing part of the gene (ldh) encoding ldh was amplified from lactococcus lactis in a polymerase chain reaction using primers designed from the partial amino acid sequence of a lactococcal ldh. this fragment was radioactively labelled and used to probe a phage lambda library of lc. lactis genomic dna. fragments containing ldh were subc ...19921452029
is the bacteriophage lambda lysozyme an evolutionary link or a hybrid between the c and v-type lysozymes? homology analysis and detection of the catalytic amino acid residues.the relationship between the bacteriophage lambda lysozyme (lambda l) and the c and v-type lysozymes has been investigated by sequence alignment, secondary structure prediction and pattern recognition methods. the alignment of the amino terminal part of lambda l with that of v-type lysozymes suggests that glu19 is a residue essential for catalysis. its mutation to gln leads to a completely inactive enzyme. in the alignment of the sequence of lambda l with those of the c-type lysozymes a strongly ...19921453462
inactivation of lambda phage with 658 nm light using a dna binding porphyrin sensitizer.exposure of lambda phage to 658 nm light in the presence of 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21h,23h-porphine, tetra-p-tosylate leads to complete (greater than 7 logs) inactivation as measured by the plaque assay. the sensitizer without light and 658 nm photolysis of lambda phage in the absence of sensitizer do not lead to a measurable decrease in viral inactivity. viral inactivation is not dependent upon the presence of oxygen.19921454872
interaction between bacteriophage lambda and its escherichia coli host.bacteriophage lambda relies to a large extent on processes requiring interactions between viral- and host-encoded proteins for its lytic growth, establishment of lysogeny, and release from the prophage state. both biochemical and genetic studies of these interactions have yielded new information about important host and lambda functions. in particular, mutations in escherichia coli that compromise lambda dna replication, genome packaging, transcription elongation, and site-specific recombination ...19921458022
molecular sieving of lambda phage dna in polyacrylamide solutions as a function of the molecular weight of the polymer.electrophoresis of lambda phage dna was carried out in solutions at various concentrations of uncrosslinked polyacrylamide of 0.6, 1, 5 and 9 x 10(6) molecular weight (mw) with narrow mw distribution. by inspection of mobilities in the various concentration ranges, it appears that mobilities decrease, and retardation increases, with increasing mw. the relation between electrophoretic retardation and the mw of the polymer was also interpreted (i) in the manner previously applied to nonlinear ferg ...19921459074
the carboxy-terminal 14 amino acids of phage lambda n protein are dispensable for transcription antitermination.the analogous n proteins encoded by lambdoid bacteriophages lambda, 21, and 22 are very different in amino acid sequence, except at their carboxy-terminal ends. since n lambda remains functional despite the deletion of most of its terminal region of homology to n21, that region of homology cannot represent a region of conserved function.19921459962
inactive o6-methylguanine-dna methyltransferase in human cells.a plasmid encoding a recombinant human o6-methylguanine-dna methyltransferase (mgmt) fused to a fragment of the bacteriophage lambda n protein has been constructed. the fusion protein retained methyltransferase activity when expressed at high levels in e.coli and was purified to essential homogeneity by a simple procedure. antisera raised against the purified fusion protein recognized mgmt in western blots of extracts of human cells. for most cell lines, there was a quantitative relation between ...19921461738
the trna(tyr) multigene family of nicotiana rustica: genome organization, sequence analyses and expression in vitro.tobacco trna(tyr) genes are mainly organized as a dispersed multigene family as shown by hybridization with a trna(tyr)-specific probe to southern blots of eco ri-digested dna. a nicotiana genomic library was prepared by eco ri digestion of nuclear dna, ligation of the fragments into the vector lambda gtwes.lambda b and in vitro packaging. the phage library was screened with a 5'-labelled synthetic oligonucleotide complementary to nucleotides 18 to 37 of cytoplasmic tobacco trna(tyr). eleven hyb ...19921463826
lysis protein t of bacteriophage t4.lysis protein t of phage t4 is required to allow the phage's lysozyme to reach the murein layer of the cell envelope and cause lysis. using fusions of the cloned gene t with that of the escherichia coli alkaline phosphatase or a fragment of the gene for the outer membrane protein ompa, it was possible to identify t as an integral protein of the plasma membrane. the protein was present in the membrane as a homooligomer and was active at very low cellular concentrations. expression of the cloned g ...19921465100
deformation of dna during site-specific recombination of bacteriophage lambda: replacement of ihf protein by hu protein or sequence-directed bends.escherichia coli ihf protein is a prominent component of bacteriophage lambda integration and excision that binds specifically to dna. we find that the homologous protein hu, a nonspecific dna binding protein, can substitute for ihf during excisive recombination of a plasmid containing the prophage attachment sites attl and attr but not during integrative recombination between attp and attb. we have examined whether ihf and hu function in excisive recombination is mediated through dna bending. o ...19921465417
spectral enhancement of proteins: biological incorporation and fluorescence characterization of 5-hydroxytryptophan in bacteriophage lambda ci repressor.we have used a tryptophan-requiring escherichia coli auxotroph to replace the three tryptophan residues of lambda ci repressor with 5-hydroxy-l-tryptophan (5-ohtrp). by using a nonleaky promoter, we have achieved > 95% replacement of tryptophan in the repressor. we show that the absorbance and fluorescence properties of 5-ohtrp-lambda ci are clearly distinct from lambda ci repressor and that the fluorescence of 5-ohtrp-lambda ci repressor can be observed selectively in the presence of exogenous ...19921465434
genescape: a relational database of escherichia coli genomic map data for macintosh computers.we present a relational database program developed in foxbase+/mac for the viewing and manipulation of ordered restriction maps and associated features of the escherichia coli genome including sequenced genes and the kohara miniset of bacteriophage lambda clones. use of this program allows easy access to the wealth of information being collected in a dataset of dna sequences, maps and genetic data known as ecoseq, ecomap and ecogene respectively.19921468012
high-yield recovery of recombinant dna from poorly growing cosmid and lambda genomic clones.certain genomic sequences cannot be recovered efficiently in cosmid or lambda bacteriophage clones, presenting a barrier to efforts to construct a contiguous cloned library of a genome. we have encountered such sequences during our efforts to isolate cosmid and bacteriophage lambda clones carrying members of the human type 2 cystatin gene family. several cosmid clones constructed in the pwe 15 vector did not survive purification, and using standard techniques, we were unable to obtain significan ...19921476724
identification and localization of microsatellite markers covering human chromosome 18.to generate microsatellite markers from chromosome 18, we have cytogenetically localized a large number of lambda phage using a deletion mapping panel of somatic cell hybrids. here we describe the identification of 65 new ca-repeat-containing phage and the localization of five markers developed in other laboratories. this approach allows the selection of a subset of markers that are well spaced across the chromosome and can be developed as genetic markers. the use of pcr-based markers should all ...19921478651
in vivo excision properties of bacteriophage lambda zap expression vectors. 19921479916
bacteriophage lambda as a cloning vector.extensive research has been directed toward the development of multipurpose lambda vectors for cloning ever since the potential of using coliphage lambda as a cloning vector was recognized in the late 1970s. an understanding of the intrinsic molecular organization and of the genetic events which determine lysis or lysogeny in lambda has allowed investigators to modify it to suit the specific requirements of gene manipulations. unwanted restriction sites have been altered and arranged together in ...19921480110
thyroid hormone receptor dimerization function maps to a conserved subregion of the ligand binding domain.thyroid hormone receptors (trs) bind as dimers to specific dna response elements. we have used a genetic approach to identify amino acid sequences required for dimerization of the tr beta isoform. bacteria expressing a chimeric repressor composed of the dna binding domain of the bacteriophage lambda cl repressor fused to the tr beta ligand binding domain are immune to lambda infection as a consequence of homodimerization activity provided by the receptor sequences. the phenotypes of deletions an ...19921480176
the fis protein: it's not just for dna inversion anymore.higher-order nucleoprotein complexes are associated with many biological processes. in bacteria the formation of these macromolecular structures for dna recombination, replication, and transcription often requires not only the participation of specific enzymes and co-factors, but also a class of dna-binding proteins collectively known as 'nucleoid-associated' or 'histone-like' proteins. examples of this class of proteins are hu, integration host factor, h-ns, and fis. fis was originally identifi ...19921484481
[detection of left-helical segments in eukaryotic dna].the method of dna binding to nitrocellulose filters was applied to dna isolated from mouse liver and ehrlich ascite carcinoma (eac), calf thymus, and lymphocytes from patients with chronic lymphoid leukemia. in those and phage pm2 dna the increase in the dna binding to the filters with a rise in nacl concentration from 0.5 up to 4.5 m was sigmoidal being suggestive of a conformational transition. no such activity was found in the case of phage lambda or single-stranded dna. the binding decreased ...19921489826
molecular cloning and expression of the xylanase gene from chainia in escherichia coli.a complete genomic library of chainia was constructed in coliphage lambda vector gt10 and was screened for the xylanase gene using an 18-mer mixed oligonucleotide probe corresponding to a six-amino acid sequence of low molecular mass chainia xylanase. inserts from 11 putative clones, showing hybridization with the oligonucleotide probe at medium stringency, were subcloned in puc8 and screened for xylanase gene expression using anti-xylanase antibodies. the restriction map of the insert (1.4 kb) ...19921490609
vh genes in tandem array comprise a repeated germline motif.in a study of human vh gene heterogeneity, we have previously used sequence-specific oligonucleotide probes to demonstrate polymorphism of 56pl and three highly homologous vh3 germline elements. we now extend these findings with vh nucleotide sequences obtained from a person who possesses restriction fragments corresponding to each of these four vh3 genes. from a lambda-phage library of genomic dna, distinct phage clones containing putative 56pl, hv3005, 1.9iii, and hv3019b9 genes were selected ...19921500714
construction of a new escherichia coli-saccharomyces cerevisiae shuttle plasmid cloning vector allowing positive selection for cloned fragments.a new e. coli-s. cerevisiae shuttle plasmid cloning vector (ppw263) with a positive type of selection, was constructed. the selection system, based on the regulatory region of lambda phage controlling the expression of tetracycline resistance, was derived from the cloning vector pun121 (nilsson et al. 1983). there are three cloning sites in the ci gene, ecori, hindiii and bglii, and, in addition, two unique sites in the neighborhood, bamhi and sali. the size of the vector is 7.8 kb. the maintena ...19921505881
in situ mapping of the gene coding for a leucine zipper dna binding protein (cdr62) to 16p12-16p13.1.a cdna clone encoding the major antigen (cdr62) associated with the antibody-induced paraneoplastic cerebellar degeneration has been used to identify the chromosomal location of the corresponding structural gene(s) by screening for its retention in a panel of rodent-human somatic cell hybrids. having established the synteny of the gene with the autosome 16, we proceeded to its precise subregional mapping by in situ fluorescence hybridization with a recombinant lambda phage containing the genomic ...19921505970
enriched sources of escherichia coli replication proteins. the dnag primase is a zinc metalloprotein.primase, the product of the escherichia coli dnag gene, is the enzyme responsible for rna primer synthesis on both template strands at replication forks during chromosomal dna synthesis. the dnag gene was modified by replacement of the natural ribosome-binding site with one complementary to the 3' end of 16s rrna, and then inserted downstream of tandem bacteriophage lambda pr and pl promoters in the puc9-derived vector pce30. following thermal induction of transcription, the resulting plasmid pp ...19921511009
the polygalacturonases of aspergillus niger are encoded by a family of diverged genes.aspergillus niger produces several polygalacturonases that, with other enzymes, are involved in the degradation of pectin. one of the two previously characterized genes coding for the abundant polygalacturonases i and ii (pgi and pgii) found in a commercial pectinase preparation was used as a probe to isolate five more genes by screening a genomic dna library in phage lambda embl4 using conditions of moderate stringency. the products of these genes were detected in the culture medium of aspergil ...19921511691
gene structure of semenogelin i and ii. the predominant proteins in human semen are encoded by two homologous genes on chromosome 20.the genes for semenogelin i and ii, the major protein constituents of the human seminal fluid, have been characterized by three overlapping clones in bacteriophage lambda, encompassing 31.5 kilobases (kb) of genomic dna. the two genes are located 11.5 kb apart in the region q12-q13.1 on chromosome 20. both genes are relatively compact, spanning only 2.7 and 3.1 kb, respectively. the transcription units are composed of three exons, of which the first encodes the signal peptide, the second encodes ...19921517240
an ordered clone bank for chromosome i of saccharomyces cerevisiae.chromosome i of saccharomyces cerevisiae dc5 rho 0 was dissected into segments with an average size of 14.0 kb and cloned into lambda phage vectors. the physical maps of the resultant clones, totaling 205.9 kb, were used to construct an ordered clone bank of this chromosome.19921522073
dna electrophoresis in uncross-linked polyacrylamide solution, studied by epifluorescence microscopy.electrophoresis of human dna fragments (approximately 1 x 10(5) to 1 x 10(7) bases in size) was conducted in a solution of uncross-linked polyacrylamide contained in a horizontally mounted 1 mm diameter glass tube and monitored by epifluorescence microscopy. in presence of the polymer, molecular conformations described as a "trailing network" of dna and a globular "head" were observed. the migration velocity varies between species differing in the size of the "head", and in the ratio between the ...19921522176
interaction of ecorii endonuclease with dna substrates containing single recognition sites.ecorii is unusual among type ii restriction enzymes in that, while it cleaves substrates such as pbr322 and bacteriophage lambda that contain several recognition sites for the enzyme efficiently, substrates such as the genomes of bacteriophages t3 and t7 which contain a small number of recognition sites are cut poorly by it. interestingly, pbr322, or a short dna duplex containing a single site for the enzyme, can activate the enzyme to cleave resistant substrates. we show here that, at low conce ...19921526995
engineered iron oxide-adhesion mutants of the escherichia coli phage lambda receptor.escherichia coli able to specifically adhere to iron oxide and not adhere to other metal oxides were constructed by genetic engineering. concatamers of random oligonucleotides were introduced into a portion of a plasmid-borne lamb gene encoding an external domain of the phage lambda receptor. bacteria able to adhere to iron oxide were selected by serial enrichment from the population of plasmid transformants. the concatameric nature of the inserted dna allows a genetic analysis analogous to exon ...19921528875
the purification and properties of the scaffolding protein of bacteriophage lambda.the nu3 gene of bacteriophage lambda resides within a cluster of genes that specify structural components of the bacteriophage head. previous experiments indicate that the nu3 gene product (gpnu3) is associated with immature proheads but is not detectable in mature proheads or bacteriophage particles, hence its classification as a scaffolding protein. the nu3 gene has been cloned and overexpressed, and its protein product has been purified. the purified protein is biologically active, as demonst ...19921530932
site-specific enthalpic regulation of dna transcription at bacteriophage lambda or.binding of ci repressor to dna fragments containing the three specific binding sites of the right operator (or) of bacteriophage lambda was studied in vitro over the temperature range 5-37 degrees c by quantitative footprint titration. the individual-site isotherms, obtained for binding repressor dimers to each site of wild-type or and to appropriate mutant operator templates, were analyzed for the gibbs energies of intrinsic binding and pairwise cooperative interactions. it is found that dimer ...19921531023
analysis of a mutation affecting the specificity domain for prohead binding of the bacteriophage lambda terminase.genetic studies have identified a specificity domain for prohead binding in the c-terminal 32 amino acids of gpa, the large subunit of bacteriophage lambda terminase (s. frackman, d. a. siegele, and m. feiss, j. mol. biol. 180:283-300, 1984). in the present work, an amber mutation, aam42, in the fifth-to-last codon of the a gene was found to be lethal in nonsuppressing hosts. the mutation, expected to generate gpa lacking the last five amino acids, caused the production of a terminase that cut c ...19921531050
identification of sbcd mutations as cosuppressors of recbc that allow propagation of dna palindromes in escherichia coli k-12.the function of an open reading frame (orf-45) located upstream of the sbcc gene of escherichia coli was investigated. mutations that inactivate sbcc improve the ability to propagate lambda red gam phage that carry a palindromic sequence in their dna. they also act with sbcb mutations as cosuppressors of the defects in recombination, dna repair, and cell viability associated with recbc mutations. a 1,282-bp cassette encoding resistance to kanamycin was used to disrupt orf-45. the mutation, which ...19921531222
effect of escherichia coli nusg function on lambda n-mediated transcription antitermination.the escherichia coli nus factors act in conjunction with the bacteriophage lambda n protein to suppress transcription termination on the lambda chromosome. nusa binds both n and rna polymerase and may also interact with other nus factors. to search for additional components of the n antitermination system, we isolated host revertants that restored n activity in nusa1 mutants. one revertant, nusg4, was mapped to the rif region of the e. coli chromosome and shown to represent a point mutation near ...19921531224
the isolation and characterization of mutants of the integration host factor (ihf) of escherichia coli with altered, expanded dna-binding specificities.the integration host factor (ihf) of escherichia coli is a small, basic protein that is required for lambda site-specific recombination and a variety of cellular processes. it is composed of two subunits, alpha and beta, that are encoded by the hima and hip (himd) genes, respectively. ihf is a sequence-specific dna-binding protein and bends the dna when it binds. we have used the bacteriophage p22-based challenge phage selection to isolate suppressor mutants with altered, expanded dna binding sp ...19921531459
unusual ribosome binding properties of mrna encoding bacteriophage lambda repressor.the mrna encoding repressor ci of phage lambda is the only known e. coli message which starts directly with the initiation aug codon. the ability of in vitro synthesized ci mrna fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. in the presence of trna(met)f, these fragments are capable of forming the ternary complexes at the 5'-terminal aug codon not only with 30s subunits but also with undissociated 70s ribosomes (70s tight couples). in ...19921531520
rexab proteins of bacteriophage lambda enhance the effect of photolyase-dimer complexes on lacz gene expression in escherichia coli.expression of the lacz gene in escherichia coli is inactivated by exposure to ultraviolet light (uv). inactivation is exceptionally effective when cells contain amplified levels of dna photolyase (which forms complexes with pyrimidine dimers in the absence of light for actual photoreversal) and a lambda prophage. without amplified photolyase, the lambda prophage or both, inactivation rates are similar and much lower. uv-inactivation of lacz gene expression in the presence of both amplified photo ...19921531692
isolation of dominant negative mutants and inhibitory antisense rna sequences by expression selection of random dna fragments.selective inhibition of specific genes can be accomplished using genetic suppressor elements (gses) that encode antisense rna, dominant negative mutant proteins, or other regulatory products. gses may correspond to partial sequences of target genes, usually identified by trial and error. we have used bacteriophage lambda as a model system to test a concept that biologically active gses may be generated by random dna fragmentation and identified by expression selection. fragments from eleven diff ...19921531871
a novel method for converting common restriction enzymes into rare cutters: integration host factor-mediated achilles' cleavage (ihf-ac).integration host factor (ihf)-mediated protection against enzymatic methylation at ihf-overlapping sites provides the basis for this novel application of the achilles' cleavage (ac) technique [koob et al., science 241 (1988) 1084-1086] for generating rare natural cleavage sites. when applying ihf-ac to plasmid, phage lambda, escherichia coli and yeast genomes, only a few of the ecori, hinfi, and mboi sites (which overlapped the ihf sites) remained cleavable after prior methylation with the cogna ...19921531969
integration host factor (ihf) binds to many sites in the a + t-rich b2 region of phage lambda dna.computer analysis of almost the entire b2 region of lambda phage (nt 22346-27475) revealed 23 consensus-like ihf sites, with eleven pointing in one direction and twelve in the opposite direction [27 bp; kur et al., gene 81 (1989) 1-15]. to confirm the significance of this finding experimentally, the region was subdivided into 21 fragments and examined for integration host factor (ihf) binding by gel retardation and a variety of footprinting methods. out of 21 fragments examined 13 were found to ...19921532160
mutations of the phage lambda nutl region that prevent the action of nun, a site-specific transcription termination factor.phage hk022 encodes a protein, nun, that promotes transcription termination within the pl and pr operons of its relative, phage lambda. the lambda sequences required for termination had previously been shown to overlap the nut sites, which are essential for transcription antitermination during normal lambda growth. to further specify the nun target and to determine its relation to the nut sites, we constructed deletion and base substitution mutations of the lambda nutl region and measured nun-de ...19921532174
ar+ plasma-induced damage to dna in bacteriophage lambda: implications for the arrangement of dna in the phage head.bacteriophage lambda was bombarded with low-energy ar+ ions with the goal of determining whether particular regions of the dna genome are found preferentially in the outer portion of the packaged dna mass. the strategy was to fragment the dna selectively near the surface of the virus by exposing intact phage to ar+ ions energetic enough to break covalent chemical bonds in dna but not energetic enough to penetrate deeply beneath the viral capsid shell. broken dna was then isolated, and its genomi ...19921532213
relevance of environmental alkylating agents to repair protein o6-alkylguanine-dna alkyltransferase: determination of individual and collective repair capacities of o6-methylguanine.the repair capacity for o6-methylguanine was determined in cell homogenates of peripheral blood lymphocytes of 35 automobile industry workers, exposed to rubber and tires, and of 35 clinical workers, handling cancer chemotherapeutic agents, compared to control groups. lambda-phage dna containing one 32p-labeled o6-methylguanine in each bamhi site was used as substrate for the repair protein o6-alkylguanine-dna alkyltransferase (agt). the clinical personnel showed in the mean a highly significant ...19921532345
deuterium exchange of operator 8ch groups as a raman probe of repressor recognition: interactions of wild-type and mutant lambda repressors with operator ol1.the rate of deuterium exchange of a purine 8ch group in dna is highly sensitive to both macromolecular secondary structure and intermolecular interactions which restrict solvent access to the major groove [lamba, o.p., becka, r., & thomas, g.j., jr. (1990) biopolymers 29, 1465-1477]. we have exploited the sensitivity of the 8ch----8cd reaction to probe dna recognition by the helix-turn-helix (hth) motif of phage lambda ci repressor. we find that purine exchanges in the 19-base-pair ol1 operator ...19921532510
functional cloning vectors for use in directional cdna cloning using cohesive ends produced with t4 dna polymerase.this paper describes the construction of 'prime' cloning vectors, which include phage lambda and plasmid vectors useful for functional cloning in oocytes, yeast, and mammalian cells, and their use in a 'prime' cloning system. the system takes advantage of the very active and precise 3' exonuclease activity of t4 dna polymerase to produce single-stranded (ss) ends (cut-back) of vector and insert dna. this results in the highly efficient directional cloning of cdna and pcr-amplified dna. the syste ...19921532564
nusg, a new escherichia coli elongation factor involved in transcriptional antitermination by the n protein of phage lambda.we have reconstituted biologically relevant transcriptional antitermination in vitro by the phage lambda n protein. this required the isolation of nusg, a newly identified escherichia coli transcription elongation factor. nusg is encoded by an e. coli gene, formerly called u and now called nusg, in which a mutation affects antitermination by n in vivo. efficient antitermination by n in our reconstituted system depends on the bacterial proteins nusg, nusa, nusb, and ribosomal protein s10 (which f ...19921532577
lambda int protein bridges between higher order complexes at two distant chromosomal loci attl and attr.the excisive recombination reaction of bacteriophage lambda involves a specific and efficient juxtaposition of two distant higher order protein-dna complexes on the chromosome of escherichia coli. these complexes, which mediate synapsis and strand exchange, consist of two dna sequences, attl and attr, the bivalent dna binding protein int, and the sequence-specific dna bending proteins, ihf, xis, and fis. the protein-protein and protein-dna interactions within, and between, these complexes were s ...19921533056
supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pl promoter.the high level of efficiency of the bacteriophage lambda pl promoter is dependent upon the topological state of the promoter dna and the binding of a dna-bending protein, ihf, to a site centered -86 base-pairs upstream from the pl transcription start site. abortive initiation assays indicate that dna supercoiling stimulates open complex formation, whereas ihf enhances promoter recognition. ihf stimulates promoter recognition to the same extent on linear and supercoiled templates. we found that t ...19921533252
large-scale subcloning of bacteriophage lambda zap clones. 19921533305
an efficient phage plaque screen for the random mutational analysis of the interaction of hiv-1 gp120 with human cd4.a lambda phage expression methodology was adapted to dissect protein/ligand interactions efficiently through the creation and rapid screening of large numbers of mutants. here we describe the method and its specific application to the interaction between the external envelope glycoprotein of the human immunodeficiency virus (hiv-1), gp120, and the human cell surface protein cd4. random substitutions were introduced throughout the gp120 binding region (amino acids 38-62) in the amino-terminal dom ...19921533631
[the lethal and mutagenic action of 3h incorporated into the 2' position of the deoxyribose in the dna of the extracellular phage lambda].the lethal and mutagenic effects of 3h decay in 2' position of deoxyribose residues in dna of extracellular lambda phage were studied, [2'-3h]-deoxyadenosine (3h-da) or [2'-3h]-thymidine (3h-dt) being used as labelled dna precursors. as estimated by the efficiency of the lethal and mutagenic actions of 3h decay in position 2' was significantly lower than that of the decay in the incorporated 3h-pyrimidines. the genetic effects of 3h decay in 2' position may be attributed to the radiation effect ...19921534626
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