Publications

role of gene 8 product in morphogenesis of bacteriophage t3.	the product of gene 8 (gp8) of t3 phage is one of the minor head proteins located at the phage head-tail junction. to determine the role of gp8, an amber (8-) and four temperature-sensitive mutants (ts8) were characterized by sedimentation analysis, polyacrylamide gel electrophoresis, and extract complementation. neither dna-containing particles nor empty particles were formed in cells infected with 8-. in addition, prohead assembly was greatly reduced. prohead assembly was also blocked in cells ...	1983	6602416
restriction of bacteriophage t3 and t7 ocr+ strains by the type ii restriction endonuclease ecorv.	when e. coli cells carrying the plasmid plg13 (coding for the newly discovered type ii restriction endonuclease ecorv) are infected with phage t3 or t7, only t7 is able to replicate normally. t3 wild-type as well as its ocr- mutants are subject to dna restriction in vivo and in vitro. the ecorv enzyme cuts t3 dna at 5 sites. t7 and its ocr- mutants have no ecorv sites in their dna. in contrast to the anti-restriction activity of the t3 and t7 ocr+ gene function against type i and iii restriction ...	1983	6308393
abortive infection of f-plasmid-containing escherichia coli cells by bacterial virus t7 is determined by the right end of t7 gene 1.	phage t7 infects male (f-plasmid-carrying) escherichia coli cells abortively, whereas the closely related phage t3 grows normally. the inability or ability of phage to replicate in male host cells depends on whether the right end of gene 1 (coding for the phage-specific rna polymerase) consists of t7 or t3 dna base sequences.	1983	6338244
on the terminally redundant sequences of bacteriophage t3 dna.	the nucleotide sequences of the termini of mature dna from t3 phage were determined. a directly repeated sequence of 230 base pairs, corresponding to the terminal redundancy of t3 dna, was found in the left and right end of the genome. the sequence of the terminal regions of t3 dna was compared with that of t7 dna. there are discrete sequences with significant homology, specifically in the regions around the two ends of the terminally redundant sequences. 5'-cctaaag and its variants appear frequ ...	1983	6297159
locations and nucleotide sequences of three major class iii promoters for bacteriophage t3 rna polymerase on t3 dna.	the dna sequences of three major class iii t3 rna polymerase promoters located at 45.0, 55.0, and 64.8% on the standard t3 genetic map have been determined. the precise rna initiation sites were also determined by 5'-terminal rna sequence analysis of the transcripts synthesized from the promoter-containing dna fragments. alignment of these three class iii promoters and a previously determined t3 rna polymerase promoter at 1.05% on t3 genetic map, with start points of transcription (+1) in regist ...	1984	6319418
virus-plasmid interactions: mutants of bacteriophage t3 that abortively infect plasmid f-containing (f+) strains of escherichia coli.	bacteriophage t7 and many closely related phages abortively infect plasmid f-containing (f+) strains of escherichia coli. however phage t3, which is also closely related to t7, grows normally in f+ hosts. mutants of phage t3 that, like t7, are subject to f-mediated restriction have been isolated. these t3 mutants lack or are defective in one or both of two genes that are nonessential for phage growth in f-, wild-type strains. our results show that the products of phage t3 gene 1.1 or 1.2, or bot ...	1984	6324192
purification and properties of gene 18 product of bacteriophage t3.	two noncapsid proteins of t3 and t7 phage, the products of gene 18(gp18) and gp19, are required for dna packaging. by using in vitro complementation for dna packaging as an assay system, t3 gp18 was purified to near homogeneity from an extract prepared cells infected with a mutant of gene 19(19- extract). the purified gp18 consisted of a single polypeptide having a molecular weight of 10,000, and was eluted as dimers and higher multimers from sephadex g-75 columns. t7 gp18 was purified by the sa ...	1984	6240154
heterogeneity of the procapsid of bacteriophage t3.	like other double-stranded dna bacteriophages, bacteriophage t3 assembles a dna-free procapsid that subsequently packages the bacteriophage dna. by agarose gel electrophoresis, it has been found that the t3 procapsid has a negative electrophoretic mobility (mu) that progressively increases in magnitude by as much as 3% after assembly of the procapsid. this increase is (i) caused by an increase in the solid support-free mu (muo) of the procapsid, not a decrease in its radius, and (ii) not prevent ...	1985	4009795
sequence and analysis of the gene for bacteriophage t3 rna polymerase.	the rna polymerases encoded by bacteriophages t3 and t7 have similar structures, but exhibit nearly exclusive template specificities. we have determined the nucleotide sequence of the region of t3 dna that encodes the t3 rna polymerase (the gene 1.0 region), and have compared this sequence with the corresponding region of t7 dna. the predicted amino acid sequence of the t3 rna polymerase exhibits very few changes when compared to the t7 enzyme (82% of the residues are identical). significant dif ...	1985	3903658
purification of characterization of gene 8 product of bacteriophage t3.	the product of gene 8 (gp8) of t3 phage was purified from proheads, heads, and extract prepared from cells infected with a mutant defective in gene 10 (major head protein) (10- extract). gp8, when purified by hydrophobic column chromatography from proheads solubilized by guanidine hydrochloride, did not show any ordered structure. gp8 from heads ruptured by sucrose shock sedimented with a sedimentation coefficient of 20 s (20 s assembly). electron micrography of 20 s assemblies showed ring struc ...	1985	3904172
isolation and characterization of bacteriophage t3/t7 hybrids and their use in studies on molecular basis of dna-packaging specificity.	in vitro dna-packaging systems of bacteriophages t3 and t7 packaged homologous dna more efficiently than heterologous dna. packaging of phage dna proceeds by way of concatemeric intermediates (h. fujisawa, j. miyazaki, and t. minagawa (1978), virology 87, 394-400). the conversion of mature homologous and heterologous dnas to concatemers was efficient in both the t3- and t7-packaging systems. in vitro complementation experiments indicate that the gene 19 product (gp19) specifies which dna enters ...	1985	2998056
genetic analysis of subunit assembly of the tail fiber of bacteriophage t3.	bacteriophage t3 virions have six tail fibers composed of the product of gene 17 (gp17). each tail fiber is a trimer of gp17 polypeptide. to characterize the assembly process of the tail fiber, temperature-sensitive (ts) mutants of gene 17 (ts17) were analyzed by sds-polyacrylamide gel electrophoresis and by extract complementation. newly synthesized gp17 polypeptide chains matured to sds-resistant native trimers with a half time of about 7.5 min at 30 degrees. although all ts17 mutants had simi ...	1985	2930941
purification and characterization of gene 17 product of bacteriophage t3.	tail fiber proteins of bacteriophage t3 are encoded by gene 17. by using in vitro complementation for phage assembly as an assay, the product of gene 17 (gp17) was purified to near homogeneity from cells infected with a double mutant of t3 defective in dna synthesis and head assembly. the purified gp17 consists of a single polypeptide having a molecular weight of 67,000. electron microscopy of the purified gp17 showed a fiber structure similar to the tail fiber in a virion. the subunit structure ...	1985	2930942
nucleotide sequence of a major class-iii phage-t3 rna-polymerase promoter located at 98.0% of phage-t3 genetic map.	the entire nucleotide sequence of a 409-bp hincii fragment, located within the mboi-e fragment on bacteriophage t3 dna and containing a major class-iii t3 rna polymerase promoter positioned at 98% on the standard t3 genetic map, has been determined. alignment of this class-iii promoter with previously determined t3 rna polymerase promoters, with start points of transcription (+1) in register, indicates high degree of sequence conservation between position -16 to +6 among all t3 rna polymerase pr ...	1985	2989096
sequence of a region near the left end of bacteriophage t3 dna that contains three promoters for the e. coli rna polymerase.		1986	3520490
expression of the unassembled capsid protein during infection of shigella sonnei by bacteriophage t7 results in dna damage that is repairable by bacteriophage t3, but not t7, dna ligase.	the abortive infection of bacteriophage t7 in shigella sonnei d2 371-48 is characterized by a premature inhibition of phage dna replication and nucleolytic breakdown of all phage dna. mutations in t7 gene 10 which are recessive to the presence of the wild-type allele can alleviate the restriction of phage growth. phage t3 productively infects s. sonnei d2 371-48, as does a t7-t3 hybrid phage that contains, in particular, a gene 10 of t7 origin. it is the presence of t3 dna ligase that allows pha ...	1986	3522545
overproduction and purification of the products of bacteriophage t3 genes 18 and 19, two genes involved in dna packaging.	the products of gene 18 (gp18) and gene 19 (gp19) of bacteriophage t3 are noncapsid proteins involved in dna packaging. a restriction fragment containing gene 18 or 19 was cloned into the plasmid vector pnt45 under the control of the inducible leftward promoter (pl) of phage lambda. induction of transcription of gene 18 or 19 by derepression of the pl promoter led to the synthesis of a high level of gp18 or gp19. by using complementation of t3 dna packaging in vitro as an assay, gp18 and gp19 we ...	1986	3962187
subunit arrangement of the tail fiber of bacteriophage t3.	a tail fiber of phage t3 is a trimer of the product of gene 17 (gp17). treatment of t3 phage particles with chymotrypsin resulted in cleavage of only the tail fiber protein, at a site near the distal end of the fiber, causing a decrease of about 10% in the size of gp17 in the treated virion. the n-terminal amino acid sequences of intact and cleaved tail fiber proteins were identical and corresponded to that deduced from the nucleotide sequence of gene 17 except for the absence of the initiation ...	1986	2943077
specific binding of monomeric bacteriophage t3 and t7 rna polymerases to their respective cognate promoters requires the initiating ribonucleoside triphosphate (gtp).	bacteriophage t3 and t7 rna polymerases are monomeric proteins of mr of about 100,000. each polymerase has stringent specificity for its own promoters that is present only on the homologous phage dna template. neither enzyme recognizes the heterologous phage promoters or escherichia coli rna polymerase promoters. in the present study, the interaction of t3 and t7 rna polymerases with their respective cognate promoters was studied by dnase i footprinting techniques. these studies revealed an abso ...	1986	2946871
genetic and biochemical analysis of shigella dysenteriae 1 o antigen polysaccharide biosynthesis in escherichia coli k-12: structure and functions of the rfb gene cluster.	the genetic organization and functions of the shigella dysenteriae 1 rfb gene cluster, which specifies the somatic o antigen in this organism, have been studied in escherichia coli k-12 by insertion and deletion mutagenesis of pss9, a pbr322 hybrid containing the shigella rfb genes. on the basis of the sensitivity/resistance to rough-specific bacteriophage t3 of e. coli k-12 derivatives containing mutant pss9 plasmids, of the banding patterns and immunoreactivity of lps isolated from such deriva ...	1986	2469933
cloning and sequencing of the genetic right end of bacteriophage t3 dna.	the genetic right end of phage t3 dna, from the beginning of gene 17, was cloned and sequenced. genes 17, 18, and 19 were identified by comparing the sequence with the genetic map and by comparing the calculated and observed molecular weights of gene products. n-terminal amino acid sequence of the gene 17 product (gp17) predicted from the nucleotide sequence was consistent with the data from the analysis of purified gp17. gene 17.5 was identified as the lysis gene on the basis of the presence of ...	1986	3010556
cloning and expression of the bacteriophage t3 rna polymerase gene.	the gene that encodes the rna polymerase of bacteriophage t3 (gene 1) has been cloned into a pbr322 derivative under the control of an inducible lacuv5 promoter. large quantities of the protein are synthesized after induction of cells that carry this plasmid. rna polymerase purified from these overproducing cells selectively initiates transcription from t3 promoter sequences as demonstrated by transcription of a dual promoter plasmid that carries both t3 and t7 promoters. cells that carry the t3 ...	1986	3011596
[bacteriophages t3 and t7: transcription-dependent mechanism of phage dna transport into the cell during infection].	the mechanism by which bacteriophage t3 dna is transported into the e. coli cell during infection was studied. the data obtained testify that bacteriophage t3, similarly to what we have earlier found for bacteriophage t7, introduces its dna into the infected cell is a transcription-dependent way. a detailed discussion is presented on the occurrence of the transcription-coupled transport of viral dna into the infected cell and on a number of general issues concerning the transport functions of te ...	1986	3517620
a defined in vitro system for packaging of bacteriophage t3 dna.	using purified components, we have constructed an in vitro system for packaging of mature phage t3 dna. in addition to mature t3 dna, the system contained t3 proheads and the products of gene 18 (gp18) and gene 19 (gp19). the reaction required mg2+, atp, and polyvinyl alcohol. spermidine was stimulatory but not absolutely required for the packaging reaction. polyvinyl alcohol could be replaced by polyethylene glycol. the packaging efficiency decreased with decreasing molecular weight of the poly ...	1986	3754362
bacteriophage t3 gene 8 product oligomer structure.	the structure of the connector of bacteriophage t3 (built up by the product of gene 8) has been studied in two dimensions by combined use of translational and rotational image filtering procedures applied to tetragonal ordered aggregates of the former oligomers. this analysis, performed up to 1/1.6 nm-1 resolution, has revealed the existence of a 12-fold symmetry in the outermost region of the specimen (mainly between radii 5.2 and 6.7 nm), a 6-fold one in the inner region (between radii 1.7 and ...	1986	3782924
characterization of the bacteriophage t3 dna packaging reaction in vitro in a defined system.	the bacteriophage t3 dna packaging system in vitro defined here is composed of purified proheads and two non-capsid proteins, the products of genes 18 and 19 (gp18 and gp19). in this system, a precursor complex (50 s complex) accumulates in the presence of adenosine 5'-o-(3'-thiotriphosphate) (atp-gamma-s), a non-hydrolyzable analog of atp. the 50 s complex is converted to a filled head in the presence of atp. the conversion of the 50 s complex, formed by preincubation with atp-gamma-s, to the m ...	1987	3316664
tau factor from escherichia coli mediates accurate and efficient termination of transcription at the bacteriophage t3 early termination site in vitro.	the termination signal that limits transcription through the early region of bacteriophage t3 (t3te) has been cloned and sequenced. the nucleotide sequence of t3te is identical with that of t7te, with the exception of a single g to u substitution in the 3' tail of the terminated transcript, and addition of an ac to the loop in the terminator stem-loop, enlarging the loop to six residues. previous studies of the properties of t3te have shown that this site is rho independent and is highly efficie ...	1987	3323530
characterization of atpase activity of a defined in vitro system for packaging of bacteriophage t3 dna.	we have developed a defined in vitro system for packaging phage t3 dna which is composed of purified proheads and the noncapsid proteins gp18 and gp19, products of genes 18 and 19 (k. hamada, h. fujisawa, and t. minagawa, 1986, virology 151, 119-123). the in vitro system displayed an atpase activity. the requirements for atpase activity were the same as those for dna packaging. atpase was inhibited by a nonhydrolyzable atp analog, adenosine-5'-o-(3'-thiotriphosphate) (atp-gamma-s). atpase activi ...	1987	2956757
[host-dependent modifications of bacteriophage t3 expressing changes in adsorption properties (serological study)].	the ability of the bacteriophage t3 to adsorb on the host cells of escherichia coli w1655 changes depending on the host strain in which the phage was propagated before. this phenomenon is termed "non-classical" host-controlled modification in contrast to "classical" dna modification. we demonstrate here that t3 phages with various non-classical modifications as well as the host range mutant t3hw differ from each other in the antigenic determinants of the phage adsorption protein.	1987	2442603
sequence of a conditionally essential region of bacteriophage t3, including the primary origin of dna replication.	the 3526 base-pair nucleotide sequence from near the end of bacteriophage t3 gene 1 to within the coding sequence of gene 2.5 is given. it includes the complete coding sequences for nine known or presumptive proteins, most of which are only conditionally essential for phage growth. the sequence includes five promoters for the phage rna polymerase, the terminator for early (host enzyme-catalyzed) transcription, and two recognition sites for rnaase iii. the primary origin of t3 dna replication tha ...	1987	3586029
early events in dna packaging in a defined in vitro system of bacteriophage t3.	we have developed a defined in vitro system for packaging phage t3 dna which is composed of purified proheads and the noncapsid proteins gp18 and gp19, products of genes 18 and 19. the reaction requires mg2+, atp, and polyethylene glycol and is inhibited by a nonhydrolyzable atp analog, adenosine-5'-o-(3'-thiotriphosphate) (atp-gamma-s) (k. hamada, h. fujisawa, and t. minagawa, 1986, virology 151, 119-123). about 30% of added mature t3 dna was packaged into heads in the defined system. a complex ...	1987	3617498
on the molecular mechanism of dna translocation during in vitro packaging of bacteriophage t3 dna.	the process of packaging of bacteriophage t3 dna in a defined in vitro system can be separated into two stages: formation of a precursor complex (50 s complex) in the presence of adenosine-5'-o-(3'-thiotriphosphate) (atp-gamma-s) and subsequent translocation of dna into the head by the addition of atp. packaged dna exits when dna translocation is interrupted by the addition of atp-gamma-s (m. shibata, h. fujisawa, and t. minagawa, 1987, virology, in press; m. shibata, h. fujisawa, and t. minagaw ...	1987	3672929
ecorii can be activated to cleave refractory dna recognition sites.	ecorii restriction sites [5'-cc(a/t)gg] in phage t3 and t7 dna are refractory to cleavage by ecorii, but become sensitive to cleavage in the presence of dnas which contain an abundance of ecorii sensitive sites (e.g. pbr322 or lambda dna). studies using fragments of pbr322 containing different numbers of ecorii sites show that the susceptibility to ecorii cleavage is proportional to the number of sites in the individual fragment. we postulate that ecorii is the prototype of restriction endonucle ...	1988	2836807
three-alpha-helical coiled-coil, as a proposed model for a thin rod segment of bacteriophage t3 tail fibers.	three-stranded alpha-helical coiled-coil was considered as a model for a thin proximal rod of t3 phage tail fiber on the basis of amino acid sequence. a segment of residues from ca. 130th to 270th was shown to have a unique feature to satisfy the required conditions of the coiled-coil, and to give the observed geometry.	1988	2963635
bacteriophage t3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions.	the bacteriophage t3 connector, which consists of 12 copies of protein gp8, has been studied by image processing of electron micrographs from negatively stained ordered aggregates. a three-dimensional reconstruction of t3 connectors was obtained by collection of tilted views and using the direct fourier method, up to 2.3 nm resolution. the reconstructed unit cell contains two connectors whose main structural features are essentially identical, but facing in opposite directions. the t3 connector ...	1988	3262165
packaging and transduction of non-t3 dna by bacteriophage t3.	a defined in vitro system for packaging t3 dna also packaged other linear dnas, including t4, lambda, and plasmid dnas. the packaging capacity was determined to be 40 kb (kilobase pairs) by measuring the packaged length of t4 dna. packaged lambda and plasmid dnas were injected into host cells to form plaques and transductants, respectively. the yield of transducers increased by using artificially ligated plasmid oligomers. the t3 mutant in gene 3 endonuclease (t3 3-) packaged plasmid dna during ...	1988	2972112
high efficiency vectors for cosmid microcloning and genomic analysis.	we describe the construction and use of cosmid vectors designed for microcloning, gene isolation and genomic mapping starting from submicrogram amounts of eukaryotic dna. these vectors contain (1) multiple cos sites to allow for simple and efficient cloning using non size-selected dna; (2) bacteriophage t3 and t7 promoter sequences flanking the cloning site to allow for the synthesis of end-specific probes for chromosome walking; (3) a selectable gene for immediate gene transfer of cosmid dna in ...	1989	2777090
mitochondrial rna polymerase: dual role in transcription and replication.	mitochondrial rna polymerases from humans, xenopus laevis and saccharomyces cerevisiae are very similar in protein composition and function. they consist of a nonspecific core rna polymerase and a protein factor that confers promoter selectivity on the core component, and they participate in transcription as well as in dna replication. amino acid sequence comparisons indicate that the yeast mitochondrial core component is related to bacteriophage t3 and t7 rna polymerases; mitochondrial and phag ...	1989	2667219
nucleotide sequence and complementation studies of the gene 10 region of bacteriophage t3.	the nucleotide sequence of bacteriophage t3 gene 10 and surrounding regulatory elements has been determined and compared to the analogous region of bacteriophage t7. t3 genes 9, 10 and 11 have been shown to complement t7 mutants. the dna sequences of t3 and t7 gene 10a are homologous, as are the amino acid sequences of the respective products. the translational shift to the -1 frame is predicted to occur at the same position in gene 10 of t3 and t7, though different nucleotide sequences are prob ...	1989	2760923
physical mapping of complex genomes by cosmid multiplex analysis.	a rapid and powerful approach for linking individual clones of a cosmid library and the assembly of a large physical map is presented, which depends on the simultaneous analysis of many cosmid clones for overlapping regions. this method uses cosmid vectors that contain endogenous bacteriophage t3 and t7 promoters to allow for the identification of overlapping clones through the synthesis of end-specific rna probes. a genomic library is constructed and organized as an ordered matrix such that eac ...	1989	2740339
synthesis of the capsid protein inhibits development of bacteriophage t3 mutants that abortively infect f plasmid-containing cells.	mutants of bacteriophage t3 that lack gene 1.2 resemble wild-type phage t7 in that they are unable productively to infect f plasmid-containing cells of escherichia coli. pseudorevertants of a t3 gene 1.2 deletion mutant that have regained the ability to plate efficiently on male cells have been isolated and characterized. at least two mutations in the gene for the major capsid protein are necessary for these phages to bypass f-mediated restriction. one mutation serves to reduce the rate of synth ...	1989	2668535
regulated expression of foreign genes in mammalian cells under the control of coliphage t3 rna polymerase and lac repressor.	systems that stringently regulate the expression of individual genes within a complex genetic background have contributed greatly to the analysis of gene function. in this report the development of a highly regulated expression system in mammalian cells is described in which transcription of a foreign gene is mediated by the bacteriophage t3 rna polymerase under the control of the escherichia coli lac repressor. rabbit kidney cell lines have been established that constitutively express the phage ...	1989	2664783
abortive initiation by bacteriophage t3 and t7 rna polymerases under conditions of limiting substrate.	initiation of rna synthesis by the phage polymerases is abortive if the concentration of pyrimidine triphosphates is limiting. under abortive initiation conditions the polymerases repeatedly initiate transcription but produce ribooligonucleotides that terminate just prior to the first occurrence of the limiting substrate. abortive initiation is most severe if the limiting substrate occurs within the first 8-12 nucleotides of the nascent rna chain and is particularly evident when ump is limiting. ...	1989	2646596
sequence of bacteriophage t3 dna from gene 2.5 through gene 9.	the nucleotide sequence of bacteriophage t3 dna, from gene 2.5 through gene 9 has been determined. in addition to regulatory sites, the sequence predicts 19 close-packed genes plus two genes that overlap, in a different reading frame, another gene. the majority of these genes are highly homologous to those in the corresponding region of bacteriophage t7. however, there are some genes that are present in one, but not the other, phage. these apparent deletions are almost exactly gene size and thus ...	1989	2614843
relative efficiency of utilization of promoter and termination sites by bacteriophage t3 rna polymerase.	bacteriophage t3 rna polymerase promoters have been classified as class ii and class iii on the basis of their relative location in t3 dna as well as on the function of the protein products encoded by the messages transcribed from them. in the present work, the efficiency of utilization of several class ii and class iii promoters by bacteriophage t3 rna polymerase was compared with regard to (a) rate of initiation of transcription as determined by [32p]ppi exchange with gtp; (b) complex formatio ...	1989	2547791
identification of a region of the bacteriophage t3 and t7 rna polymerases that determines promoter specificity.	bacteriophages t7 and t3 encode dna-dependent rna polymerases that are 82% homologous, yet exhibit a high degree of specificity for their own promoters. a region of the rna polymerase gene (gene 1) that is responsible for this specificity has been localized using two approaches. first, the rna polymerase genes of recombinant t7 x t3 phage that had been generated in other laboratories in studies of phage polymerase specificity were characterized by restriction enzyme mapping. this approach locali ...	1990	2204707
discrimination between bacteriophage t3 and t7 promoters by the t3 and t7 rna polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site.	the bacteriophage t3 and t7 rna polymerases are closely related, yet are highly specific for their own promoter sequences. to understand the basis of this specificity, t7 promoter variant that contain substitutions of t3-specific base-pairs at one or more positions within the t7 promoter consensus sequence were synthesized and cloned. template competition assays between variant and consensus promoters demonstrate that the primary determinants of promoter specificity are located in the region fro ...	1990	2204706
specific interaction of the murine transcription termination factor ttf i with class-i rna polymerases.	the 18-base-pair sequence element aggtcgaccagtactccg (the sal box) signals termination of mouse ribosomal gene transcription. this sequence is recognized by a sequence-specific dna-binding protein, ttf i, which mediates the termination of transcription by rna polymerase i (pol i). subsequently, the ends of the primary transcripts are trimmed by 10 nucleotides in a sequence-dependent 3'-terminal processing reaction. we have now investigated whether ttf i bound to its target sequence will block el ...	1990	2181320
directional cloning of cdna using a selectable sfii cassette.	to increase the efficiency of directionally cloning cdna, we have constructed a pair of vectors and devised a cdna cloning strategy that improves upon previously published methods. the vectors, plib: az and plib: za, have two unique (distinct religation specificities; ggccn/nnnnggcc) sfii sites (sfii.a and sfii.b) flanking a stuffer fragment which contains the tetracycline-resistance element. these vectors permit the directional cloning of cdna in both sense (plib: az) and antisense (plib: za) o ...	1990	2165017
synthesis of functional mrna in mammalian cells by bacteriophage t3 rna polymerase.	we found that the 5' nontranslated leader sequence from encephalomyocarditis virus (emcv) allowed transcripts that were synthesized by the t3 rna polymerase in mammalian cells to be translated in a cap-independent fashion. stable mouse cell lines that carry the t3 rna polymerase gene expressed the chloramphenicol acetyltransferase (cat) gene under the control of a phage promoter when the cat gene was fused to the emcv leader and introduced into the cells by transient dna uptake. the level of gen ...	1990	2167433
regulated expression of nuclear genes by t3 rna polymerase and lac repressor, using recombinant vaccinia virus vectors.	recombinant vaccinia viruses that express the bacteriophage t3 rna polymerase (vv-t3pol) or the escherichia coli lac repressor (vv-laci) under control of the early-late vaccinia promoter p7.5 were constructed. to determine whether phage polymerase and lac repressor can function in the nucleus of mammalian cells, the bacterial chloramphenicol acetyltransferase (cat) gene was cloned downstream of a t3 promoter (pt3-cat) or downstream of a t3 promoter-lac operator fusion element (pt3olac-cat), and ...	1990	2204724
in vitro cleavage of the concatemer joint of bacteriophage t3 dna.	mature dna from phage t3 or t7 is a linear duplex dna with direct repeats at its ends known as "terminally redundant sequences." the dna of these phages is synthesized as concatemers in which unit length molecules are joined together in a head-to-tail fashion through the terminally redundant sequences and processed to form mature dna with coupling to dna packaging. when linearized plasmid dna carrying a concatemer joint, a terminally redundant sequence and its flanking sequences from the concate ...	1990	2294641
infectious measles virus from cloned cdna.	the study of measles virus (mv) and of negative strand rna viruses in general has been hampered by the lack of an experimental system for genetic manipulation. here we describe a procedure for generating infectious mv from cloned mv cdna. first we assembled a genetically marked dna copy of the mv genome in plasmids, under the control of phage t3 or t7 promoters, allowing production of transcripts almost identical to the mv genome or antigenome. incubation of these linearized plasmid dnas with th ...	1990	2303032
bacteriophage t7 morphogenesis and gene 10 frameshifting in escherichia coli showing different degrees of ribosomal fidelity.	bacteriophage t7 infection has been studied in escherichia coli strains showing both increased and decreased ribosome fidelity and in the presence of streptomycin, which stimulates translational misreading, in an effort to determine effects on the apparent programmed translational frameshift that occurs during synthesis of the gene 10 capsid protein. quantitation of the protein bands from sds-page failed to detect any significant effects on the amounts of the shifted 10b protein relative to the ...	1991	1766436
genes 1.2 and 10 of bacteriophages t3 and t7 determine the permeability lesions observed in infected cells of escherichia coli expressing the f plasmid gene pifa.	infections of f plasmid-containing strains of escherichia coli by bacteriophage t7 result in membrane damage that allows nucleotides to exude from the infected cell into the culture medium. only pifa of the f pif operon is necessary for "leakiness" of the t7-infected cell. expression of either t7 gene 1.2 or gene 10 is sufficient to cause leakiness, since infections by phage containing null mutations in both of these genes do not result in permeability changes of the f-containing cell. even in t ...	1991	1917875
frameshifting in gene 10 of bacteriophage t7.	gene 10 of bacteriophage t7, which encodes the most abundant capsid protein, has two products: a major product, 10a (36 kda), and a minor product, 10b (41 kda). 10b is produced by frameshifting into the -1 frame near the end of the 10a coding frame and is incorporated into the capsid. the frameshift occurs at a frequency of about 10% and is conserved in bacteriophage t3. this study shows that sequences important to frameshifting include the originally proposed frameshift site, consisting of over ...	1991	1938901
analysis of interactions among factors involved in the bacteriophage t3 dna packaging reaction in a defined in vitro system.	during head assembly of phage t3, dna is packaged into the cavity of a preformed protein shell, called the prohead, with the aid of noncapsid, packaging proteins, the products of genes 18 and 19 (gp18 and gp19). gp18 and gp19 separately form complexes with dna and proheads, respectively. these complexes associate to form a precursor which can be converted to filled heads by the addition of atp. interactions among factors involved in dna packaging were analyzed. in the presence of atp, gp19 forme ...	1991	1962450
dissection of functional domains of the packaging protein of bacteriophage t3 by site-directed mutagenesis.	intracellular phage t3 dna is synthesized as a concatemer in which unit-length molecules are joined together in head-to-tail fashion through terminally redundant sequences. during packaging of dna, mature monomers are cut from the concatemer. the cutting is obligatorily coupled to dna packaging. the packaging of phage dna is under the control of a pair of noncapsid proteins, called packaging proteins, gp 18 and gp19. gp19 is an atp-binding protein that plays multiple roles in dna packaging. gp19 ...	1991	1989388
amino acid sequence of the bacteriophage t5 gene a2 protein.	the complete amino acid sequence of the bacteriophage t5-encoded gene a2 protein was determined by protein sequencing. the 134-residue sequence is closely similar to that reported for the product of gene a2-a3 of bacteriophage bf23. segments of the sequence are similar to segments of bacteriophage t4 gene 32 protein, bacteriophage t3 rna polymerase, and the protein encoded by the host gene responsible for isoenzyme conversion of alkaline phosphatase. the similarity of residues 26-46 to a portion ...	1991	2059212
dna-dependent rna polymerase from bacteriophage t3 transcribes and amplifies an rna template in vitro.	rna-based amplification systems that have been recently described are dependent upon the presence of more than one enzyme. in an attempt to minimize the number of polymerases required for efficient amplification, we have studied the template specificity of bacteriophage t3 rna polymerase. a synthetic bacteriophage t3 promoter was covalently attached to an rna template. the t3 promoter-rna complex was found to be selective for its native polymerase, and dependent upon the presence of all four rib ...	1991	1718821
substitution of the conserved tryptophan 31 in escherichia coli thioredoxin by site-directed mutagenesis and structure-function analysis.	all prokaryotic and eukaryotic thioredoxins contain a conserved tryptophan residue, exposed at the active site disulfide/dithiol. the role of this w31 in escherichia coli thioredoxin (trx) was studied by site-directed mutagenesis. four mutant trx with w31y, w31f, w31h, and w31a replacements were characterized. very low tryptophan fluorescence emission from the remaining w28 was observed in all mutant trx; reduction resulted in large, but variable increases (up to 11-fold) of fluorescence, to lev ...	1991	1999401
specific contacts between the bacteriophage t3, t7, and sp6 rna polymerases and their promoters.	the specificity and structural simplicity of the bacteriophage t3, t7, and sp6 rna polymerases make these enzymes particularly well suited for studies of polymerase-promoter interactions. to understand the initial recognition process between the enzyme and its promoters, dna fragments that carry phage promoters were chemically modified by three different methods: base methylation, phosphate ethylation, and base removal. the positions at which these modifications prevented or enhanced binding by ...	1991	1985921
the rnase protection assay.	a sensitive method for quantitation of mrna in gene transfer studies is mrna protection using end-labeled dna probes. in addition, this technique also provides structural information about the transcript under study (1). in vitro labeled antisense rnacan be used as an alternative to end-labeled dna probes (2,3. rna probes have attained wide popularity because of the ease of synthesis and high yield of probe in a labeling reaction. this has been made possible by the recent characterization of sin ...	1991	21416363
absence of a gene dosage effect during bacteriophage t3- and t7-coded rna polymerase synthesis.	the rates of synthesis of phage-coded rna polymerase upon infection of escherichia coli by bacteriophages t3 or t7 were measured at different mois under permissive and non-permissive conditions. at mois from 1 to 15, these rates did not vary appreciably, at mois of about 20 there was a slight depression in the synthesis rate. the reason for this absence of a positive gene dosage effect is unknown.	1992	1740385
substitution of a single bacteriophage t3 residue in bacteriophage t7 rna polymerase at position 748 results in a switch in promoter specificity.	the bacteriophage t3 and t7 rna polymerases (rnap) are closely related, yet exhibit high specificity for their own promoter sequences. in this work the primary determinant of t7 versus t3 promoter specificity has been localized to a single amino acid residue at position 748 in the t7 rnap. substitution of this residue (asn) with the corresponding residue found in t3 rnap (asp) results in a switch in promoter specificity, and specifically alters recognition of the base pairs (bp) at positions -11 ...	1992	1453460
three-dimensional structure of t3 connector purified from overexpressing bacteria.	the bacteriophage t3 connector has been purified from overexpressed protein in escherichia coli, harboring a plasmid containing the gene encoding p8 protein. the connector, which is composed of 12 copies of p8, has been crystallized in two-dimensional sheets and studied by electron microscopy from negatively stained specimens. a two-dimensional fourier filtering and averaging procedure was performed with crystalline specimens. in addition, single particle averaging techniques were used with othe ...	1992	1548694
topology and phosphorylation of soybean nodulin-26, an intrinsic protein of the peribacteroid membrane.	soybean nodulin-26, a homologue of bovine eye lens major intrinsic protein (mip-26), is an integral protein of the peribacteroid membrane in symbiotic root nodules. it comprises 271 amino acids with six potential transmembrane domains and lacks an amino-terminal signal sequence. a full-length nodulin-26 cdna and its various deletion derivatives were transcribed in vitro after linking them to bacteriophage t3 promoter. in vitro translation of these transcripts in a rabbit reticulocyte lysate, in ...	1992	1629242
partial characterization of coliphage wpk and a comparison with coliphage t3.	coliphage wpk was originally isolated from sewage in kiel, germany, because its plaque diameter continued to expand for days. electron microscopy revealed an isometric capsid with dimensions of 54 nm between opposite apices, and a short, noncontractile tail 16 nm long, placing phage wpk into morphogroup c1. the nucleic acid of phage wpk was linear double stranded dna. the host ranges of phages wpk and t3 were identical. of ten e. coli strains tested for host range, two were resistant and of eigh ...	1992	1584081
structure analysis of the 5' external transcribed spacer of the precursor ribosomal rna from saccharomyces cerevisiae.	full-length precursor ribosomal rna molecules were produced in vitro using as a template, a plasmid containing the yeast 35 s pre-rrna gene under the control of the phage t3 promoter. the higher-order structure of the 5'-external transcribed spacer (5' ets) sequence in the 35s pre-rrna molecule was studied using dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate, rnase t1 and rnase v1 as structure-sensitive probes. modified residues were detected by primer ...	1992	1469716
dna sequences necessary for packaging bacteriophage t3 dna.	a recombinant plasmid, puce1-tr, carrying a target for processing of the concatemer joint (tr) and sequences to the left of the target (e1), is efficiently packaged into transducing particles during t3 phage infection. using this plasmid packaging/transduction system, the minimal sequences necessary for packaging of t3 dna were determined. the tr sequence contains the targets for initiation cleavage and termination cleavage of concatemer processing (paccr and paccl, respectively). a plasmid lack ...	1992	1546467
[study of the activation mechanism of ecorii restriction endonuclease using synthetic dna duplexes].	efficiency of the cleavage of dna duplexes with one recognition site by ecorii restriction endonuclease decreases with the increase in substrate length. dna duplexes more than 215 base pairs long are practically not cleaved by this enzyme. it has been found that in the presence of substrates 11-14 base pairs long acceleration of hydrolysis of extended single-site substrates by ecorii enzyme is observed. the level of hydrolysis stimulation is dependent on the length and concentration of the secon ...	1993	8316237
dna packaging atpase of bacteriophage t3.	a defined in vitro dna packaging system of phage t3, which is composed of purified proheads and two packaging proteins, the products of genes 18 and 19 (gp18 and gp19, respectively), displayed a dna-dependent atpase activity. atp was hydrolyzed to adp and pi. the atpase activity was stimulated by nonpackageable dna, such as single-stranded or circular dna, or rna (nonpac-atpase). among the inhibitors of dna packaging, actinomycin d specifically inhibited the atpase activity that was tightly coup ...	1993	8460483
analysis of functional domains of the packaging proteins of bacteriophage t3 by site-directed mutagenesis.	intracellular phage t3 dna is synthesized as a concatemer in which unit-length molecules are jointed together in head-to-tail fashion through terminally redundant sequences. the concatemeric dna is processed and packaged into the prohead with the aid of non-capsid proteins, gp18 and gp19. we have developed a defined system, composed of purified gp18, gp19 and proheads, and a crude system, composed of lysates of t3 infected cells, for in vitro packaging of t3 dna. the defined system displays an a ...	1994	8289246
a novel method for generating nested deletions using the in vitro bacteriophage t3 dna packaging system.	to sequence a dna segment inserted into a cosmid vector under the directed sequencing strategy, we established a simple and rapid method for generating nested deletions which uses the in vitro packaging system of bacteriophage t3 dna. the principle is based on the previous finding that this system can translocate any linear double-stranded dna up to 40 kb into the phage capsid in a time-dependent manner and the encapsulated dna becomes dnase-resistant. for this purpose, we constructed a cosmid v ...	1994	7719924
a novel tn10 tetracycline regulon system controlling expression of the bacteriophage t3 gene encoding s-adenosyl-l-methionine hydrolase.	to study the effects of in vivo dna methylation, we have developed an inducible system to control the intracellular concentration of s-adenosyl-l-methionine (adomet). the product of the bacteriophage t3 adomet hydrolase-encoding gene (amh), which degrades adomet to l-homoserine and 5'-methylthioadenosine, was employed to lower adomet concentrations in vivo. the amh gene was placed downstream from the inducible teta promoter of the tn10 tetracycline regulon substituting for most of the teta gene. ...	1994	7926842
gene expression mediated by bacteriophage t3 and t7 rna polymerases in transgenic trypanosomes.	messenger rnas of higher eukaryotes share a functionally essential 5' monomethyl cap structure generated during a reaction that is linked exclusively to rna polymerase ii transcription. in unicellular parasites belonging to the kinetoplastida, however, mrnas acquire their 5' cap through a trans-splicing reaction which effectively uncouples pol ii transcription and capping. consequently functional mrnas can be produced by endogenous rna polymerase i. here we demonstrate the extension of this flex ...	1994	7937108
sequence-specific transcription arrest by peptide nucleic acid bound to the dna template strand.	the effects of pna (peptide nucleic acid) bound to double-stranded (ds) dna targets positioned downstream from phage t3 or t7 promoters in pbluescriptks+ derived plasmids on transcription by rna polymerases t3 or t7 have been studied. the dsdna targets a10, 5'-a5ga4 or 5'-a2ga2ga4, and the corresponding pnas t10, t5ct4 and t2ct2ct4 were used and the target-pna strand displacement complexes were performed in low-salt buffer, since pna does not bind efficiently to ds dna in higher salt than 50 mm. ...	1994	7958978
a functional chimeric dna primase: the cys4 zinc-binding domain of bacteriophage t3 primase fused to the helicase of bacteriophage t7.	two colinear bacteriophage t7 gene 4 proteins provide helicase and primase functions in vivo. t7 primase differs from t7 helicase by an additional 63 residues at the amino terminus. this terminal domain contains a zinc-binding motif which mediates an interaction with the basic primase recognition sequence 3'-ctg-5'. we have generated a chimeric primase in which the 81 amino-terminal residues are derived from the primase of phage t3 and the 484 carboxyl-terminal residues are those of phage t7 hel ...	1994	7991626
reduced ethylene synthesis by transgenic tomatoes expressing s-adenosylmethionine hydrolase.	we have utilized a gene from bacteriophage t3 that encodes the enzyme s-adenosylmethionine hydrolase (samase) to generate transgenic tomato plants that produce fruit with a reduced capacity to synthesize ethylene. s-adenosylmethionine (sam) is the metabolic precursor of 1-aminocyclopropane-1-carboxylic acid, the proximal precursor to ethylene. samase catalyzes the conversion of sam to methylthioadenosine and homoserine. to restrict the presence of samase to ripening fruit, the promoter from the ...	1994	7999994
conservative substitutions in the hydrophobic core of rhodobacter sphaeroides thioredoxin produce distinct functional effects.	the internal residue phe 25 in rhodobacter sphaeroides thioredoxin was changed to five amino acids (ala, val, leu, ile, tyr) by site-directed mutagenesis, and the mutant proteins were characterized in vitro and in vivo using the mutant trxa genes in an escherichia coli trxa- background. the substitution f25a severely impaired the functional properties of the enzyme. strains expressing all other mutations can grow on methionine sulfoxide with growth efficiencies of 45-60% that of the wild type at ...	1995	8580841
versatile, multi-featured plasmids for high-level expression of heterologous genes in escherichia coli: overproduction of human and murine cytokines.	we describe the construction, expression characteristics and some applications of a versatile dual-promoter expression plasmid for heterologous gene expression in escherichia coli which contains both lambda pl and pt7 promoters. furthermore, the plasmid is optimized to allow the expression of mature coding sequences without compromising the strength of the highly efficient pt7 or of the t7g10 ribosome-binding site. the effect of the the naturally occurring rna loops at both the 5' and 3' ends of ...	1995	7590329
structural and functional domains of the large subunit of the bacteriophage t3 dna packaging enzyme: importance of the c-terminal region in prohead binding.	during head assembly of phage t3, dna is packaged into a preformed protein shell, called the prohead, with the aid of non-capsid packaging proteins, the products of genes 18 and 19 (gp18 and gp19). we have developed a defined system, composed of purified gp18,gp19 and proheads for in vitro packaging of t3 dna. our previous results using the defined in vitro system indicate the sequential events in dna packaging: the packaging proteins, gp18 and gp19, bind dna and proheads, respectively. these co ...	1995	7844832
analysis of the fine structure of the prohead binding domain of the packaging protein of bacteriophage t3 using a hexapeptide, an analog of a prohead binding site.	a large subunit of bacteriophage t3 packaging enzyme, a product of gene 19 (gp19, 586 amino acid residues), binds a prohead prior to dna translocation in dna packaging. its c-terminal region (571 to 576, region i) is of crucial importance for prohead binding. to elucidate the functional role(s) of region i in dna packaging, a hexapeptide (6pt3) corresponding to the region i sequence and its variants were synthesized and their effects on dna packaging in a defined in vitro system were examined. 6 ...	1995	7645255
the significance of distance and orientation of restriction endonuclease recognition sites in viral dna genomes.	studies on phage t3 and t7 have shown that these viruses avoid restriction not only by the phage-coded ocr (and s-adenosylmethionine hydrolase) protein functions or by the complete loss of specific recognition sites for certain restriction endonucleases from their genomes, but also that there are two additional modes: resistance towards ecop15 (which recognizes a non-symmetrical sequence) is achieved by an identical orientation of all the recognition sites in the virus genome (strand bias) and i ...	1995	7669344
an improved cosmid vector for the nested deletion method using the bacteriophage t3 dna packaging system.	we constructed a new cosmid vector suitable for the previously developed nested deletion method which used the in vitro dna packaging system of bacteriophage t3. the first step of this method is linearization of a cosmid clone to be packaged, and we previously introduced cleavage at the cos site using lambda-terminase, but optimization of the reaction conditions was required for complete digestion because of its instability. in the newly constructed vector, pat5, the sites of 4 different restric ...	1996	8724852
in vitro transcripts from cloned cdnas of the lettuce infectious yellows closterovirus bipartite genomic rnas are competent for replication in nicotiana benthamiana protoplasts.	full-length cloned cdnas of lettuce infectious yellows closterovirus (liyv) rnas 1 and 2 were constructed and fused to the bacteriophage t3 rna polymerase promoter. to assess rna replication, nicotiana benthamiana protoplasts were inoculated with liyv virion rnas and liyv cdna-derived in vitro transcripts. analysis of protoplasts inoculated with liyv virion rnas or capped (m7gpppg) in vitro transcripts from liyv rna 1 and 2 cdnas showed accumulation of liyv genomic and putative subgenomic rnas ( ...	1996	8806497
sequences homologous to yeast mitochondrial and bacteriophage t3 and t7 rna polymerases are widespread throughout the eukaryotic lineage.	although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial rna polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage t3 and t7 rna polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast dna. to broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (pcr) approach designed to ampl ...	1996	8604305
a bacteriophage t3 promoter can be linked to a lethal gene without detectable toxicity for eukaryotic cells. interest for inducible transgenes.	the bacteriophage t3 promoter can be selectively transcribed by the corresponding rna polymerase in eukaryotic cells. a toxic gene can in principle be linked to this promoter in a "dormant" and innocuous transgene in a transgenic animal. in this scheme, the activating strain expresses the rna polymerase. when expression of the gene is needed in the progeny, the 2 lines are crossed. however, when a single molecule is sufficient to kill the cell--as with the diphtheria toxin--transcriptional "leak ...	1996	9091177
the gly74-->ser and ser3-->ala mutations in rhodobacter sphaeroides y thioredoxin: effects on active site reactivity and protein interaction.	in this study, we report the effects of two different substitutions in rhodobacter sphaeroides thioredoxin on two regions of the protein: the n-terminus end and the hydrophobic area implicated in protein/protein interactions. we have produced by site-directed mutagenesis r. sphaeroides thioredoxin single and double mutants in which the glycine residue at position 74 is changed to a serine and the serine at position 3 is changed to an alanine; the three mutant proteins have been purified. the two ...	1996	8654421
hypermutagenic in vitro transcription employing biased ntp pools and manganese cations.	in vitro dna-dependent rna transcription using bacteriophage t3 rna polymerase may be rendered hypermutagenic by employing biased nucleoside triphosphate (ntp) concentrations and manganese cations. using the e. coli r67 plasmid-encoded dihydrofolate reductase (dhfr) gene as target substitution rates approaching 4 x 10(-2) per base per reaction could be achieved, on a par with hypermutagenic reverse transcription. in all cases the majority of substitutions was that expected from the ntp pool bias ...	1997	9047346
[a nested deletion method for cosmid dna using the bacteriophage t3 in vitro packaging system].		1997	9185481
transcription termination by bacteriophage t3 and sp6 rna polymerases at rho-independent terminators.	transcription termination of t3 and sp6 dna-dependent rna polymerases have been studied on the dna templates containing the threonine (thr) attenuator and its variants. the thr attenuator is from the regulatory region of the thr operon of escherichia coli. the dna template, encoding the thr attenuator, contains specific features of the rho-independent terminators. it comprises a dg + dc rich dyad symmetry, encoding a stem-and-loop rna, which is followed by a poly(u) region at the 3'-end. thirtee ...	1997	9476351
in vivo evidence that s-adenosylmethionine and fatty acid synthesis intermediates are the substrates for the luxi family of autoinducer synthases.	many gram-negative bacteria synthesize n-acyl homoserine lactone autoinducer molecules as quorum-sensing signals which act as cell density-dependent regulators of gene expression. we have investigated the in vivo source of the acyl chain and homoserine lactone components of the autoinducer synthesized by the luxi homolog, trai. in escherichia coli, synthesis of n-(3-oxooctanoyl)homoserine lactone by trai was unaffected in a fadd mutant blocked in beta-oxidative fatty acid degradation. also, cond ...	1998	9573148
testing promoter activity in the trypanosome genome: isolation of a metacyclic-type vsg promoter, and unexpected insights into rna polymerase ii transcription.	in trypanosomes, most genes are arranged in polycistronic transcription units. individual mrnas are generated by 5'-trans splicing and 3' polyadenylation. remarkably, no regulation of rna polymerase ii transcription has been detected although many rnas are differentially expressed during kinetoplastid life cycles. demonstration of specific class ii promoters is complicated by the difficulty in distinguishing between genuine promoter activity and stimulation of trans splicing. using vectors that ...	1998	9709032
stereospecific differences in repair by human cell extracts of synthesized oligonucleotides containing trans-opened 7,8,9, 10-tetrahydrobenzo[a]pyrene 7,8-diol 9,10-epoxide n2-dg adduct stereoisomers located within the human k-ras codon 12 sequence.	the potent environmental carcinogen benzo[a]pyrene (bap), following enzymatic activation to enantiomeric pairs of bay-region 7,8-diol 9, 10-epoxides (the benzylic 7-hydroxyl group and epoxide oxygen are cis for de-1 diastereomers and trans for de-2 diastereomers), reacts with dna to form covalent adducts predominately at the exocyclic amino groups of purines. specific adducts, corresponding to the trans opening of each of the four optically active bap de isomers at c-10 by the n 2-amino group of ...	1999	9888796
influence of s-adenosylmethionine pool size on spontaneous mutation, dam methylation, and cell growth of escherichia coli.	escherichia coli strains that are deficient in the ada and ogt dna repair methyltransferases display an elevated spontaneous g:c-to-a:t transition mutation rate, and this increase has been attributed to mutagenic o(6)-alkylguanine lesions being formed via the alkylation of dna by endogenous metabolites. here we test the frequently cited hypothesis that s-adenosylmethionine (sam) can act as a weak alkylating agent in vivo and that it contributes to endogenous dna alkylation. by regulating the exp ...	1999	10542178
bacteriophage phiyeo3-12, specific for yersinia enterocolitica serotype o:3, is related to coliphages t3 and t7.	bacteriophage phiyeo3-12 is a lytic phage of yersinia enterocolitica serotype o:3. the phage receptor is the lipopolysaccharide o chain of this serotype that consists of the rare sugar 6-deoxy-l-altropyranose. a one-step growth curve of phiyeo3-12 revealed eclipse and latent periods of 15 and 25 min, respectively, with a burst size of about 120 pfu per infected cell. in electron microscopy phiyeo3-12 virions showed pentagonal outlines, indicating their icosahedral nature. the phage capsid was sh ...	2000	10960095
structural analysis of the bacteriophage t3 head-to-tail connector.	the connector protein of bacteriophage t3, p8, has been overexpressed in escherichia coli. purification of the oligomers built by several copies of p8 reveals a mixed population of dodecamers and tridecamers. the percentages of these two types of oligomers differ in every culture growth, indicating that assembly of this protein depends upon the conditions of the expression system. those cultures that generated a majority of dodecamers allowed, after purification of the connectors, the two-dimens ...	2000	11042085
lowering s-adenosylmethionine levels in escherichia coli modulates c-to-t transition mutations.	deoxycytosine methylase (dcm) enzyme activity causes mutagenesis in vitro either directly by enzyme-induced deamination of cytosine to uracil in the absence of the methyl donor, s-adenosylmethionine (sam), or indirectly through spontaneous deamination of [5-methyl]cytosine to thymine. using a lac reversion assay, we investigated the contribution of the first mechanism to dcm mutagenesis in vivo by lowering the levels of sam. escherichia coli sam levels were lowered by reducing sam synthetase act ...	2001	11208790
sea urchin mtdbp is a two-faced transcription termination factor with a biased polarity depending on the rna polymerase.	the sea urchin mitochondrial displacement (d)-loop binding protein mtdbp has been previously identified and cloned. the polypeptide (348 amino acids) displays a significant homology with the human mitochondrial transcription termination factor mterf. this similarity, and the observation that the 3' ends of mitochondrial rnas coded by opposite strands mapped in correspondence of mtdbp-binding sites, suggested that mtdbp could function as transcription termination factor in sea urchin mitochondria ...	2001	11713324