Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| bacteriophage lambda dna packaging: dna site requirements for termination and processivity. | bacteriophage lambda chromosomes are processively packaged into preformed shells, using end-to-end multimers of intracellular viral dna as the packaging substate. a 200 bp long dna segment, cos, contains all the sequences needed for dna packaging. the work reported here shows that efficient dna packaging termination requires cos's i2 segment, in addition to the required termination subsite, cosq, and the nicking site, cosn. efficient processivity requires cosb, in addition to cosq and cosn. an i ... | 2001 | 11478856 |
| simultaneous topographic and fluorescence imaging of single dna molecules for dna analysis with a scanning near-field optical/atomic force microscope. | high-resolution fluorescence imaging of lambda-phage dna molecules, intercalated with the dye yoyo-1, has been performed by a snom/afm based on a bent-type optical fiber probe. a modified design of the optical probe has been made, and successful near-field optical resolution has been obtained for the strongly stretched lambda-phage dna molecules. the best optical resolution was estimated at 45 nm for the dye-intercalated single lambda-dna molecules by a mean width evaluation. in our comparison b ... | 2001 | 11791570 |
| structure of the hodgkin's lymphoma-associated human cd30 gene and the influence of a microsatellite region on its expression in cd30(+) cell lines. | the cd30 antigen is a member of the tumor necrosis factor receptor (tnfr) family which is overexpressed on the surface of the tumor cells of hodgkin's lymphoma, anaplastic large cell lymphoma (alcl), and embryonal carcinoma of the testis. in this study the entire cd30 gene which is more than 24000 bp long and organized in eight exons was characterized by analyzing cosmid and phage lambda clones from human placental libraries with long-range polymerase chain reaction (pcr) and sequencing. differe ... | 2001 | 11418184 |
| numerical comparison of several approximations of the word count distribution in random sequences. | the exact distribution of word counts in random sequences and several approximations have been proposed in the past few years. the exact distribution has no theoretical limit but may require prohibitive computation time. on the other hand, approximate distributions can be rapidly calculated but, in practice, are only accurate under specific conditions. after making a survey of these distributions, we compare them according to both their accuracy and computational cost. rules are suggested for ch ... | 2001 | 11571071 |
| octamerization of lambda ci repressor is needed for effective repression of p(rm) and efficient switching from lysogeny. | the ci repressor of bacteriophage lambda is a model for the role of cooperativity in the efficient functioning of genetic switches. pairs of ci dimers interact to cooperatively occupy adjacent operator sites at o(r) and at o(l). these ci tetramers repress the lytic promoters and activate transcription of the ci gene from p(rm). ci is also able to octamerize, forming a large dna loop between o(r) and o(l), but the physiological role of this is unclear. another puzzle is that, although a dimer of ... | 2001 | 11711436 |
| cryoelectron microscopy of lambda phage dna condensates in vitreous ice: the fine structure of dna toroids. | dna toroids produced by the condensation of lambda phage dna with hexammine cobalt (iii) have been investigated by cryoelectron microscopy. image resolution obtained by this technique has allowed unprecedented views of dna packing within toroidal condensates. toroids oriented coplanar with the microscope image plane exhibit circular fringes with a repeat spacing of 2.4 nm. for some toroids these fringes are observed around almost the entire circumference of the toroid. however, for most toroids ... | 2001 | 11734630 |
| genotype versus phenotype: conflicting results in mapping a lung tumor susceptibility locus to the g7c recombination interval in the mouse mhc class iii region. | susceptibility to chemically induced lung tumorigenesis has previously been mapped to a genomic interval of 27 kb in the mhc class iii region of the mouse using two h2 (a/b) intra- h2 recombinants, b10.a(1r) and b10.a(2r). three genes are located within this interval, g7e (encoding a viral envelope protein), g7a/ vars2 (encoding valyl-trna synthetase), and g7c (a gene with unknown function). a 70 kb contig, spanning the 27 kb region and extending 20 kb either side, was constructed from lambda ph ... | 2001 | 11797099 |
| inheritance of the replication complex: a unique or common phenomenon in the control of dna replication? | early models of the regulation of initiation of dna replication by protein complexes predicted that binding of a replication initiator protein to a replicator region is required for initiation of each dna replication round, since after the initiation event the replication initiator should dissociate from dna. it was, therefore, assumed that binding of the replication initiator is a signal for triggering dna replication. however, more recent investigations have revealed that in many replicons thi ... | 2001 | 11285745 |
| polymerase chain reaction in polymeric microchips: dna amplification in less than 240 seconds. | there is much interest in developing methods amenable to amplifying nucleic acids by the polymerase chain reaction (pcr) in small volumes in microfabricated devices. the use of infrared-mediated temperature control to accurately thermocycle microliter volumes in microchips fabricated from polyimide is demonstrated. amplification of a 500-base-pair fragment of lambda-phage dna was achieved in a 1.7-microl chamber containing a thermocouple that allowed for accurate control of temperature. while pr ... | 2001 | 11262165 |
| biophysical characterization of the dna binding domain of gpnu1, a viral dna packaging protein. | terminase enzymes are common to double-stranded dna viruses. these enzymes "package" the viral genome into a pre-formed capsid. terminase from bacteriophage lambda is composed of gpa (72.4 kda) and gpnu1 (20.4 kda) subunits. we have described the expression and biochemical characterization of gpnu1deltak100, a construct comprising the n-terminal 100 amino acids of gpnu1 (yang, q., de beer, t., woods, l., meyer, j., manning, m., overduin, m., and catalano, c. e. (1999) biochemistry 38, 465-477). ... | 2001 | 11279084 |
| the solution structure of bacteriophage lambda protein w, a small morphogenetic protein possessing a novel fold. | protein w (gpw) from bacteriophage lambda is required for the stabilization of dna within the phage head and for attachment of tails onto the head during morphogenesis. although comprised of only 68 residues, it likely interacts with at least two other proteins in the mature phage and with dna. thus, gpw is an intriguing subject for detailed structural studies. we have determined its solution structure using nmr spectroscopy and have found it to possesses a novel fold consisting of two alpha-hel ... | 2001 | 11302702 |
| a structural view of cre-loxp site-specific recombination. | structural models of site-specific recombinases from the lambda integrase family of enzymes have in the last four years provided an important new perspective on the three-dimensional nature of the recombination pathway. members of this family, which include the bacteriophage p1 cre recombinase, bacteriophage lambda integrase, the yeast flp recombinase, and the bacterial xercd recombinases, exchange strands between dna substrates in a stepwise process. one pair of strands is exchanged to form a h ... | 2001 | 11340053 |
| increased bar minigene mrna stability during cell growth inhibition. | bacteriophage lambda is unable to grow vegetatively on escherichia coli mutants defective in peptidyl-trna hydrolase (pth) activity. mutations which allow phage growth on the defective host have been located at regions named bar in the lambda genome. expression of wild-type bar regions from plasmid constructs results in inhibition of protein synthesis and lethality to pth-defective cells. two of these wild-type bar regions, bari+ and barii+, contain minigenes with similar aug-aua-stop codon sequ ... | 2001 | 11136457 |
| a new expression cloning strategy for isolation of substrate-specific kinases by using phosphorylation site-specific antibody. | signal transduction from cell surface receptors to the nucleus is regulated in most part by protein phosphorylation. for the purpose of identification of kinases which play an important role at a particular phosphorylation step in a series of signal transduction pathways, we have developed a new expression-screening method using a phosphorylation site specific antibody and a vector encoding substrate polypeptide. we have applied this method for screening kinases which phosphorylate stat3 at seri ... | 2001 | 11150545 |
| the initiation codon affects ribosome binding and translational efficiency in escherichia coli of ci mrna with or without the 5' untranslated leader. | translational efficiency of an aug, cug, gug, or uug initiation codon was measured for the naturally leaderless ci mrna from bacteriophage lambda. in a ci-lacz translational fusion, only aug supported a high level of expression; gug supported a low level of expression, while uug and cug expression was barely above background levels. addition of an untranslated lac leader and shine-dalgarno sequence to ci increased expression but still showed a dependence on an aug for maximum expression. ci-lacz ... | 2001 | 11157940 |
| genetic footprinting in bacteria. | in vivo genetic footprinting was developed in the yeast saccharomyces cerevisiae to simultaneously assess the importance of thousands of genes for the fitness of the cell under any growth condition. we have developed in vivo genetic footprinting for escherichia coli, a model bacterium and pathogen. we further demonstrate the utility of this technology for rapidly discovering genes that affect the fitness of e. coli under a variety of growth conditions. the definitive features of this system incl ... | 2001 | 11160101 |
| growth and recombination of phage lambda in the presence of exonuclease v from bacillus subtilis. | when expressed in escherichia coli, the addab exonuclease/recombinase from bacillus subtilis blocks the growth of phage lambda. mutants of lambda that are deleted for ea47, a gene of unknown function which is expressed early in the lytic cycle, are not blocked for growth. the blocked-growth phenotype of lambda ea47+ in the presence of addab is expressed only when phage dna replication is permitted. | 2001 | 11212927 |
| tethered-function analysis reveals that elf4e can recruit ribosomes independent of its binding to the cap structure. | the cap-binding complex elf4f is involved in ribosome recruitment during the initiation phase of translation and is composed of three subunits: elf4e, -4g, and -4a. the m7gpppn cap-binding subunit eif4e binds the n-terminal region of eif4g, which in turn contacts eif4a through its central and c-terminal regions. we have previously shown, through a tethered-function approach in transfected hela cells, that the binding of eif4g to an mrna is sufficient to drive productive translation (de gregorio ... | 2001 | 11214172 |
| occurrence and characterization of escherichia coli o157 isolated from cattle in norway. | faecal samples from 504 imported beef cattle were screened to investigate the occurrence of escherichia coli o157. the results were compared with those from a previous screening of norwegian dairy cattle, and the occurrence was found to be higher in the imported beef cattle. the e. coli o157 isolates from the previous and present studies were characterized for the genes encoding for shigatoxin 1 (stx1), shigatoxin 2 (stx2), the intimin protein (eae) and the flagellar protein h7 (flic) using pcr ... | 2001 | 11214668 |
| the neurospora crassa genome: cosmid libraries sorted by chromosome. | a neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector plorist6xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. the electrophoretic karyotype of the seven chromosomes comprising the 42.9-mb n. crassa genome was resolved using two translocation strains. using gel-purified chromosomal ... | 2001 | 11238388 |
| regulation of the switch from early to late bacteriophage lambda dna replication. | there are two modes of bacteriophage lambda dna replication following infection of its host, escherichia coli. early after infection, replication occurs according to the theta (theta or circle-to-circle) mode, and is later switched to the sigma (sigma or rolling-circle) mode. it is not known how this switch, occurring at a specific time in the infection cycle, is regulated. here it is demonstrated that in wild-type cells the replication starting from orilambda proceeds both bidirectionally and u ... | 2001 | 11238961 |
| selection of rna-binding peptides using mrna-peptide fusions. | we have been working to apply in vitro selection to isolate novel rna-binding peptides. to do this, we use mrna-protein fusions, peptides covalently attached to their own mrna. here, we report selection protocols developed using the arginine-rich domain of bacteriophage lambda-n protein and its binding target, the boxb rna. systematic investigation of possible paths for a selection round has allowed us to design a reliable and efficient protocol to enrich rna-binding peptides from nonfunctional ... | 2001 | 11243841 |
| papain does not cleave operator-bound lambda repressor: structural characterization of the carboxy terminal domain and the hinge. | the circular dichroism spectra of three different purified carboxy terminal fragments 93-236, 112-236 and 132-236 of the bacteriophage lambda ci repressor have been measured and compared with those of the intact repressor and the amino terminal fragment 1-92. all three carboxy terminal fragments contain mostly beta-strands and loops, a minor helix content increasing with the size of the fragment, showing that the 93-131 region previously called a hinge is structured. fourier transformed infrared ... | 2001 | 11245251 |
| dominant-negative mutants of prgx: evidence for a role for prgx dimerization in negative regulation of pheromone-inducible conjugation. | prgx negatively regulates prgq transcriptional readthrough in the pheromone-inducible enterococcal conjugative plasmid pcf10. we isolated and characterized 13 dominant-negative prgx mutants, all of which mapped in either the n- or the c-terminus of prgx. in all mutants, the in vivo level of qa rna, an antisense rna to prgq rna, was greatly reduced. when oligomerization of prgx was tested with a phage lambda ci repressor fusion system, the oligomerization domain was found to be between amino acid ... | 2001 | 11251846 |
| hepatitis b virus x protein acts as a tumor promoter in development of diethylnitrosamine-induced preneoplastic lesions. | chronic infection with hepatitis b virus (hbv) is one of the major etiological factors in the development of human hepatocellular carcinoma. transgenic mice that express the hbv x protein (hbx) have previously been shown to be more sensitive to the effects of hepatocarcinogens. although the mechanism for this cofactor role remains unknown, the ability of hbx to inhibit dna repair and to influence cell cycle progression suggests two possible pathways. to investigate these possibilities in vivo, w ... | 2001 | 11264374 |
| methylation by a mutant t2 dna [n(6)-adenine] methyltransferase expands the usage of reca-assisted endonuclease (rare) cleavage. | properties of a mutant bacteriophage t2 dna [n:(6)-adenine] methyltransferase (t2 dam mtase) have been investigated for its potential utilization in reca-assisted restriction endonuclease (rare) cleavage. steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type t4 dam, both wild-type t2 dam and mutant t2 dam p126s had a 1.5-fold higher k(cat) in methylating canonical gatc sites. additionally, t2 dam p126s showed increased efficiencies in methylation of non ... | 2001 | 11266550 |
| foreign dna integration. genome-wide perturbations of methylation and transcription in the recipient genomes. | in hamster cells transgenic for the dna of adenovirus type 12 (ad12) or for the dna of bacteriophage lambda, the patterns of dna methylation in specific cellular genes or dna segments remote from the site of transgene insertion were altered. in the present report, a wide scope of cellular dna segments and genes was analyzed. the technique of methylation-sensitive representational difference analysis (ms-rda) was based on a subtractive hybridization protocol after selecting against dna segments t ... | 2001 | 11278495 |
| revisiting the lysogenization control of bacteriophage lambda. identification and characterization of a new host component, hfld. | upon infection to the escherichia coli cell, the genome of bacteriophage lambda either replicates to form new progenies (lytic growth) or integrates into the host chromosome (lysogenization). the lambda cii protein is a key determinant in the lysis-lysogeny decision. it is a short-lived transcription activator for the lambda genes essential for lysogeny establishment. in this study, we isolated a new class of hfl (high frequency lysogenization) mutants of e. coli, using a new selection for enhan ... | 2001 | 11278968 |
| bacteriophage lambda: alive and well and still doing its thing. | the lambda (lambda) family of bacteriophages continues to provide significant insights into the understanding of basic biological processes, as well as useful technological innovations. areas in which recent advances have occurred include transcription elongation, repressor interactions, genomics and post-transcriptional regulation. the homologous lambda recombination functions have been exploited as an efficient in vivo recombinant engineering system for functional genomic studies. the virulenc ... | 2001 | 11282477 |
| elevated mutant frequencies and increased c : g-->t : a transitions in mlh1-/- versus pms2-/- murine small intestinal epithelial cells. | mutations in dna mismatch repair (mmr) genes are associated with increased genomic instability and susceptibility to cancer. mice rendered deficient in either mlh1 or pms2 as a result of gene targeting are prone to tumorigenesis, particularly, lymphomas. in addition, although mlh1-/- mice also develop small intestinal adenomas and adenocarcinomas, pms2-/- animals remain free of such tumors. to establish whether this phenotypic dichotomy might be associated with a quantitative and/or qualitative ... | 2001 | 11313994 |
| sequence analysis of insecticidal genes from xenorhabdus nematophilus pmfi296. | three strains of xenorhabdus nematophilus showed insecticidal activity when fed to pieris brassicae (cabbage white butterfly) larvae. from one of these strains (x. nematophilus pmfi296) a cosmid genome library was prepared in escherichia coli and screened for oral insecticidal activity. two overlapping cosmid clones were shown to encode insecticidal proteins, which had activity when expressed in e. coli (50% lethal concentration [lc(50)] of 2 to 6 microg of total protein/g of diet). the complete ... | 2001 | 11319082 |
| bacteriophage lambda ciii gene product has an additional function apart from inhibition of cii degradation. | for lysogenization of escherichia coli cells by bacteriophage lambda, functions of three lambda genes called c are necessary. the ci gene codes for a repressor that blocks activities of lytic promoters. however, early after infection, expression of ci is dependent on the function of the cii gene, coding for a specific transcriptional activator. the cii protein is unstable in e. coli cells due to ftsh-mediated proteolysis. the ciii gene product is an inhibitor of the ftsh protease. here we demons ... | 2001 | 11324748 |
| the herpesvirus alkaline exonuclease belongs to the restriction endonuclease pd-(d/e)xk superfamily: insight from molecular modeling and phylogenetic analysis. | the pd-(d/e)xk superfamily of deoxyribonucleases (enases) comprises restriction endonucleases, exonucleases and nicking enzymes, which share a common fold and the architecture of the active site. their extreme divergence generally hampers identification of novel members based solely on sequence comparisons. here we report a remote similarity between the phage lambda exonuclease (lambda-exo), branching out early in the evolutionary history of enases (3), with the family of alkaline exonucleases ( ... | 2001 | 11324759 |
| cloning, expression, and characterization of a family 52 beta-xylosidase gene (xysb) of a multiple-xylanase-producing bacterium, aeromonas caviae me-1. | a lambda phage genomic library of aeromonas caviae me-1, a multiple-xylanase-producing bacterium, was screened for xylan degradation activities. we isolated one clone, b65, which had weak xylanase activity, by the dns method, but gave no visible bands on zymogram assay using sds-xylan-page. based on tlc analyses of enzymatic products and some glycosidase assays using p-nitrophenyl substrates, we established that pb65 encodes a beta-xylosidase gene. in the nucleotide sequence analysis, we found a ... | 2001 | 11330658 |
| crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-n-acetylchitohexaose. | the three-dimensional structure of the lytic transglycosylase from bacteriophage lambda, also known as bacteriophage lambda lysozyme, complexed to the hexasaccharide inhibitor, hexa-n-acetylchitohexaose, has been determined by x-ray crystallography at 2.6 a resolution. the unit cell contains two molecules of the lytic transglycosylase with two hexasaccharides bound. each enzyme molecule is found to interact with four n-acetylglucosamine units from one hexasaccharide (subsites a-d) and two n-acet ... | 2001 | 11341831 |
| unusual evolutionary history of the trna splicing endonuclease enda: relationship to the laglidadg and pd-(d/e)xk deoxyribonucleases. | the trna splicing endoribonuclease enda from methanococcus jannaschii is a homotetramer formed via heterologous interaction between the two pairs of homodimers. each monomer consists of two alpha/beta domains, the n-terminal domain (ntd) and the c-terminal domain (ctd) containing the rnase a-like active site. comparison of the enda coordinates with the publicly available protein structure database revealed the similarity of both domains to site-specific deoxyribonucleases: the ntd to the laglida ... | 2001 | 11344334 |
| protein transduction domain of hiv-1 tat protein promotes efficient delivery of dna into mammalian cells. | the plasma membrane of mammalian cells is one of the tight barriers against gene transfer by synthetic delivery systems. various agents have been used to facilitate gene transfer by destabilizing the endosomal membrane under acidic conditions, but their utility is limited, especially for gene transfer in vivo. in this article, we report that the protein transduction domain of human immunodeficiency virus type 1 tat protein (tat peptide) greatly facilitates gene transfer via membrane destabilizat ... | 2001 | 11346640 |
| the structure of the coliphage hk022 nun protein-lambda-phage boxb rna complex. implications for the mechanism of transcription termination. | nun protein from coliphage hk022 binds to phage boxb rna and functions, in contrast to phage lambda n protein, as a transcriptional terminator. the basic nun-(10-44) peptide contains the boxb rna binding arginine rich motif, arm. the peptide binds boxb rna and competes with the phage lambda arm peptide n-(1-36) as indicated by nuclear magnetic resonance (nmr) spectroscopy titrations. in two-dimensional nuclear overhauser enhancement spectroscopy experiments boxb rna in complex with nun-(20-44) e ... | 2001 | 11356847 |
| [changes in rigidity of the polymeric chain of the lambda-phage dna in aqueous solutions with low ionic strength over the ph range 4-9.5]. | it was shown that the decrease in the rigidity (persistent length) of phage lambda dna, revealed previously by laser correlation spectroscopy, occurs in an aqueous solution at concentrations of sodium salts less than 10(-2) m in the ph range 4-9.5. dna coils of anomalously small size (approximately twofold less than the size reported by other authors) are formed. the formation of these coils is likely to be due to the separation of "normal", i.e., rigid dna coils into two phases, which occurs as ... | 2001 | 11357334 |
| molecular nature of ultraviolet b light-induced deletions in the murine epidermis. | depletion of the stratospheric ozone layer leads to an increase in ambient uv loads, which are expected to raise skin cancer incidences. tumor development in the skin could be a multistep process in which various genetic alterations, such as point mutations and deletions, occur successively. here, we demonstrate that uvb irradiation efficiently induces deletions in the epidermis using a novel transgenic mouse, gpt delta. in this mouse model, deletions in lambda dna integrated in the chromosome a ... | 2001 | 11358805 |
| facilitation of bacteriophage lambda dna injection by inner membrane proteins of the bacterial phosphoenol-pyruvate: carbohydrate phosphotransferase system (pts). | infection of escherichia coli by bacteriophage lambda depends on two membrane protein complexes: (i) maltoporin (lamb) in the outer membrane for adsorption and (ii) the iic(man)-iid(man) complex of the mannose transporter in the inner membrane for dna penetration. iic(man) and iid(man) are components of the phosphoenolpyruvate: sugar phosphotransferase system (pts) which together with the iiab(man) subunit mediate transport and phosphorylation of sugars. to identify structural determinants impor ... | 2001 | 11361066 |
| cloning and expression analysis of nhl1, a gene encoding an extracellular lipase from the fungal pea pathogen nectria haematococca mp vi (fusarium solani f. sp. pisi) that is expressed in planta. | the filamentous fungus nectria haematococca (anamorph fusarium solani f. sp. pisi) resides in soil, and attacks pea seedlings in the area of the underground epicotyl and upper tap root, causing foot rot disease. we detected lipase activity during in vitro growth of n. haematococca. subsequently, a lipase gene was cloned and functionally characterised by heterologous expression in saccharomyces cerevisiae. the full-length cdna of 1152 bp was cloned using a 3' race-pcr approach coupled with cdna l ... | 2001 | 11361331 |
| functional analysis of the phage t4 holin in a lambda context. | phage lambda hybrids were constructed by inserting the t gene of phage t4 in place of the lambda holin gene, s. induction of the hybrid phage resulted in lysis that was just as abrupt as, but occurred much earlier in the vegetative cycle than, that obtained with lambda, indicating that t is indeed a holin gene. moreover, it was possible to impose lysis inhibition (lin) on induction of the hybrid phage, but not of the parental lambda phage, by superinfection with lin-competent t4. the imposition ... | 2001 | 11361346 |
| two novel pao-like retrotransposons (kamikaze and yamato) from the silkworm species bombyx mori and b. mandarina: common structural features of pao-like elements. | to characterize the structural features common to pao-like retrotransposons, we analyzed two lambda phage clones which contain the pao-like elements from the silkworm species bombyx mori and b. mandarinia, and copies of pao itself and ninja of drosophila simulans, amplified by pcr. we previously identified two randomly amplified polymorphic dnas (rapds), w-kamikaze and w-yamato, from b. mori and b. mandarina, which are part of two novel pao-like retrotransposons, kamikaze and yamato, respectivel ... | 2001 | 11361350 |
| chromosomal location of murine disabled-2 gene and structural comparison with its human ortholog. | disabled-2 (dab2) is one of the two mammalian orthologs of the drosophila disabled. the three spliced forms, p96, p93, and p67 of murine dab2 cdnas were first isolated as phosphoproteins functioning in the macrophage csf-1 signal transduction pathway. subsequently, the involvement of dab2 in ovarian cancer development has been investigated: dab2 expression is lost or greatly diminished in breast and ovarian cancers, and gene deletions have been found. regulation of disabled-2 expression is also ... | 2001 | 11368898 |
| high efficiency mutagenesis, repair, and engineering of chromosomal dna using single-stranded oligonucleotides. | homologous dna recombination is a fundamental, regenerative process within living organisms. however, in most organisms, homologous recombination is a rare event, requiring a complex set of reactions and extensive homology. we demonstrate in this paper that beta protein of phage lambda generates recombinants in chromosomal dna by using synthetic single-stranded dnas (ssdna) as short as 30 bases long. this ssdna recombination can be used to mutagenize or repair the chromosome with efficiencies th ... | 2001 | 11381128 |
| activities of vire1 and the vire1 secretion chaperone in export of the multifunctional vire2 effector via an agrobacterium type iv secretion pathway. | agrobacterium tumefaciens uses a type iv secretion system to deliver oncogenic nucleoprotein particles and effector proteins, such as the multifunctional vire2 protein, to plant cells. in this study, we examined the function of vire1 and its product, the vire1 secretion chaperone, in mediating vire2 export. a nonpolar vire1 null mutant accumulated low levels of vire2, and trans expression of vire1 in this mutant only partially restored vire2 abundance. deletion of vire1 did not affect transcript ... | 2001 | 11395448 |
| a small protein-protein interaction domain common to klcb and global regulators kora and trba of promiscuous incp plasmids. | the kor regulon of broad host-range, incompatibility group p (incp) plasmids uses the kora, korb, and korc repressors to regulate expression of genes for replication, conjugation, segregation, and host range. one operon, kilc, encodes the korc repressor and two genes of unknown function (klca and klcb). the predicted sequences of the 51.1 kda klcb protein, the 11.3 kda kora repressor, and another small (13.5 kda) regulatory protein, trba, show a highly related 35 amino acid residue segment (v-l- ... | 2001 | 11419936 |
| unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. | single chromatin fibers were assembled directly in the flow cell of an optical tweezers setup. a single lambda phage dna molecule, suspended between two polystyrene beads, was exposed to a xenopus laevis egg extract, leading to chromatin assembly with concomitant apparent shortening of the dna molecule. assembly was force-dependent and could not take place at forces exceeding 10 pn. the assembled single chromatin fiber was subjected to stretching by controlled movement of one of the beads with t ... | 2001 | 11427891 |
| specific and non-specific interactions of integration host factor with dna: thermodynamic evidence for disruption of multiple ihf surface salt-bridges coupled to dna binding. | site-specific dna binding of architectural protein integration host factor (ihf) is involved in formation of functional multiprotein-dna assemblies in escherichia coli, while non-specific binding of ihf and other histone-like proteins serves to structure the nucleoid. here, we report an isothermal titration calorimetry study of the thermodynamics of binding ihf to a 34 bp fragment composed entirely of the specific h' site from lambda-phage dna. at low to moderate [k(+)] (60-100 mm), strong compe ... | 2001 | 11428896 |
| the double mechanism of incompatibility between lambda plasmids and escherichia coli dnaa(ts) host cells. | for plasmids derived from bacteriophage lambda, the initiation of bidirectional dna replication from orilambda depends on the stimulation of transcription from the p(r) promoter by the host replication initiator protein dnaa. certain escherichia coli dnaa(ts) mutants cannot be transformed by wild-type lambda plasmids even at the temperature permissive to cell growth. this plasmid-host incompatibility appeared to be due to inefficient stimulation of transcription from the p(r) promoter by the mut ... | 2001 | 11429468 |
| a plasmid cloning vector with precisely regulatable copy number in escherichia coli. | we have developed a genetic system allowing for precise regulation of plasmid copy number in escherichia coli cells. a cloning vector based on this system is described in this article. the ptc lambda 3 plasmid is a lambda replicon, but transcription controlling initiation of plasmid dna replication starts from the pteta promoter instead of phage lambda pr promoter. additionally, activity of pteta promoter is negatively controlled by the tetr repressor whose gene is located on the same plasmid ve ... | 2001 | 11434307 |
| bacteriophage lambda-based expression vectors. | bacteriophage lambda has been in use as a cloning vector for over 25 years, and has been used extensively as an expression vector. the efficiency of packaging and infection, and the simplicity of plaque screening are advantages of lambda as a cloning vector. a number of ingenious modifications help overcome the disadvantages associated with its mode of growth and its size. some lambda vectors have been designed to be readily converted into plasmids or phagemids, and there are a variety of promot ... | 2001 | 11434310 |
| seqa, the escherichia coli origin sequestration protein, is also a specific transcription factor. | the seqa protein is a negative regulator of initiation of dna replication in the escherichia coli chromosome. here, we demonstrate that seqa stimulates transcription from the bacteriophage lambda pr promoter both in vivo and in vitro. the activity of the lambda pl promoter was found not to be affected by this protein. seqa-mediated stimulation of pr was dependent on the state of template methylation: transcription was activated on fully methylated and hemimethylated templates but not on an unmet ... | 2001 | 11442835 |
| what makes the bacteriophage lambda red system useful for genetic engineering: molecular mechanism and biological function. | recent studies have generated interest in the use of the homologous recombination system of bacteriophage lambda for genetic engineering. the system, called red, consists primarily of three proteins: lambda exonuclease, which processively digests the 5'-ended strand of a dsdna end; beta protein, which binds to ssdna and promotes strand annealing; and gamma protein, which binds to the bacterial recbcd enzyme and inhibits its activities. these proteins induce a 'hyper-rec' state in escherichia col ... | 2001 | 11445160 |
| regulation of microcin c51 operon expression: the role of global regulators of transcription. | expression of the microcin c51 operon in escherichia coli cells is regulated as a function of the phase of growth; it is stimulated during the decelerating phase of growth. using single-copy p(mcc)-lac transcriptional fusion (the promoter region of the microcin c51 operon fused to a promoterless lac operon in lambda phage), we showed that transcription from the microcin operon promoter is dependent on sigma(s) (rpos) factor. however, some level of p(mcc)-lac expression is possible in rpos null m ... | 2001 | 11446515 |
| single-strand interruptions in replicating chromosomes cause double-strand breaks. | replication-dependent chromosomal breakage suggests that replication forks occasionally run into nicks in template dna and collapse, generating double-strand ends. to model replication fork collapse in vivo, i constructed phage lambda chromosomes carrying the nicking site of m13 bacteriophage and infected with these substrates escherichia coli cells, producing m13 nicking enzyme. i detected double-strand breaks at the nicking sites in lambda dna purified from these cells. the double-strand break ... | 2001 | 11459959 |
| identification of the high affinity mn2+ binding site of bacteriophage lambda phosphoprotein phosphatase: effects of metal ligand mutations on electron paramagnetic resonance spectra and phosphatase activities. | bacteriophage lambda phosphoprotein phosphatase (lambdapp) has structural similarity to the mammalian ser/thr phosphoprotein phosphatases (ppps) including the immunosuppressant drug target calcineurin. ppps possess a conserved active site containing a dinuclear metal cluster, with metal ligands provided by a phosphoesterase motif plus two additional histidine residues at the c-terminus. multiple sequence alignment of lambdapp with 28 eubacterial and archeal phosphoesterases identified active sit ... | 2001 | 11467953 |
| cell toxicity caused by products of the p(l) operon of bacteriophage lambda. | induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of functions from the lambda p(l) operon. we genetically modified the lambda prophage to determine which lambda p(l) operon functions were involved in cell killing. viability assays and flow cytometry were used to monitor cell death and filamentation. the kil gene was shown to cause cell death and filamentation as described previously. another killing ac ... | 2001 | 11470529 |
| viral haemorrhagic septicaemia virus induces vig-2, a new interferon-responsive gene in rainbow trout. | an mrna differential display methodology was used to study the rainbow trout response to viral infection. a new transcript (vig-2) induced by viral haemorrhagic septicaemia virus (vhsv) in rainbow trout leucocytes was identified from the head-kidney. vig-2 was also induced in vivo during experimental infection and following dna immunisation with a plasmid containing a gene encoding the viral glycoprotein. viral induction of vig-2 was blocked by cycloheximide (chx), indicating its dependency on a ... | 2001 | 11478515 |
| expression of unphosphorylated form of human double-stranded rna-activated protein kinase in escherichia coli. | interferon (ifn)-inducible, double-stranded (dsrna)-activated protein kinase (pkr) is a key mediator of the antiviral and antiproliferative effects of ifn. pkr is present within cells in a latent state. in response to binding dsrna, the enzyme becomes activated, causing autophosphorylation and an increase in specific kinase activity. in order to study pkr and its inhibitors, a large amount of the enzyme in its latent, unphosphorylated state is required. when pkr is fused to glutathione s-transfe ... | 2001 | 11396973 |
| repression of transcription initiation at 434 p(r) by 434 repressor: effects on transition of a closed to an open promoter complex. | the lambdoid bacteriophage repressors function both as transcription activators and repressors. regulation of transcription at the adjacent, but divergent promoters, p(rm) and p(r), determines the phage's choice between the lytic and lysogenic development pathways. here, we demonstrate that 434 repressor bound at 434 o(r)1 alone is not sufficient to repress transcription from 434 p(r,) but that 434 repressor bound at 434 o(r)2 alone is necessary and sufficient to repress p(r )transcription. this ... | 2001 | 11397081 |
| defining cosq, the site required for termination of bacteriophage lambda dna packaging. | bacteriophage lambda is a double-stranded dna virus that processes concatemeric dna into virion chromosomes by cutting at specific recognition sites termed cos. a cos is composed of three subsites: cosn, the nicking site; cosb, required for packaging initiation; and cosq, required for termination of chromosome packaging. during packaging termination, nicking of the bottom strand of cosn depends on cosq, suggesting that cosq is needed to deliver terminase to the bottom strand of cosn to carry out ... | 2001 | 11404316 |
| efficient transformation of filamentous fungus pleurotus ostreatus using single-strand carrier dna. | the effects of carrier dnas on the transformation of the basidiomycete pleurotus ostreatus were analyzed. when lambda phage dna was added to a transformation mixture containing protoplasts and cbxr vector plasmid, an increased number of drug-resistant transformants was observed on a screening plate containing 2 microg carboxin/ml. the highest efficiency (about 200 transformants/microg vector plasmid) was obtained by the addition of heat-denatured lambda dna, which gave yields approximately 50-fo ... | 2001 | 11414321 |
| variable range hopping and electrical conductivity along the dna double helix. | we present a model to describe electrical conductivity along the dna double helix. in this model, dna is considered as a one-dimensional disordered system, and electrons are transported via variable range hopping between localized states. thermal structural fluctuations in dna further localize electronic wave functions, giving rise to a temperature-dependent localization length. the model quantitatively explains the temperature dependence of the conductivity observed in the lambda phage dna (lam ... | 2001 | 11415418 |
| selection of ligands by panning of domain libraries displayed on phage lambda reveals new potential partners of synaptojanin 1. | one of the goals of functional genomics is the description of reliable and complete protein interaction networks. to facilitate ligand discovery from complex protein mixtures, we have developed an improved approach that is affected by a negligible fraction of false positives. we have combined a novel technique based on the display of cdna libraries on the capsid of bacteriophage lambda and an efficient plaque assay to reveal phage displaying ligands that are enriched after only a couple of affin ... | 2001 | 11292345 |
| the tgv transgenic vectors for single-copy gene expression from the escherichia coli chromosome. | plasmid-based cloning and expression of genes in escherichia coli can have several problems: plasmid destabilization; toxicity of gene products; inability to achieve complete repression of gene expression; non-physiological overexpression of the cloned gene; titration of regulatory proteins; and the requirement for antibiotic selection. we describe a simple system for cloning and expression of genes in single copy in the e. coli chromosome, using a non-antibiotic selection for transgene insertio ... | 2001 | 11483365 |
| the use of competitive pcr mimic to evaluate a limulus lambda phage genomic dna library. | 1. a lambda phage genomic dna library for limulus (l.) polyphemus brain was constructed using the agem-12 vector and the host strain kw251. 2. the primary library contained approximately 1.275 x 10(6) independent clones, increasing upon amplfication to 6.66 x 10(9) pfu/ml in a total volume of 58 ml. 3. a total of 28 clones was randomly chosen for a determination of the average size of inserts in the library. all clones contained inserts and the average size was 14.9 kb, ranging from 11.7 to 28.0 ... | 2000 | 10901270 |
| novel fold and capsid-binding properties of the lambda-phage display platform protein gpd. | the crystal structure of gpd, the capsid-stabilizing protein of bacteriophage lambda, was solved at 1.1 a resolution. data were obtained from twinned crystals in space group p21 and refined with anisotropic temperature factors to an r-factor of 0.098 (rfree = 0. 132). gpd (109 residues) has a novel fold with an unusually low content of regular secondary structure. noncrystallographic trimers with substantial intersubunit interfaces were observed. the c-termini are well ordered and located on one ... | 2000 | 10700283 |
| affinity selection of dna-binding proteins displayed on bacteriophage lambda. | two transcription factors, human atf1, its dna-binding domain (atf1bd), and the dna-binding domain (gal4bd) of the yeast gal4 protein, were displayed on the surface of bacteriophage lambda vectors and efficiently selected by dna fragments immobilized in microtiter wells. the dna-binding proteins are fused to the carboxy terminus of the tail protein gpv and head protein gpd of the vectors, lambdafoo and lambdafoodc, respectively. after a single round of affinity selection, the fusion phages were ... | 2000 | 10833275 |
| changes in the 17 bp spacer in the p(r) promoter of bacteriophage lambda affect steps in open complex formation that precede dna strand separation. | tau plots and temperature-shift experiments were used to determine which step in the formation of transcriptionally-competent open complexes is affected by changing the length of the 17 bp spacer separating the -10 and -35 consensus regions of the p(r) promoter of bacteriophage lambda. abortive initiation assays at 37 degrees c indicate that the primary effect of insertion of a base-pair, thereby increasing spacer length to 18 bp, is a decrease in k(f), the rate constant for conversion from clos ... | 2000 | 10860742 |
| alu-associated interstitial deletions and chromosomal re-arrangement in 2 human multidrug-resistant cell lines. | previous studies have shown that gene re-arrangements play a significant role in tumorigenesis. gene re-arrangements involving the human multidrug resistance-1 (mdr1) gene have been identified as a mechanism for mdr1 over-expression in human malignant cells. in 2 multidrug-resistant human cancer sublines with high levels of mdr1 and p-glycoprotein (mcf7/tx400 and s48-3s/adr10), hybrid mrnas containing sequences from mdr1 and an unrelated gene have previously been identified. to characterize and ... | 2000 | 10797263 |
| antitermination in bacteriophage lambda. the structure of the n36 peptide-boxb rna complex. | the solution structure of a 15-mer nutrboxb rna hairpin complexed with the 36-mer n-terminal peptide of the n protein (n36) from bacteriophage lambda was determined by 2d and 3d homonuclear and heteronuclear magnetic resonance spectroscopy. these 36 amino acids include the arginine-rich motif of the n protein involved in transcriptional antitermination of phage lambda. upon complex formation with boxb rna, the synthetic n36 peptide binds tightly to the major groove of the boxb hairpin through hy ... | 2000 | 10759866 |
| mechanical stability of single dna molecules. | using a modified atomic force microscope (afm), individual double-stranded (ds) dna molecules attached to an afm tip and a gold surface were overstretched, and the mechanical stability of the dna double helix was investigated. in lambda-phage dna the previously reported b-s transition at 65 piconewtons (pn) is followed by a second conformational transition, during which the dna double helix melts into two single strands. unlike the b-s transition, the melting transition exhibits a pronounced for ... | 2000 | 10733978 |
| the structural basis for enhanced stability and reduced dna binding seen in engineered second-generation cro monomers and dimers. | it was previously shown that the cro repressor from phage lambda, which is a dimer, can be converted into a stable monomer by a five-amino acid insertion. phe58 is the key residue involved in this transition, switching from interactions which stabilize the dimer to those which stabilize the monomer. structural studies, however, suggested that phe58 did not penetrate into the core of the monomer as well as it did into the native dimer. this was strongly supported by the finding that certain core- ... | 2000 | 10686105 |
| complete structural characterisation of the mammalian and drosophila traf genes: implications for traf evolution and the role of ring finger splice variants. | the complete murine traf2 gene was obtained using a lambda phage and pcr cloning strategy. the gene was found to consist of ten coding and one 5' non-coding exon spread over 28 kbp of dna. we also report the basic structure of the human traf5 and traf6 genes obtained by analysis of the genomic dna database. comparison of these three gene structures, along with those previously described for traf1, traf3 and traf4, revealed the evolutionary relationship between the six known mammalian trafs. the ... | 2000 | 11275257 |
| recent advances in the protocols of transgenic mouse mutation assays. | transgenic mutation assays were developed to detect gene mutations in multiple organs of mice or rats. the assays permit (1) quantitative measurements of mutation frequencies in all tissues/organs including germ cells and (2) molecular analysis of induced and spontaneous mutations by dna sequencing analysis. the protocols of recently developed selections in the lambda phage-based transgenic mutation assays, i.e. cii, spi(-) and 6-thioguanine selections, are described, and a data set of transgeni ... | 2000 | 11113476 |
| a tyrosine hydroxylase-neurofilament chimeric promoter enhances long-term expression in rat forebrain neurons from helper virus-free hsv-1 vectors. | helper virus-free herpes simplex virus (hsv-1) plasmid vectors are attractive for neural gene transfer, but a promoter that supports neuronal-specific, long-term expression is required. although expression from many promoters is unstable, a 6.8-kb, but not a 766-bp, fragment of the tyrosine hydroxylase (th) promoter supports long-term expression. thus, 5' upstream sequences in this promoter may enhance expression. in this study, we evaluated expression from vectors that contain 5' upstream seque ... | 2000 | 11113528 |
| genomic organization of the 5' region of the human thyroglobulin gene. | the purpose of the present work is to establish the intron-exon organization from exon 12 to exon 23 of the human thyroglobulin gene and to construct a physical map of the 5' terminal half of the gene. | 2000 | 11124863 |
| specificity-enhanced hot-start pcr: addition of double-stranded dna fragments adapted to the annealing temperature. | a new method to produce hot-start conditions in pcr is described. short double-stranded dna fragments were found to inhibit the activity of dna polymerases from thermus aquaticus and thermus flavus. this inhibition is not sequence specific, but exclusively dependent on the melting temperature of the fragments as shown by its correlation to their melting curves as measured. this property is exploited by adding fragments of the appropriate length to the pcr mixture during the reaction setup and th ... | 2000 | 10683737 |
| is911 transposition is regulated by protein-protein interactions via a leucine zipper motif. | efficient intermolecular transposition of bacterial insertion sequence is911 involves the activities of two element-encoded proteins: the transposase, orfab, and a regulatory factor, orfa. orfa shares the majority of its amino acid sequence with the n-terminal part of orfab. this includes a putative helix-turn-helix and three of four heptads of a leucine zipper motif. orfa strongly stimulates orfab-mediated intermolecular transposition both in vivo and in vitro. the present results support the n ... | 2000 | 10677279 |
| bacteriophage lambda display of complex cdna libraries: a new approach to functional genomics. | we describe the construction and characterization of two lambda surface displayed cdna expression libraries derived from human brain and mouse embryo. cdna inserts were obtained by tagged random-priming elongation of commercially available cdna libraries and cloned into a novel lambda vector at the 3' end of the d capsid protein gene, which produced highly complex repertoires (1x10(8) and 2x10(7) phage). these libraries were affinity selected with a monoclonal antibody against the neural specifi ... | 2000 | 10669604 |
| function of transcription cleavage factors grea and greb at a regulatory pause site. | gre proteins of prokaryotes, and sii proteins of eukaryotes and archaea, are transcription elongation factors that promote an endogenous transcript cleavage activity of rna polymerases; this process promotes elongation through obstructive regions of dna, including transcription pauses that act as sites of genetic regulation. we show that a regulatory pause in the early part of the late gene operon of bacteriophage lambda is subject to such cleavage and resynthesis. in cells lacking the cleavage ... | 2000 | 11163202 |
| characterization and genomic sequence of the murine 60 kd ro gene. | autoantibodies binding 60 kd ro (or ss-a) are commonly found in patients with systemic lupus erythematosus and sjögren's syndrome. while many studies have examined the autoimmune response directed against this rna-protein, its function is still uncertain. as part of a broad effort to better understand animal models of anti-ro autoimmunity we have characterized the murine 60 kd ro gene. southern blot analysis of mouse genomic dna suggests that the 60 kd ro gene is a single copy gene. the complete ... | 2000 | 11196703 |
| characterization of bacteriophage lambda excisionase mutants defective in dna binding. | the bacteriophage lambda excisionase (xis) is a sequence-specific dna binding protein required for excisive recombination. xis binds cooperatively to two dna sites arranged as direct repeats on the phage dna. efficient excision is achieved through a cooperative interaction between xis and the host-encoded factor for inversion stimulation as well as a cooperative interaction between xis and integrase. the secondary structure of the xis protein was predicted to contain a typical amphipathic helix ... | 2000 | 11004181 |
| three spliced mrnas of tt virus transcribed from a plasmid containing the entire genome in cos1 cells. | a permuted whole-genome construct of a tt virus (ttv), named vt416, had 3,852 nucleotides (nt) 98.2% similar to the prototype ta278 genome. to allow the transcription of ttv from the internal promoter, pbk*vt416(1.3g), carrying 1.3 units of vt416, was constructed. the poly(a)(+) rnas expressed in cos1 cells 48 h posttransfection contained three ttv mrna species 3.0, 1.2, and 1.0 kb in length, which were recovered in the 13 dna clones from a lambda phage cdna library. these mrnas in the antigenom ... | 2000 | 11024126 |
| dimerization between the holin and holin inhibitor of phage lambda. | holins are integral membrane proteins that control the access of phage-encoded muralytic enzymes, or endolysins, to the cell wall by the sudden formation of an uncharacterized homo-oligomeric lesion, or hole, in the membrane, at a precisely defined time. the timing of lambda-infected cell lysis depends solely on the 107 codon s gene, which encodes two proteins, s105 and s107, which are the holin and holin inhibitor, respectively. here we report the results of biochemical and genetic studies on t ... | 2000 | 11029427 |
| detection of mutations in transgenic fish carrying a bacteriophage lambda cii transgene target. | to address the dual needs for improved methods to assess potential health risks associated with chemical exposure in aquatic environments and for new models for in vivo mutagenesis studies, we developed transgenic fish that carry multiple copies of a bacteriophage lambda vector that harbors the cii gene as a mutational target. we adapted a forward mutation assay, originally developed for lambda transgenic rodents, to recover cii mutants efficiently from fish genomic dna by lambda in vitro packag ... | 2000 | 11035814 |
| the alpha subunit of e. coli rna polymerase activates rna binding by nusa. | the escherichia coli nusa protein modulates pausing, termination, and antitermination by associating with the transcribing rna polymerase core enzyme. nusa can be covalently cross-linked to nascent rna within a transcription complex, but does not bind rna on its own. we have found that deletion of the 79 carboxy-terminal amino acids of the 495-amino-acid nusa protein allows nusa to bind rna in gel mobility shift assays. the carboxy-terminal domain (ctd) of the alpha subunit of rna polymerase, as ... | 2000 | 11040219 |
| [antioxidant features of fungal melanin pigments]. | fungal melanin pigments were shown to display a high antioxidant activity. an increase in the number of methyl substituents in benzidine molecules of melanins obtained from micromycetes and macromycetes was accompanied by a decrease in the efficiency of inhibition of peroxidase-catalyzed oxidation. melanins were found to have considerable gene-protecting properties. pigments isolated from macromycetes and applied at a much lower concentration than those obtained from micromycetes prevented damag ... | 2000 | 11042882 |
| cooperativity: action at a distance in a classic system. | a new high resolution crystal structure of the phage lambda repressor reveals the basis for repressor dimer formation and, together with biochemical data, provides insights into the mechanism of repressor tetramer formation, a process essential to the cooperative binding and gene regulatory activities of this protein. | 2000 | 11050405 |
| affinity selection of cdna libraries by lambda phage surface display. | bacteriophage lambda surface display was used to isolate cdna clones encoding autoantigens recognized by sera from patients with sjögren's syndrome (ss). we made cdna libraries from human hela and hepg2 cells, using the expression vector lambdafoo. by repeating affinity selection of the libraries with the sera immobilized in microtiter wells, we isolated three clones that encode previously unknown antigens as well as four clones previously known as ss autoantigens. the newly identified autoantig ... | 2000 | 11054552 |
| assignment of the 1h, 13c, and 15n resonances of the dna binding domain of gpnu1, a genome packaging protein from bacteriophage lambda. | 2000 | 11061230 | |
| endonuclease and helicase activities of bacteriophage lambda terminase: changing nearby residue 515 restores activity to the gpa k497d mutant enzyme. | terminase, the dna packaging enzyme of bacteriophage lambda, is a heteromultimer of gpnu1 and gpa subunits. in an earlier investigation, a lethal mutation changing gpa residue 497 from lysine to aspartic acid (k497d) was found to cause a mild change in the high-affinity atpase that resides in gpa and a severe defect in the endonuclease activity of terminase. the k497d terminase efficiently sponsored packaging of mature lambda dna into proheads. in the present work, k497d terminase was found to h ... | 2000 | 11062051 |
| the r-type pyocin of pseudomonas aeruginosa is related to p2 phage, and the f-type is related to lambda phage. | pseudomonas aeruginosa produces three types of bacteriocins: r-, f- and s-type pyocins. the s-type pyocin is a colicin-like protein, whereas the r-type pyocin resembles a contractile but non-flexible tail structure of bacteriophage, and the f-type a flexible but non-contractile one. as genetically related phages exist for each type, these pyocins have been thought to be variations of defective phage. in the present study, the nucleotide sequence of r2 pyocin genes, along with those for f2 pyocin ... | 2000 | 11069649 |
| a rapid method for efficient gene replacement in the filamentous fungus aspergillus nidulans. | the construction of mutant fungal strains is often limited by the poor efficiency of homologous recombination in these organisms. higher recombination efficiencies can be obtained by increasing the length of homologous dna flanking the transformation marker, although this is a tedious process when standard molecular biology techniques are used for the construction of gene replacement cassettes. here, we present a two-step technology which takes advantage of an escherichia coli strain expressing ... | 2000 | 11071951 |
| the pcr plateau phase - towards an understanding of its limitations. | the dna polymerases from thermus aquaticus and thermus flavus were recently found to bind to short double-stranded dna fragments without sequence specificity [kainz et al. (2000) biotechniques 28, 278-82]. in the present study, it is shown that the accumulation of amplification products during later pcr cycles also exerts an inhibitory effect on several enzymes tested. to simulate later cycle conditions, a 1.7 kb sequence from phage lambda dna was amplified in the presence of various amounts of ... | 2000 | 11072065 |
| the multifunctional bacteriophage p2 cox protein requires oligomerization for biological activity. | the cox protein of bacteriophage p2 is a multifunctional protein of 91 amino acids. it is directly involved in the site-specific recombination event leading to excision of p2 dna out of the host chromosome. in this context, it functions as an architectural protein in the formation of the excisome. cox is also a transcriptional repressor of the p2 pc promoter, thereby ensuring lytic growth. finally it promotes derepression of prophage p4, a nonrelated defective satellite phage, by activating the ... | 2000 | 11073917 |
| folding kinetics of phage 434 cro protein. | folding kinetics for phage 434 cro protein are examined and compared with those reported for lambda(6-85), the n-terminal domain of the repressor of phage lambda. the two proteins have similar all-helical structures consisting of five helices but different stabilities. in contrast to lambda(6-85), sharp and distinct aromatic (1)h nmr signals without exchange broadening characterize the native and urea-denatured 434 cro forms at equilibrium at 20 degrees c, indicating slow interconversion on the ... | 2000 | 11076539 |
| mechanism for a transcriptional activator that works at the isomerization step. | transcriptional activators in prokaryotes have been shown to stimulate different steps in the initiation process including the initial binding of rna polymerase (rnap) to the promoter and a postbinding step known as the isomerization step. evidence suggests that activators that affect initial binding can work by a cooperative binding mechanism by making energetically favorable contacts with rnap, but the mechanism by which activators affect the isomerization step is unclear. a well-studied examp ... | 2000 | 11087868 |