Publications

chi-stimulated patches are heteroduplex, with recombinant information on the phage lambda r chain.	generalized recombination in escherichia coli is elevated near chi sites. in vitro, recbcd enzyme can nick chi a few nucleotides 3' of the terminal gg of the chi sequence (5'-gctggtgg). the simplest model in which this nick at chi participates in chi function predicts that in phage lambda, chi-stimulated recombinants not crossed-over for flanking markers (patches) should be heteroduplex, with recombinant information on the lambda i chain. i report here that patches are heteroduplex, but that rec ...	1987	2949853
purification and properties of gal repressor:pl-galr fusion in pkc31 plasmid vector.	the galr gene, which encodes the gal repressor protein in escherichia coli, has been fused to the strong pl promoter of bacteriophage lambda in plasmid pkc31. the pl promoter is kept repressed by a thermolabilie lambda repressor, cits857, to prevent cell killing. heat induction of the pl-galr fusion plasmid synthesizes large amounts of active gal repressor. the protein has been purified to homogeneity in three steps. the purification is greatly aided by the reversible insolubility of active repr ...	1987	2950087
degradation in vitro of bacteriophage lambda n protein by lon protease from escherichia coli.	lon protease from escherichia coli degraded lambda n protein in a reaction mixture consisting of the two homogeneous proteins, atp, and mgcl2 in 50 mm tris, ph 8.0. genetic and biochemical data had previously indicated that n protein is a substrate for lon protease in vivo (gottesman, s., gottesman, m., shaw, j. e., and pearson, m. l. (1981) cell 24, 225-233). under conditions used for n protein degradation, several lambda and e. coli proteins, including native proteins, oxidatively modified pro ...	1987	2950089
structures of mismatched base pairs in dna and their recognition by the escherichia coli mismatch repair system.	the escherichia coli mismatch repair system does not recognize and/or repair all mismatched base pairs with equal efficiency: whereas transition mismatches (g x t and a x c) are well repaired, the repair of some transversion mismatches (e.g. a x g or c x t) appears to depend on their position in heteroduplex dna of phage lambda. undecamers were synthesized and annealed to form heteroduplexes with a single base-pair mismatch in the centre and with the five base pairs flanking each side correspond ...	1986	2951250
genetic functions promoting homologous recombination in escherichia coli: a study of inversions in phage lambda.	we have studied homologous recombination in a derivative of phage lambda containing two 1.4-kb repeats in inverted orientation. inversion of the intervening 2.5-kb segment occurred efficiently by the escherichia coli recbc pathway but markedly less efficiently by the lambda red pathway or the e. coli rece or recf pathways. inversion by the recbcd pathway was stimulated by chi sites located to the right of the invertible segment; this stimulation decreased exponentially by a factor of about 2 for ...	1987	2951295
synthesis of a trans-acting inhibitor of dna maturation by prohead mutants of phage lambda.	bacteriophage lambda with mutations in genes that control prohead assembly and other head precursors cannot mature their dna. in this paper we present evidence that the failure of these phage mutants to mature dna is a reflection of a mechanism that modulates terminase nicking activity during normal phage development. we have constructed plasmids that contain the lambda-cohesive end site (cos) and the genes that code for dna terminase, the enzyme that matures dna by cutting at cos. the dna termi ...	1987	2951296
gene fusion in vivo using transductional cointegrates.	a method is described which allows the efficient construction of hybrids between homologous genes. the technique is based on the phenomenon of cointegrate transduction in which the homology between cloned sequences present on a bacteriophage lambda vector and a plasmid vector is exploited to allow the packaging of a plasmid-phage recombinant. the size of the cointegrate molecule can be far beyond the normal packaging limit of lambda and still allow the transduction of plasmid-borne drug-resistan ...	1986	2951299
structure of physarum actin gene locus arda: a nonpalindromic sequence causes inviability of phage lambda and reca-independent deletions.	previously we reported that approx. 80% of the genome from the plasmodial slime mold physarum polycephalum, including all the actin genes, can be cloned only in recbc- sbcb- escherichia coli hosts [nader et al., proc. natl. acad. sci. usa 82 (1985) 2698-2702]. we have now sequenced the actin gene locus arda. the nucleotide sequence of its coding region is flanked by the typical putative regulatory sequences for transcription initiation and polyadenylation. the coding region is interrupted by fiv ...	1986	2951301
isolation and analysis of escherichia coli mutants that allow increased replication of bacteriophage lambda.	escherichia coli mutants were isolated that supported the growth of a lambda ots and, in at least one case, a lambda bts phage at the normally nonpermissive temperature of 39 degrees c. in one such strain, ots and bts suppression ability appeared to be a function of the guab gene. ots suppression by the mutant guab strain was prevented if high levels of guanine or xanthine were present in the medium. no other base had any effect on ots suppression in this strain. other strains carrying spontaneo ...	1987	2951367
the mannose permease of escherichia coli consists of three different proteins. amino acid sequence and function in sugar transport, sugar phosphorylation, and penetration of phage lambda dna.	the mannose permease of the bacterial phosphotransferase system mediates sugar transport across the cytoplasmic membrane concomitant with sugar phosphorylation. it also functions as a receptor for bacterial chemotaxis and is required for infection of the cell by bacteriophage lambda where it most likely functions as a pore for penetration of lambda dna. the permease consists of three different subunits, iiiman, ii-pman, and ii-mman, which are encoded in a single transcriptional unit ptslpm. the ...	1987	2951378
mutational analysis of integrase arm-type binding sites of bacteriophage lambda. integration and excision involve distinct interactions of integrase with arm-type sites.	integrative recombination between specific attachment (att) regions of the bacteriophage lambda genome (attp) and the escherichia coli genome (attb) results in a prophage flanked by the hybrid recombinant sites attl and attr. each att site contains sequences to which proteins involved in recombination bind. using site-directed mutagenesis, we have constructed a related set of point mutations within each of the five int "arm-type" binding sites located within attp, attl and attr. footprint analys ...	1986	2951525
in vivo cloning of dna into multicopy cosmids by mini-mu-cosduction.	a general in vivo procedure for cloning escherichia coli genes into cosmids has been developed. the method we describe here uses a deleted mu phage (a mini-mu) to transpose e. coli genes into cosmids during mini-mu replication. the resulting cosmids clones are packaged in vivo into lambda phage particles. plasmids carrying a particular dna sequence can be selectively recovered after infection of a new host with the in vivo constructed genomic cosmid library. this system was used successfully to ...	1986	2951581
large palindromes in the lambda phage genome are preserved in a rec+ host by inhibiting lambda dna replication.	a large palindrome carried by phage lambda has been shown to prevent growth of the phage on a rec+ strain of escherichia coli. the phage do form plaques on recbc sbcb strains, but the palindrome is not stable--deletions that either destroy the palindrome or diminish its size overgrow the original engineered palindrome-containing phage. we have prepared stocks of lambda carrying a palindrome that is 2 x 4200 base pairs long. these phage stocks are produced by induction of a lysogen in which the t ...	1987	2951734
analysis of a cdna clone expressing a human autoimmune antigen: full-length sequence of the u2 small nuclear rna-associated b" antigen.	a u2 small nuclear rna-associated protein, designated b'', was recently identified as the target antigen for autoimmune sera from certain patients with systemic lupus erythematosus and other rheumatic diseases. such antibodies enabled us to isolate cdna clone lambda hb''-1 from a phage lambda gt11 expression library. this clone appeared to code for the b'' protein as established by in vitro translation of hybrid-selected mrna. the identity of clone lambda hb''-1 was further confirmed by partial ...	1987	2951739
direct evidence for dna bending at the lambda replication origin.	replication initiation in bacteriophage lambda appears to require wrapping of origin dna on an approximately 50 angstrom radius in or around the complex with the initiator protein o. since short lengths of dna are not that flexible, it may be that runs of coherently spaced deoxyadenylate residues constitute bend sites in the ori sequence that facilitate the process. earlier data showed that ori dna has electrophoretic anomalies characteristic of bend sites and that these are augmented by initiat ...	1987	2951850
bacteriophage lambda as a model system.		1986	2952113
a bacteriophage transcription terminator permits the cloning of a mammalian expression vector carrying the human preprorenin gene in e. coli.	we constructed a plasmid-based expression vector carrying the murine metallothionein gene promoter, the human preprorenin gene, the tn5 neomycin phosphotransferase ii gene, and a complete bovine papilloma virus genome. we were unsuccessful in cloning the preprorenin gene in e. coli when it was inserted into a plasmid vector 3' to the metallothionein gene promoter. this result was consistent with our previous data suggesting that expression of the preprorenin gene is toxic to e. coli (weighous, t ...	1987	2952120
the distinct role of catalase and dna repair systems in protection against hydrogen peroxide in escherichia coli.	the katekatg mutant of e. coli, um1, had no assayable catalase activities in the extract and showed increased (about 20 fold) sensitivity to killing by h2o2 when compared with its parental strain csh7. the mutant strain was able to reactivate h2o2-damaged lambda phage. on the other hand, reca and pola mutants were also highly sensitive to h2o2, but they had normal level of catalase activities. reca derivatives of um1 were much more sensitive to h2o2 than um1 and reca strains. the induction of um ...	1987	2952121
dimerization of the operator binding domain of phage lambda repressor.	dimerization of lambda repressor is required for its binding to operator dna. as part of a continuing study of the structural basis of the coupling between dimer formation and operator binding, we have undertaken 1h nmr and gel filtration studies of the dimerization of the n-terminal domain of lambda repressor. five protein fragments have been studied: three are wild-type fragments of different length (1-102, 1-92, and 1-90), and two are fragments bearing single amino acid substitutions in resid ...	1987	2952164
host/vector interactions which affect the viability of recombinant phage lambda clones.	a class of recombinant phage lambda clones are recovered from human genomic libraries on escherichia coli recb21 recc22 sbcb15 cells, which fail to form plaques on wild-type cells. we report experiments which address the mechanism of this inhibition. the introduction of the recombination-stimulating sequence chi into one such clone allows growth of this phage on rec+ cells. in addition, the insertion of lambda gam+ gene into a rec+-inhibited clone results in the ability of the phage to form plaq ...	1986	2952553
factors which equalize the representation of genome segments in recombinant libraries.	genomic segments which contain inverted repetitions longer than 300 bp are frequently lost from recombinant libraries grown on rec+ hosts. we have found that 9% of phage lambda clones that contain 15-20-kb insertions of human or drosophila dna are inhibited on rec+ hosts and as a result will become under-represented in amplified genomic libraries. we have therefore examined several factors of both host and vector origin which affect the fidelity of representation of genomic sequences in recombin ...	1986	2952554
a broad-host-range expression vector based on the pl promoter of coliphage lambda: regulated synthesis of human interleukin 2 in erwinia and serratia species.	we report the construction of a broad-host-range expression vector based on an rsf1010-derived replicon. the vector carries the strong leftward promoter (pl) of coliphage lambda as well as the ci857 allele, which codes for a thermolabile repressor protein. the coding region of mature human interleukin 2, which is preceded by the ner ribosome binding site of phage mu, was cloned downstream from the pl promoter. the plasmid was introduced into erwinia and serratia species by means of mobilization. ...	1987	2952635
bacteriophage lambda receptor site on the escherichia coli k-12 lamb protein.	we have analyzed eight new phage-resistant missense mutations in lamb. these mutations identify five new amino acid residues essential for phage lambda adsorption. two mutations at positions 245 and 382 affect residues which were previously identified, but lead to different amino acid changes. three mutations at residues 163, 164, and 250 enlarge and confirm previously proposed phage receptor sites. two different mutations at residue 259 and one at 18 alter residues previously suggested as facin ...	1987	2952637
determination of bacteriophage lambda tail length by a protein ruler.	how the size and shape of living structures are determined by genetic information is one of the fundamental problems in biology. here i describe a study in which the size of a biological supramolecular structure was changed in a predictable way by in vitro genetics, with the size both before and after manipulation being exactly determined. i have studied the tail of bacteriophage lambda, whose length is determined by the length of the 'ruler protein', the product of gene h. the length of the tai ...	1987	2952887
electron microscopic studies of giant nucleus-like structure formed by lambda dna introduced into the cytoplasm of xenopus laevis fertilized eggs and embryos.	when bacteriophage lambda dna was injected into the cytoplasm of the fertilized egg of xenopus laevis, giant nucleus-like structures were assembled around the injected dna. these nucleus-like structures survived during cleavage and were partitioned into blastomeres at the blastula stage. the nucleus-like structures formed in the uncleaved fertilized eggs and the blastula cells were both surrounded by a bilayer nuclear membrane with nuclear pore complexes. the ultrastructural features of the lamb ...	1987	2953439
mutations that affect the efficiency of translation of mrna for the cii gene of coliphage lambda.	starting with the lambda pre-strain lambda ctr1 cy3008, which forms clear plaques, we have isolated two mutant strains, lambda dya2 ctr1 cy3008 and lambda dya3 ctr1 cy3008, that form plaques with very slightly turbid centers. the dya2 and dya3 mutations lie in the region of overlap between the pre promoter and the ribosome recognition region of the cii gene, and have nucleotide alterations at positions -1 and +5 of pre, and alterations in cii mrna at -16 and -21 nucleotides before the initial au ...	1987	2953647
mutations that improve the pre promoter of coliphage lambda.	the dya5 mutation, a c----t change at position -43 of the lambda pre promoter, results in a twofold increase in pre activity in vivo. smaller increases in pre activity are found for the dya2 mutation, a t----c change at position -1 of pre, and the dya3 mutation, an a----g change at +5 of pre. the mutant pre promoters retain complete dependence on cii protein for activity. these observations argue, at least for pre-like promoters, that promoter activities are influenced by nucleotide sequences at ...	1987	2953648
repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence.	heteroduplexes with single base pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda dna and used to transfect escherichia coli. a series of transition (g:t and a:c) and transversion (g:a and c:t) mismatches located throughout most of the bacteriophage lambda ci gene has been examined. the results suggest that the transition mismatches are generally better repaired than the transversion mismatches and that, at least for the transversion mismatche ...	1987	2953650
boundaries of the nutl antiterminator of coliphage lambda and effects of mutations in the spacer region between boxa and boxb.	to study the relationship of sequence to function for the phage lambda nutl transcriptional antiterminator, we cloned the 354-bp hincii lambda dna fragment (coordinates 35261-35615; daniels et al., in lambda ii, 1983, pp. 485-486 and 618-619) between the plac promoter and rho-dependent or rho-independent terminators (t) in the plac-t-galk plasmid derived from vector pko3, and assayed the galk expression in escherichia coli hosts in the presence or absence of the n gene product. the 354-bp fragme ...	1986	2953653
generation of lambda phage concatemers for use as pulsed field electrophoresis size markers.		1987	2954030
role of homology in site-specific recombination of bacteriophage lambda: evidence against joining of cohesive ends.	bacteriophage lambda integration and excision take place at specific loci called attachment sites. earlier work has shown that efficient recombination requires the identical sequence to be present in both attachment sites throughout the seven-base-pair region between the points of strand exchange. a plausible model for the role of homology postulates that int, the site-specific recombinase, makes double-strand breaks at attachment sites such that each broken end has a short single-strand protrus ...	1987	2954163
the functional boundaries of the q-utilization site required for antitermination of late transcription in bacteriophage lambda.	expression of the late genes of bacteriophage lambda requires, in addition to the host functions, the lambda p'r promoter, the antiterminator sequence qut, and the product of gene q which interacts with the q utilization (qut) site. in the absence of the q function or qut site, the p'r-initiated transcription is blocked by the t'r terminator at the 194th nucleotide downstream of the start point, s'r, producing a short 6 s mrna. in this study the position and boundaries of the qut site were deduc ...	1987	2954301
organization and sequence of the human alpha-lactalbumin gene.	a recombinant bacteriophage containing the entire alpha-lactalbumin gene was isolated from a human genomic library constructed in bacteriophage lambda l47. within this recombinant the 2.5 kb alpha-lactalbumin gene is flanked by about 5 kb of sequence on either side. the complete nucleotide sequence of the gene and its immediate flanking sequences were determined and compared with those of the rat alpha-lactalbumin gene. these studies showed that the size, organization and sequence of the exons h ...	1987	2954544
pseudogene in the genome of bacteriophage lambda?	we find a region in the non-coding part of bacteriophage lambda genome that codes for the conserved fold which repressors and other proteins use for specific dna binding. the region is involved in a long open reading frame exceeding one kilobase and is read in the same frame as gene a in the opposite strand. the putative translation product of this open reading frame has a highly ordered secondary structure with a predominance of alpha helices, which is typical of repressors. in addition, codon ...	1987	2954549
in vivo dna cloning with a mini-mu replicon cosmid and a helper lambda phage.	a mini-mu bacteriophage, containing the cohesive-end packaging site (cos) from a lambda-phi 80 hybrid phage, a high-copy-number plasmid replicon, and a kanamycin-resistance gene for independent selection, was constructed to clone genes in vivo. this mini-mu element can be derepressed to transpose at a high frequency. dna segments that become flanked by copies of this mini-mu element in the same orientation can be packaged by a helper lambda phage. the resulting lambda lysate can be used to infec ...	1987	2954879
isolation of the cd7 gene from the dna of transfected l cells.	using dna from l cells which expressed high levels of the cd7 (leu-9 or huly-m2) antigen obtained after two cycles of transfection, a genomic library was constructed in the lambda phage charon 4a. recombinant clones containing the gene coding for this antigen were identified by first screening the library with both the hsv-tk gene and a probe detecting the human repetitive (alu) sequences. dna from 10 tk+ and 12 alu+ recombinant clones was used to transfect l cells which were analyzed for the ce ...	1987	2954903
enzymology of the pre-priming steps in lambda dv dna replication in vitro.	we have examined some of the early pre-priming steps of bacteriophage lambda dv dna replication in vitro. previous experiments have shown that bacteriophage lambda replication requires host rna polymerase-dependent rna synthesis near or at the origin of replication (ori lambda) to initiate dna synthesis. using a crude fraction ii enzymatic system we have shown that during rna polymerase action, at least the bacteriophage lambda o and lambda p replication proteins as well as the host dnab protein ...	1987	2954949
syrinx 2a: an improved lambda phage vector designed for screening dna libraries by recombination in vivo.	the syrinx 2a phage and pi an13 plasmid were designed for screening of dna libraries by homologous recombination in vivo. syrinx 2a carries multiple cloning sites and a recently identified lambda gene, rap (recombination adept with plasmid), required for efficient phage-plasmid recombination. we describe a rapid, reliable, and technically easy method to screen syrinx 2a libraries, expand the resulting phage-plasmid cointegrates, and subclone plasmid in as little as 2 days. recombination screenin ...	1987	2955406
analysis of nutr, a site required for transcription antitermination in phage lambda.	deletions extending from the cro gene into boxa and nutr of the rho-dependent tr1 terminator of bacteriophage lambda have been generated and cloned between promoters and the galk gene of escherichia coli on a multicopy plasmid. terminators placed between the promoters and galk restrict transcription and expression of galk on these plasmids. however, when lambda n protein is provided, and if a functional n interaction site, nutr, is intact, transcription antitermination occurs and galk expression ...	1987	2955408
carcinoembryonic antigen family: expression in a mouse l-cell transfectant and characterization of a partial cdna in bacteriophage lambda gt11.	genomic dna and mrna from the adenocarcinoma cell line lovo were used to generate l-cell transfectants and a bacteriophage lambda gt11 cdna clone that express epitopes of carcinoembryonic antigen (cea). primary and secondary l-cell transfectants expressing cea were selected with a fluorescence-activated cell sorter (facs). these transfectants, including some clones that were selected for high-level cea expression by multiple rounds of facs sorting, express a surface protein of 150 kda that react ...	1987	2955415
construction of a dna-polymerase i overproducing plasmid and isolation of the enzyme.	the pola gene of escherichia coli coding for dna polymerase i was cloned under the control of bacteriophage lambda promoter pl and gene n in a high copy number plasmid vector. the chromosomally located lambda cits repressor gene kept the synthesis of the pola gene product at 28 degrees c at a low level. raising the temperature to 43 degrees c resulted in inactivation of the repressor and overproduction of dna polymerase i, which could easily be purified to homogeneity.	1987	2955618
mismatch repair and recombination in e. coli.	the involvement of the e. coli methyl-directed and very short patch (vsp) mismatch repair systems in bacteriophage lambda recombination has been studied. genetic crosses and heteroduplex transfection experiments were performed using lambda phages with sequenced mutations in the cl gene. the results indicate that methyl-directed repair does operate during bacteriophage lambda recombination but generally does not contribute to the formation of recombinants involving close markers. vsp repair appar ...	1987	2955904
mismatch repair of deaminated 5-methyl-cytosine.	deamination of 5-methyl-cytosine in double-stranded dna produces a g-t mismatch. heteroduplexes of bacteriophage lambda dna containing a g-t mismatch at the site of a g-5-mec base-pair in one of the parental phages were constructed and used to transfect escherichia coli cells. genetic analysis of the progeny phages derived from such heteroduplexes suggests that, in e. coli, mismatches resulting from the deamination of 5-methyl-cytosine are repaired by a system requiring the e. coli dcm methylase ...	1987	2956428
tests of the double-strand-break repair model for red-mediated recombination of phage lambda and plasmid lambda dv.	the double-strand-break repair (dsbr) model was formulated to account for various aspects of yeast mitotic and meiotic recombination. in this study three features of the dsbr model are tested for red-mediated recombination between phage lambda and lambda dv, a plasmid that is perfectly homologous to about 10% of lambda. the results support the applicability of the dsbr model to lambda's red system: (1) creating a double-strand-break (dsb) within the region of homology shared by phage and plasmid ...	1987	2957271
detection of heterologous fusion proteins in escherichia coli with a monoclonal antibody.	several laboratories have constructed expression vectors for the production of heterologous fusion proteins containing the n-terminal 13 amino acids of the bacteriophage lambda cii-coded protein in escherichia coli. we have prepared a monoclonal antibody to a synthetic peptide having this cii amino acid sequence and have found that this antibody reacts with authentic cii protein in western blot tests and with most cii peptide-containing fusion proteins in both radioimmunoprecipitation and wester ...	1987	2957274
aberrant regulation of synthesis and degradation of viral proteins in coliphage lambda-infected uv-irradiated cells and in minicells.	the patterns of bacteriophage lambda proteins synthesized in uv-irradiated escherichia coli cells and in anucleate minicells are significantly different; both systems exhibit aberrations of regulation in lambda gene expression. in unirradiated cells or cells irradiated with low uv doses (less than 600 j/m2), regulation of lambda protein synthesis is controlled by the regulatory proteins ci, n, cii, ciii, cro, and q. as the uv dose increases, activation of transcription of the ci, rexa, and int g ...	1987	2957511
homology-dependent interactions in phage lambda site-specific recombination.	general recombination shows a dependence on large regions of homology between the two participating segments of dna. many site-specific recombination systems also exhibit a dependence on homology, although in these systems the requirement is limited to a short region (less than 10 base pairs (bp]. we have used the in vitro phage lambda integration reaction to study the role of homology in this model site-specific recombination system. we find that certain non-homologous pairings which are strong ...	1987	2957599
preparation of high titer lambda phage lysates.		1987	2957644
minipreps of dna from bacteriophage lambda.		1987	2957647
rnase iii stimulates the translation of the ciii gene of bacteriophage lambda.	the bacteriophage lambda ciii gene product regulates the lysogenic pathway by stabilizing the lambda cii regulatory protein. our results show that the expression of the lambda ciii gene is subject to specific requirements. tests of a set of ciii-lacz gene and operon fusions reveal that a sequence upstream of the ciii ribosome binding site is needed for ciii translation. the sequence contains an inefficient rnase iii processing site. furthermore, expression of ciii is drastically reduced in cells ...	1987	2957696
[reduced restriction of phage lambda in escherichia coli k-12 cells after gamma-irradiation].	in gamma-irradiated cells of escherichia coli k-12 restriction alleviation of an unmodified phage lambda is only observed in ab1157 strain. no restriction alleviation by gamma-rays is registered in ab1157 mutants (rec a and ssb-1).	1987	2957724
new mutations in the prm promoter of bacteriophage lambda.	a prm-ci-lacz fusion inserted into the b2 region of bacteriophage lambda imm21 was used to isolate mutations in the lambda prm promoter. among the mutations causing defects in synthesis of both repressor (ci gene product) and beta-galactosidase, new promoter mutations were identified at positions -11 and -32 relative to the ci transcription start point. both mutations are changes in conserved (consensus) nucleotides in prm, but the mutation at -11, which alters a more highly conserved nucleotide ...	1987	2958391
activated reca protein may induce expression of a gene that is not controlled by the lexa repressor and whose function is required for mutagenesis and repair of uv-irradiated bacteriophage lambda.	the activated form of the reca protein (reca) is known to be involved in the reactivation and mutagenesis of uv-irradiated bacteriophage lambda and in the expression of the sos response in escherichia coli k-12. the expression of the sos response requires cleavage of the lexa repressor by reca and the subsequent expression of lexa-controlled genes. the evidence presented here suggests that reca induces the expression of a gene(s) that is not under lexa control and that is also necessary for maxi ...	1987	2958446
deletion analysis of the dna sequence required for the in vitro initiation of replication of bacteriophage lambda.	supercoiled dna containing the replication origin of bacteriophage lambda can be replicated in vitro. this reaction requires purified lambda o and p replication proteins and a partially purified mixture of escherichia coli proteins (tsurimoto, t., and matsubara, k. (1982) proc. natl. acad. sci. u.s.a. 79, 7639-7643; wold, m. s., mallory, j.b., roberts, j. d., lebowitz, j. h., and mcmacken, r. (1982) proc. natl. acad. sci. u.s.a. 79, 6176-6180). the lambda origin region has four repeats of a 19-b ...	1987	2958451
characterization of glucosyltransferase expressed from a streptococcus sobrinus gene cloned in escherichia coli.	the gene encoding a glucosyltransferase which synthesized water-insoluble glucan, gtfi, previously cloned from streptococcus sobrinus strain mfe28 (mutans serotype h) into a bacteriophage lambda vector, was subcloned into the plasmid pbr322. the recombinant plasmid was stable in escherichia coli and gtfi was efficiently expressed. the gtf-i expressed in e. coli was compared to the corresponding enzymes in s. sobrinus strains mfe28 (serotype h), b13 (serotype d) and 6715 (serotype g) and shown to ...	1987	2958599
cutting of chi-like sequences by the recbcd enzyme of escherichia coli.	chi, 5' g-c-t-g-g-t-g-g 3', stimulates coliphage lambda recombination mediated by the major recombination pathway of escherichia coli, the recbc pathway. purified recbcd enzyme makes a single strand endonuclease cleavage four to six nucleotides to the 3' side of the chi sequence. three sequences similar to chi, 5' a-c-t-g-g-t-g-g 3', 5' g-t-t-g-g-t-g-g 3' and 5' g-c-t-a-g-t-g-g 3', have partial recombinational hotspot activity in genetic crosses. we report here that purified recbcd enzyme prefer ...	1987	2958631
double-chain-cut sites are recombination hotspots in the red pathway of phage lambda.	the red recombination pathway of phage lambda is shown to target recombination to double-chain ends of dna. a double-chain cut, delivered in vivo to only one of two parents participating in a lambda lytic cross by a type ii restriction endonuclease, increases the proportion of crossing over in the interval containing the cut compared with other intervals. the stimulating effect of a cut is evident whether replication is inhibited or permitted. cut stimulation can move away from the initial cut-s ...	1987	2958632
protein-protein interactions in a higher-order structure direct lambda site-specific recombination.	the highly directional site-specific recombination of bacteriophage lambda is tightly regulated by the binding of three different proteins to a complex array of sites. the manner in which these reactions are both stimulated and inhibited by co-operative binding of proteins to specific sites on the p arm of attp and attr has been elucidated by correlation of nuclease protection with recombination studies of both wild-type and mutant dnas. in addition to co-operative forces, there is a specific co ...	1987	2958633
sequence of amino acids in lamb responsible for spontaneous ejection of bacteriophage lambda dna.	the dna sequence of the promoter-distal half of lamb from shigella sonnei 3070 has been determined and compared with the known sequence for the escherichia coli k12 gene. the only predicted amino acid changes in this region of lamb, the receptor protein for bacteriophage lambda, lie between positions 381 and 390, where seven of the ten amino acids are altered. evidence is presented that indicates that this region is responsible for the ability of the s. sonnei receptor, but not the e. coli recep ...	1987	2958635
kinetic studies on cro repressor-operator dna interaction.	the six operators of phage lambda and their consensus sequence were synthesized as 21 base-pair dnas and their interactions with cro repressor were studied using a filter binding assay. the measured equilibrium dissociation constants suggest that cro has the highest affinity to the consensus operator (kd = 1.2 x 10(-12) m) and then the or3 operator (kd = 2.0 x 10(-12) m), after that the affinity becomes lower in the following order: or1, ol1, ol2, ol3, or2. the competition experiments show that ...	1987	2958636
[the role of sensitive bacteria in determining the count of phage negative colonies on solid growth media].	the purpose of the work was to study how the number of phage negative colonies on a solid growth medium depended on the concentration of a sensitive bacterial strain. for the system of phage lambda and a sensitive e. coli cell, the number of negative colonies was maximal at a concentration of ca. 4 x 10(8) cells/ml.	1987	2958685
missing contact probing of dna-protein interactions.	we have examined the positions of contact between lambda phage repressor protein and operator or1 dna by scanning populations of lightly depurinated or depyrimidated dna for bases essential to or irrelevant to repressor binding. this global scanning technique delineates the apparent contact region between lambda repressor and operator and shows bases previously demonstrated or predicted to be contacted plus some additional bases. a mutant repressor, previously shown to contact dna as wild-type r ...	1987	2958845
translational polarity of a mutation in the initiator aug codon of the lambda ci gene.	a prm-ci-lacz fusion inserted into the b2 region of bacteriophage lambda was used to isolate mutations affecting expression of both the lambda ci gene and the lacz gene. one such mutation, a change in the ci initiator codon from aug to aua, reduces immunity of a lambda prophage to superinfection, and causes a 60-70% reduction in beta-galactosidase synthesis, even when repressor is supplied in trans. the effect of the mutation on lacz gene expression is eliminated in a rho- bacterial strain, and ...	1987	2959588
bacterial genes mutl, muts, and dcm participate in repair of mismatches at 5-methylcytosine sites.	certain amber mutations in the ci gene of bacteriophage lambda appear to recombine very frequently with nearby mutations. the aberrant mutations included c-to-t transitions at the second cytosine in 5'cc(a/t)gg sequences (which are subject to methylation by bacterial cytosine methylase) and in 5'ccag and 5'cagg sequences. excess ci+ recombinants arising in crosses that utilize these mutations are attributable to the correction of mismatches by a bacterial very-short-patch (vsp) mismatch repair s ...	1987	2959653
isolation of escherichia coli rpob mutants resistant to killing by lambda cii protein and altered in pyre gene attenuation.	escherichia coli mutants simultaneously resistant to rifampin and to the lethal effects of bacteriophage lambda cii protein were isolated. the sck mutant strains carry alterations in rpob that allow them to survive cii killing (thus the name sck), but that do not impair either the expression of cii or the activation by cii of the lambda promoters pe and pi. the sck-1, sck-2, and sck-3 mutations modify transcription termination. the growth of lambda, but not of the n-independent lambda variant, l ...	1987	2959654
resolution of dna molecules greater than 5 megabases by contour-clamped homogeneous electric fields.	excellent resolution of chromosomal dna molecules from saccharomyces cerevisiae, candida albicans and schizosaccharomyces pombe has been obtained using alternating contour-clamped homogeneous electric field (chef) gel electrophoresis. the largest of these molecules is greater than 5 mb in size and is resolved after 130 hours in a 0.6% agarose gel at a field strength of 1.3 v/cm and a switching interval of 1 hour. separation of concatamers of phage lambda dna reveals four regions of resolution in ...	1987	2959907
inhibition of streptomycin-dependent mutation in escherichia coli on the lytic growth of bacteriophage lambda.	spontaneous streptomycin-dependent mutants (strda) were isolated from escherichia coli c600. on c600 strd, the lytic growth of phage lambda nam and lambda ci857 was inhibited. after e. coli lysogenic strain 1.1485 (lambda ci857) mutated to strda, induction of lambda was decreased greatly. on strda of e. coli strains c600 and 1.1485 (lambda ci857), the plating efficiencies and burst sizes of phage t4 and t7 remained normal. since strda is a mutation in the structural gene for ribosomal protein s1 ...	1987	2960017
active human erythropoietin expressed in insect cells using a baculovirus vector: a role for n-linked oligosaccharide.	biologically active recombinant human erythropoietin has been expressed at high levels in an insect cell background. expression involved the preparation of a human erythropoietin cdna, the transfer of this cdna to the autographa californica nuclear polyhedrosis virus (acnpv) genome under the polyhedrin gene promoter, and the subsequent infection of spodoptera frugiperda cells with recombinant acnpv. erythropoietin cdna was prepared through the expression of the human erythropoietin gene in cos c ...	1987	2960381
the occurrence of 2'-5' oligoadenylates in escherichia coli.	the use of a highly specific radioimmunoassay and of hplc permitted us to confirm the occurrence of 2'-5' oligoadenylates [p chi (a2'p5')na] in several strains of escherichia coli. cellular concentrations of 2'-5' oligoadenylates ranged from 50 nm to 300 nm. the mixture of 2'-5' oligoadenylates consisted primarily of pppa2'p5'a, pa2'p5'a,a2'p5'ap and a2'p5'a under normal conditions of growth. none of them activated rnase l. infection of the bacteria with the single-stranded dna phage m13 or indu ...	1987	2960522
transcription antitermination by phage lambda gene q protein requires a dna segment spanning the rna start site.	the gene q protein of phage lambda is a transcription antiterminator that modifies rna polymerase near the phage late gene promoter and thereby causes antitermination at distant sites. to define the site of action of q protein, we have reconstructed the regulatory system on plasmids that allow the intracellular concentration of q protein to be regulated, and that allow the effect of q protein on transcription from variant promoter segments to be measured in vivo and in vitro. we show that dna se ...	1987	2960589
control of cloned gene expression by promoter inversion in vivo: construction of improved vectors with a multiple cloning site and the ptac promoter.	we have constructed three gene-expression plasmids which contain (an) invertible promoter(s) and a multiple cloning site. we used either the plac promoter or the ptac-plac tandem promoters, the latter directing a more than fourfold increase in expression of the galk reporter gene in escherichia coli host. all these plasmids were derived from the pnh7a expression plasmid of podhajska et al. [gene 40 (1985) 163-168]. like pnh7a, these vectors have three novel properties: (i) in the 'off phase', th ...	1987	2960590
an open reading frame in the escherichia coli bacteriophage lambda genome encodes a protein that functions in assembly of the long tail fibers of bacteriophage t4.	assembly of the long tail fibers of the escherichia coli bacteriophage t4 requires the catalytic action of two auxiliary proteins. it was found that a gene of the entirely unrelated phage lambda codes for a protein which can substitute for one of these t4 polypeptides, protein 38. the lambda gene was designated tfa (tail fiber assembly). protein 38 consists of 183 residues, and the tfa protein consists of 194 residues; the two polypeptides are about 40% homologous. although the tfa gene is dispe ...	1987	2960666
[vectors--derivatives of phage lambda for construction and analysis of genome libraries].	basic features of lambda phage derived, cosmid and plasmid vectors are described. plasmid vectors combine the most useful features of phage and plasmid vectors. plasmids can exist in vivo as a plasmid or as a phage. plasmid vectors are similar to large capacity phage vectors, but can be maintained in vivo without a stuffer fragment. that is why plasmids are easier in preparation for cloning than phage vectors. the yield of recombinants is higher with plasmid vectors (up to 3.10(6)) and the backg ...	1987	2960881
a novel in vitro dna packaging system demonstrating a direct role for the bacteriophage lambda fi gene product.	a new in vitro bacteriophage lambda dna packaging system is described in which all the proteins necessary for head morphogenesis are supplied by extracts of plasmid-transformed cells. this assay is used to demonstrate that the lambda fi gene product (gpfi) is necessary for maximal packaging efficiency when proheads and terminase are present in limiting amounts. a 100- to 200-fold decrease in packaging is seen when gpfi is omitted. gpfi is shown to act at and/or after the stage in packaging where ...	1987	2961121
promoter recognition by escherichia coli rna polymerase: effects of base substitutions in the -10 and -35 regions.	we have constructed the prm promoter of phage lambda and eight variants, which represents intermediates in the conversion of this promoter to one that has complete homology to the consensus sequences in the -10 and -35 regions. the in vivo activity of these promoters was determined from the beta-galactosidase or galactokinase activities in cells harboring plasmids, in which the cloned promoters were driving the expression of these genes. additionally, the kinetics of the interaction of escherich ...	1987	2961367
evidence that the normal route of replication-allowed red-mediated recombination involves double-chain ends.	recombination mediated by the red pathway of bacteriophage lambda is focused towards sites of double-chain cuts. double-chain ends created either by type ii restriction enzymes acting at unmodified recognition sites or by lambda's packaging enzyme, terminase, acting at cos are utilized in a manner similar to the double-chain break repair pathway of recombination in yeast. when lambda is allowed to recombine during replicative growth, spontaneous recombination is approximately evenly distributed ...	1987	2961561
some features of base pair mismatch and heterology repair in escherichia coli.	we have used artificially constructed heteroallelic heteroduplex molecules of bacteriophage lambda dna to transfect escherichia coli, and e. coli mutants deficient in various functions involved in the adenine methylation-directed mismatch repair system, mutl, muts, muth, and uvrd (mutu). analysis of the allele content of single infective centers shows that this repair system often acts on several mismatches, separated by as many as 2000 bp, on one of the strands of a heteroduplex molecule. when ...	1987	2961649
bacteriophage lambda n gene leader rna. rna processing and translational initiation signals.	the positions of rna processing events mediated by rnase iii and of two ribosome binding sites have been defined in an in vitro transcript of 321 nucleotides initiated at the major leftward promoter (pl) of bacteriophage lambda. purified rnase iii makes two specific endonucleolytic cleavages in the transcript at points 88 and 197 nucleotides from the pl start. the positions of these cuts suggest a secondary structure for the rnase iii recognition site which is similar to other rnase iii sites in ...	1987	2961741
t lymphocyte response to bacteriophage lambda repressor ci protein. recognition of the same peptide presented by ia molecules of different haplotypes.	the murine t cell response to bacteriophage lambda ci repressor protein has been investigated. isolation and characterization of class ii-restricted t cell hybridomas from balb/c and a/j mice undergoing a primary response has revealed that a single region of the protein, residues 12-26, is the immunodominant site. fine specificity analysis using truncated peptides (p12-24 and p15-26) reveals a great deal of heterogeneity at the clonal level of i-ad-restricted t cells. i-ek-restricted t cells are ...	1987	2961803
rapid processing of nitrocellulose filter lifts of bacteriophage lambda libraries.		1987	2962069
lambda cro repressor complex with or3 dna: 15n nmr observations.	15n nmr studies of the coliphage lambda cro repressor are presented. the protein has been uniformally labeled with 15n, and individual amino acids have been incorporated. although the four c-terminal residues (63-66) were not located in the original crystallographic studies of the protein [anderson, w.f., ohlendorf, d.h., takeda, y., & matthews, b.w. (1981) nature (london) 290, 754], it has been proposed that the c-terminus is involved in dna binding [ohlendorf, d.h., anderson, w.f., fisher, r.g ...	1987	2962634
induction of the heat shock response of e. coli through stabilization of sigma 32 by the phage lambda ciii protein.	the ciii protein of phage lambda favors the lysogenic response to infection by inhibiting the degradation of the lambda cii protein, which exerts the primary control on the developmental decision for lysis or lysogeny. to study the mechanism and scope of ciii-mediated regulation, we have used plasmid systems to examine the specific effect of ciii overproduction on the growth of escherichia coli and the synthesis of bacterial proteins. we have found that maximal production of ciii prolongs the he ...	1987	2962898
oop rna, produced from multicopy plasmids, inhibits lambda cii gene expression through an rnase iii-dependent mechanism.	oop rna is a major short (77 bases) transcript that is made from bacteriophage lambda dna both in vivo and in vitro. oop rna is synthesized in the opposite direction to mrna for the lambda cii gene, and the final 55 bp of the oop region overlaps the 3' end of the cii gene. we find that a multicopy plasmid containing an oop dna fragment inhibits cii expression from a derepressed prophage by approximately 100-fold, using an in vivo assay in which cii protein activates galactokinase synthesis from ...	1987	2962901
molecular cloning of treponema pallidum outer envelope fibronectin binding proteins, p1 and p2.	phages directing the synthesis of treponema pallidum fibronectin binding adhesin proteins, p1 and p2, were isolated from an embl-3 bacteriophage lambda library of t pallidum deoxyribonucleic acid (dna). the recombinant phages were identified using antisera generated to treponemal proteins purified in fibronectin-sepharose. recombinant p1 and p2 proteins possessed the same relative molecular weights as the native surface polypeptides of spirochaetes. the structural genes for these proteins were s ...	1987	2962928
[phenomenon of restriction alleviation in escherichia coli strains].	the alleviation of foreign dna restriction after treatment of cells by uv and gamma-rays or ocr+-gene product of t3, t7 phages has been studied. both uv and gamma-radiation were shown to induce in restriction alleviation of unmodified phage. the results of restriction alleviation caused by t3 and t7 ocr+-gene products have been evaluated by f-lac+ transfer efficiencies in heterologic crosses and plating of unmodified phage lambda. the phenomenon of restriction alleviation was established to depe ...	1987	2963212
nucleotide sequence of a human liver cytochrome p-450 related to the rat male specific form.	p-450 human-2 is a human cytochrome p-450 that is immunochemically related to a constitutive male-specific cytochrome p-450 (p-450-male) and the phenobarbital-inducible p-450b/e in rat liver. by screening a human liver cdna library in bacteriophage lambda gt11, we isolated a clone with an insert length of 1,847 bases (phy13). the clone was sequenced and shown to code for a protein of 487 amino acids. the n-terminal 11-amino-acid sequence was in agreement with the protein sequence of p-450 human- ...	1987	2963808
efficient recabc-dependent, homologous recombination between coliphage lambda and plasmids requires a phage ninr region gene.	a phage lambda gene that gives a 100-fold increase in recombinant frequencies for recabc pathway-mediated, phage-plasmid homologous recombination (shen and huang 1986) maps to ning (orf 204) of lambda. we call this gene rap, for recombination adept with plasmid. a similar determinant exists in charon 4a and maps in phi 80-derived sequences, between nin5 and the rz homology with lambda. the absence of the rap+ phenotype from certain lambda vectors explains the inefficiency of screening the result ...	1987	2963943
an improved method for mapping recombinant lambda phage clones.		1988	2964000
a fluorescence photobleaching study of the microsecond reorientational motions of dna.	we have conducted a polarized fluorescence photobleaching recovery (fpr) study of the rotational dynamics of ethidium azide labeled dna. polarized photobleaching experiments provide data on microsecond and millisecond molecular reorientation that complement the information available from nanosecond fluorescence depolarization studies. in polarized fpr experiments an anisotropic angular concentration of fluorophore is created by bleaching dye molecules in a preferred orientation with a short, int ...	1988	2964258
molecular cloning of an enhancer binding protein: isolation by screening of an expression library with a recognition site dna.	a novel strategy has been used to isolate a cdna clone that encodes a dna binding domain whose recognition properties overlap those of the mammalian transcription factors h2tf1 and nf-kappa b. these two factors are distinguished by their cell type distributions and their relative affinities for related sequence elements in the enhancers of the major histocompatibility complex (mhc) class i and immunoglobulin kappa chain genes. the human cdna clone was detected by screening a lambda phage express ...	1988	2964277
the relationship between lipophilic-hydrophilic balance, uptake and anti-bacteriophage lambda activity of experimental anti-tumour bisquaternary salts.	the uptake by escherichia coli of a series of bisquaternary experimental anti-tumour agents (quinolinium 4-[p-9(-pyridylamino)phenylcarbamoyl]-aniline-bisalkyl dibromides) has been measured both by association of radiolabelled compounds and their inhibition of the vegetative replication of bacteriophage lambda (after heat inactivation of the phage repressor) as a measure of biologically effective intracellular drug concentration. uptake of these compounds was correlated with biological effect, a ...	1988	2964283
[construction and properties of the expression vector based on the temperature-regulated p'r promoter in phage lambda dna].	plasmid expression vector using the temperature-regulated promoter p'r of bacteriophage lambda is described. the vector carries a combination of two regions of lambda ci857indgenome, that contain: 1) gene ci and promoter pr, and 2) gene q and promoter p'r. transcription or gene q is initiated at promoter pr, which is controlled by ci857 repressor. the q gene product acts as a positive regulator of rna synthesis from p'r. at 37 degrees c, sufficient amounts of protein q are synthesised to initiat ...	1987	2964824
the overproduction of dna terminase of coliphage lambda.	an artificial operon containing the genes coding for the two subunits of lambda dna terminase, nul and a, has been constructed. derivatives of plasmid pbr322 served as the cloning vehicles. the transcription is driven by the pl promoter of phage lambda, and translation of the terminase genes was made efficient by the replacement of the wild-type ribosome-binding sites for those of lambda genes cii and/or d. the operon also carries the ol operator, and this enables regulation of its expression by ...	1987	2965061
functional elements of dna upstream from the integrase operon that are conserved in bacteriophages 434 and lambda.	a 1488-bp restriction fragment of bacteriophage 434 dna contains the integrase promoter and an adjacent nucleotide sequence (t'i) resembling a rho-independent terminator. to identify and quantitate transcription termination, dna segments were cloned into a plasmid between the galactose promoter and assayable galactokinase gene and tested for termination. whereas the entire fragment effectively terminated transcription, a 331-bp restriction fragment containing the t'i terminator had only weak ter ...	1987	2965063
structure of the rabbit fast-twitch skeletal muscle ca2+-atpase gene.	we have isolated two genomic clones which together encode the ca2+-atpase of rabbit fast-twitch skeletal muscle sarcoplasmic reticulum. one of the two 16.5 kilobase (kb) genomic inserts in the lambda phage vector charon 4a contains 23 exons extending from the polyadenylation site at the 3' end of the atpase gene to within 38 nucleotides of the translation initiation codon in the 5' exon. an overlapping genomic insert of 16.5 kb contains the remainder of the 5' exon and a further 8 kb of upstream ...	1988	2965149
prediction of an atp reactive center in the small subunit, gpnu1, of the phage lambda terminase enzyme.	the small subunit of the bacteriophage lambda terminase enzyme, the product of the phage's nu1 gene, is shown to contain amino acid segments homologous to those present in a large number of atpases. in keeping with these predictions, the purified protein has been found to hydrolyze atp with a relatively low turnover number. terminase holoenzyme is a known atpase, and the biochemical significance of an atp-interactive center situated in the gpnu1 subunit is discussed.	1988	2965248
dominance in lambda s mutations and evidence for translational control.	phenotypic analysis of a collection of point mutations in the lysis gene s of bacteriophage lambda indicates that many of the s alleles exhibit at least partially dominant character, suggesting that the s gene product (gps) must oligomerize to achieve its lethal membrane effect. moreover, mutations found 5' to the coding sequence also show a dominant character and appear to define a site, designated sdi (structure directed initiation) where mrna secondary structure controls the choice of initiat ...	1988	2965249
bacteriophage lambda dna packaging. the product of the fi gene promotes the incorporation of the prohead to the dna-terminase complex.	lambda dna packaging in vitro can be examined in stages. in a first step, lambda dna interacts with terminase to form a dna-enzyme complex, called complex i. upon addition of proheads, in a second step, a ternary complex, complex ii, containing dna, terminase and the prohead is formed. finally, upon addition of the rest of the morphogenetic components, complete phages are assembled. we have investigated the effect of the fi gene product (gpfi) in these reactions and found that a stimulation in p ...	1988	2965251
evidence for prokaryotic transcription and translation control regions in the human factor ix gene.	a human factor ix cdna clone isolated from a liver cdna library constructed in phage lambda gt11 vector was shown to express factor ix protein in escherichia coli. a factor ix immunospecific protein of 46.8 kda was expressed, but was not a beta-galactosidase-factor ix fusion protein. expression was seen when the factor ix cdna was cloned into two different vector systems, lambda gt11 and puc9, in both orientations with respect to the vector lacz promoter. the expression of factor ix was not unde ...	1987	2965665
dna damage and mutagenesis of lambda phage induced by gamma-rays.	lambda phage dna was gamma-irradiated in aqueous solution and the amount of radiation-induced strand breakage [double- and single-strand breaks and alkali-labile sites (dsb, ssb, als)] was determined. twice as much minor structural damage (ssb and als) per lethal hit was found in this dna compared with dna from irradiated phage suspensions. the in vitro irradiated dna was re-packaged into infectious particles ('pack-phage'). the induction of mutations in the ci or cii cistron was scored using so ...	1988	2965783