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PubMed1984

A novel in vitro transcription-translation system: accurate and efficient synthesis of single proteins from cloned DNA sequences.

A system is described which permits the efficient synthesis of single proteins in vitro. The essential element in this expression system is a strong promoter derived from coliphage T5 which produces, with high efficiency, specific RNAs in capped or uncapped form, depending upon the experimental conditions used. The transcription-coupled capping of RNA allows the direct translation of the RNA in eukaryotic extracts from wheat germ as well as from HeLa cells. The synthesis of three different proteins is reported, including lysozyme, which is shown to be translocated across membranes when appropriate assay conditions are used. The simplicity of the experimental procedure, the high purity and specific activity of the [35S]methionine-labelled proteins produced offer a number of possibilities for the study of structure-function relationships of proteins.

Cell-Free System↗
PubMed1986

Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures.

The strength in vivo of 14 promoters was determined in a system which permits the quantitation of RNA synthesis with high accuracy. Up to 75-fold differences in promoter strength were measured and the most efficient signals are promoters from coliphages T7 and T5. Their activity approaches the strength of fully induced promoters of the rRNA operons which may be close to the functional optimum of a single sequence. By contrast, a synthetic 'consensus promoter' belongs to the less efficient signals. Our data show that optimal promoter function can be achieved by alternate structures and strongly suggest that information outside of the 'classical' promoter region contributes to promoter activity.

Base Sequence↗
PubMed1987

Transcriptional termination at a fully rho-independent site in Escherichia coli is prevented by uninterrupted translation of the nascent RNA.

We have examined the possibility that translation reading through a fully rho-independent transcriptional terminator in Escherichia coli might prevent termination, as already established for rho-dependent terminators. Plasmids were constructed with and without interposition of the rho-independent coliphage T7 'early' terminator between a promoter and galK. Our constructions ensured either that there was no upstream translation, or that translation (initiated at the galE ribosome binding site) stopped upstream of, or at the normal position (the T7 gene 1.3 stop codon) with respect to, the transcriptional terminator; or else downstream of both this stop codon and the terminator. Our galactokinase enzyme and mRNA measurements on strains harbouring these plasmids indicate that 'readthrough translation' eliminates transcriptional termination at the T7 site. This effect is suppressed if the rate of ribosome movement is reduced with fusidic acid.

Base Sequence↗
PubMed2004

Heavy-metal and microbial depuration of the clam Ruditapes decussatus and its effect on bivalve behavior and physiology.

The bivalve Ruditapes decussatus was evaluated as a possible biomonitor of heavy-metal contamination. Concentrations of copper (Cu), cobalt (Co), iron (Fe), nickel (Ni), and manganese (Mn) were measured in R. decussatus. Water and sediment samples were collected at two stations of Timsah Lake in Ismailia, Egypt, from October to November 2002, using atomic absorption spectrophotometry (AAS). Results from the heavy-metal and microbial analyses indicated that site II was less contaminated than site I. The bivalve showed accumulation of metals, with a bioaccumulation factor (BAF) greater than 4. The bioaccumulation of metals varied strongly according to the sampling site. After 48 h of depuration, Fe, Ni, Co, Cu, and Mn were reduced significantly, to 46.8% and 47.7%, 19.9% and 20.3%, 27.3% and 27.9%, 35.9% and 36.6%, and 18.2% and 26.6%, compared with the initial concentrations, in clam tissue at the two stations. In bivalves from site II the counts of total bacteria, fecal coliforms, and bacterial pathogens were reduced by more than 90%, whereas phage counts were only reduced by 56% after 4 days of depuration. The depuration of bivalves collected from the heavily polluted site (I) was not effective, as coliforms were reduced only by 85% after 4 days, whereas counts of pathogens and pathogenic indicators such as Vibrio, fecal Streptococcus, and coliphage decreased to less than 50% of the initial concentration. The time necessary to decrease contamination to 10%, 50%, and 90% for clams at both stations was consistently shorter for heavy metals than for microorganisms. Investigation of the effects of heavy-metal and microbiological depuration on valve movement and physiological rates (oxygen consumption and ammonia excretion) was carried out on R. decussatus to test the utility of physiological stress indices in assessing the health of depurated animals. Clams in the experimental tanks exhibited various states of activity, which were rated by identifying and scoring (0-4) the different parameters, including shell gap, siphon extension, and foot protrusion. Moreover, an increase in ammonia excretion was usually associated with an increase in respiration rate. The oxygen-to-nitrogen ratio provided a sensitive indicator of bivalve health. It can be concluded that shellfish monitoring and depuration data depended on the initial concentration of the pollutants. There were differences in the physiological responses of clams from the two sites during the periods of pre- and postdepuration of the contaminants. There was a significant correlation between reduction of metal concentration in clam tissue and enhancement of valve movement, as well as activity and increasing respiration rate.

Ammonia↗
PubMed1994

An additional role of transcriptional activation of ori lambda in the regulation of lambda plasmid replication in Escherichia coli.

Initiation of replication of plasmids derived from coliphage lambda in vivo is dependent on transcription at or near the replication origin, ori lambda. However, this transcriptional activation is dispensable for lambda plasmid DNA replication reconstituted in vitro from purified lambda and Escherichia coli proteins. It was proposed previously that histone-like protein HU interferes with the assembly or function of the pre-primosomal complex, and transcription at or near ori lambda abolishes HU-mediated inhibition of lambda DNA replication. We found that during lambda plasmid replication driven by the previously assembled replication complex (in amino acid-starved relA mutants), when the inhibition by HU protein should not be observed, the synthesis of lambda DNA was still dependent on transcriptional activation. Moreover, in hupA hupB double mutants the transcription is necessary for the initiation of lambda plasmid DNA replication perpetuated by the replication complex inherited by one of two daughter copies after a replication round. We conclude that transcriptional activation of ori lambda has an additional role in the initiation of lambda plasmid DNA replication beside the abolition of HU-mediated inhibition.

Bacterial Proteins↗
PubMed1993

The refined structure of bacteriophage MS2 at 2.8 A resolution.

Bacteriophage MS2 is an icosahedral virus with 180 copies of a coat protein forming a shell around a single-stranded RNA molecule. The coat protein subunits form a lattice with the triangulation number T = 3. The coat protein has a fold which is different from the fold of all other viral coat proteins so far known. It consists of a five-stranded beta sheet facing the inside of the particle, and a hairpin and two helices on the outside. The crystal structure has been refined at 2.8 A resolution. The final R-factor was 0.189 for reflections with F > 2 sigma, and the root-mean-square deviation from idealized bond lengths and bond angles was 0.015 A and 2.9 degrees, respectively. The three chemically identical conformers A, B and C are largely similar. The B conformer has a unique conformation in one loop, which is involved in 5-fold interactions, while the A and C conformers, which are involved in the quasi-6-fold contacts, are similar throughout the structure. One cis-proline has been identified in the B conformer but the corresponding prolines in A and C are of the trans isomer. This residue is conserved within small RNA coliphages and it is proposed that this isomerization enables a less elongated loop (FG) around the 5-fold axis, thus creating a channel. The extensive dimer contact supports the idea of dimers as initial building blocks. An assembly pathway is proposed where five dimers converge into a pentamer and 12 pentamers are linked together with free dimers creating a complete particle.

Amino Acid Sequence↗
PubMed1995

The bacteriophage N4-coded single-stranded DNA-binding protein (N4SSB) is the transcriptional activator of Escherichia coli RNA polymerase at N4 late promoters.

Transcription of the 72kb linear double-stranded DNA genome of coliphage N4 is carried out by the sequential activity of three different RNA polymerases. Early and middle viral transcripts are synthesized by two phage-coded RNA polymerases while late transcription is carried out by the Escherichia coli sigma 70-RNA polymerase. We have determined the sequences and sites of initiation of several N4 late transcripts; N4 late promoters share weak homology with the E. coli sigma 70 promoter consensus sequence. Indeed, N4 late promoters are weak templates for the host enzyme. We present evidence that the phage-coded, single-stranded DNA-binding protein (N4SSB), a protein that is required for phage DNA replication and recombination and does not bind with sequence specificity to DNA, is the activator of E. coli RNA polymerase at late N4 promoters. Models for the mechanism of action of N4SSB as a transcriptional activator are discussed.

Base Sequence↗
PubMed1994

Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites.

Cooperative binding of specific DNA-binding proteins plays crucial roles in gene regulatory circuitry, and is a model system for interactions between proteins bound to DNA. We have studied coliphage HK022 repressor, which binds to two adjacent operators with a cooperativity parameter of approximately 2000. We examined the effect of changing the spacing between these two operators on cooperativity and on the conformation of the complex. Maximum cooperativity was seen with the wild-type spacing; considerable cooperativity was retained for most spacing variants, but was abolished when the operators lay on opposite faces of the DNA helix. Most spacing variants conferred changes in the conformation of the DNA-protein complex. Our data indicate that the pairwise cooperativity observed with the wild-type spacing results from a conformation that prevents protein-protein contacts with flanking bound dimers. We conclude that protein-DNA complexes involving the same specific binding sites and the same protein molecules can adopt many different conformations, depending on the spacing between the binding sites. This conclusion may be broadly applicable to protein-DNA interactions in other systems.

Allosteric Regulation↗
PubMed1996

Secondary structure model for the first three domains of Q beta RNA. Control of A-protein synthesis.

We present a secondary structure model for the first 860 nucleotides of Q beta RNA. The model is supported by phylogenetic comparison, nuclease S1 structure probing and computer prediction using energy minimization and a Monte Carlo approach. To provide the necessary data for the comparative analysis we have sequenced the single-stranded RNA coliphages MX1, M11 and NL95. Together with the known sequences of Q beta and SP, this yields five sequences with sufficient sequence diversity to be useful for the analysis. The part of the Q beta genome examined contains the 60 nucleotide 5' untranslated region and the first 800 nucleotide of the maturation protein gene. The RNA adopts a highly ordered structure in which all hairpins are held in place by a network of long-distance interactions, which form three-way and four-way junctions. Only the 5'-terminal hairpin is unrestrained, while connected by a few single-stranded nucleotides to the body of the RNA. The start region of the A-protein gene, which is part of the network of long-distance interactions, is base-paired to three non-contiguous downstream sequences. As a result, translation is expected to be progressively quenched when the length of the nascent chains increases. This feature explains the previous observation that A-protein synthesis on Q beta RNA can start only on short nascent strands. Translational control of the A protein in the distantly related phage MS2 was recently shown to be controlled by the kinetics of RNA folding. This basic difference and its possible biological purpose can be explained by the different RNA folding pathways in Q beta and MS2. Interestingly, due to the presence of G-U pairs, structure prediction for the minus strand differs in some aspects from that for the plus strand. More specifically, there is a minus-strand specific, long-distance interaction bordering the minus-strand equivalent of the 5'-terminal hairpin. This interaction extends at the expense of the lower part of the terminal helix, thereby exposing the terminal C residues at which replication starts. This long-distance interaction, which was recently shown to be required for minus-strand replication, is strongly supported by our comparative data.

Allolevivirus↗
PubMed1996

Stoichiometry and domainal organization of the long tail-fiber of bacteriophage T4: a hinged viral adhesin.

The long-tail fibers (LTFs) form part of bacteriophage T4's apparatus for host cell recognition and infection, being responsible for its initial attachment to susceptible bacteria. The LTF has two parts, each approximately 70 to 75 nm long; gp34 (140 kDa) forms the proximal half-fiber, while the distal half-fiber is composed of gp37 (109 kDa), gp36(23 kDa) and gp35 (30 kDa). LTFs have long been thought to be dimers of gp34, gp37 and gp36, with one copy of gp35. We have used mass mapping by scanning transmission electron microscopy (STEM), quantitative SDS-PAGE, and computational sequence analysis to study the structures of purified LTFs and half-fibers of both kinds. These data establish that the LTF is, in fact, trimeric, with a stoichiometry of gp34: gp37: gp36: gp35 = 3:3:3:1. Averaged images of stained and unstained molecules resolve the LTF into a linear stack of 17 domains. At the proximal end is a globular domain of approximately 145 kDa that becomes incorporated into the baseplate. It is followed by a rod-like shaft (33 x 4 mm; 151 kDa) which correlates with a cluster of seven quasi repeats, each 34 to 39 residues long. The proximal half-fiber terminates in three globular domains. The distal half-fiber consists of ten globular domains of variable size and spacing, preceding a needle-like end domain (15 x 2.5 nm; 31 kDa). The LTF is rigid apart from hinges between the two most proximal domains, and between the proximal and distal half-fibers. The latter hinge occurs at a site of local non-equivalence (the "kneecap") at which density, correlated with the presence of gp35, bulges asymmetrically out on one side. Several observations indicate that gp34 participates in the sharing of conserved structural modules among coliphage tail-fiber genes to which gp37 was previously noted to subscribe. Two adjacent globular domains in the proximal half-fiber match a pair of domains in the distal half-fiber, and the rod domain in the proximal half-fiber resembles a similar domain in the T4 short tail-fiber (gp12). Finally, possible structures are considered; combining our data with earlier observations, the most likely conformation for most of the LTF is a three-stranded beta-helix.

Amino Acid Sequence↗
PubMed1997

Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qbeta replicase efficiently binds small RNAs by recognizing pyrimidine residues.

Binding of small RNAs by the RNA-dependent RNA polymerase of coliphage Qbeta was studied utilizing a fluorometric assay. A DNA oligonucleotide probe of sequence 5'-d(TTTTTCC) was 5'-end-labeled with pyrene. In this construct, the proximal thymine residues efficiently quench the fluorophore emission in solution. Upon stoichiometric binding of one probe per polymerase molecule, the pyrene steady-state fluorescence increases by two orders of magnitude, the fluorescence anisotropy increases, and a long fluorescence lifetime component of 140 ns appears. With addition of replicable RNA, steady-state fluorescence decreases in a concentration dependent manner and the long lifetime component is lost. This observation most likely reflects displacement of the pyrene-labeled probe from the proposed nucleic acid binding site II of Qbeta replicase. The effect was utilized to access binding affinities of different RNAs to this site in a reverse titration assay format. In 10 mM sodium phosphate (pH 7.0), 100 mM NaCl, at 16 degrees C, equilibrium dissociation constants for different template midi- and minivariant RNAs were calculated to be in the nanomolar range. In general, the minus and plus strands, concomitantly synthesized by Qbeta replicase during replication, exhibited discriminative affinities, while their hybrid bound less efficiently than either of the single strands. Different non-replicable tRNAs also bound to the polymerase with comparable dissociation constants. By titration with DNA homo-oligonucleotides it was shown that the probed site on Qbeta replicase does not require a 2' hydroxyl group for binding nucleic acids, but recognizes pyrimidine residues. Its interaction with thymine is lost in an A.T base-pair, while that with cytosine is retained after Watson-Crick base-pairing. These findings can explain the affinities of RNA-Qbeta replicase interactions reported here and in earlier investigations. The sensitivity of the described fluorometric assay allows detection of RNA amplification by Qbeta replicase in real-time.

Base Sequence↗
PubMed1993

Comparative analysis of the pC194 group of rolling circle plasmids.

pC194-type plasmids have been isolated from widely divergent species of bacteria: Gram positive, Proteobacteria, Spirochaetes and Cyanobacteria. We have examined the three essential replication elements of these plasmids, i.e., the Rep protein, and the origins of double and single stranded synthesis. Comparative analysis of Rep protein sequences from these plasmids indicates that they are highly divergent. Those isolated from Gram positive species fall into five groups: a Bacillus group, a Lactobacillus group, a Streptococcus group and two Staphylococcus aureus groups. The two S. aureus clusters are quite separate, suggesting that there has been at least one plasmid transfer between divergent Gram positive species. The double stranded origin of replication and the active site of the Rep protein display similarities across species indicating that these motifs can function in very divergent hosts. In contrast the single stranded origin of replication is typical of the host from which the plasmid is isolated. This is exemplified by (i) pKYM where the single stranded origins are similar to the minus origins found on the single-stranded coliphages, and (ii) pTD1 (isolated from a Spirochaete), pNostoc, pMA1 and pRF1 (all isolated from Cyanobacteria) which have no sequence homology to the minus origins identified in Gram positive or Gram negative species. This points to the single stranded origin as a feature critical to the determination of the host range of the plasmid.

Amino Acid Sequence↗
PubMed1994

Differential replication of plasmids during stringent and relaxed response of Escherichia coli.

Stringent control of DNA replication has been demonstrated for a few replicons like oriC, pBR322, and plasmids derived from coliphage lambda. In this study we investigated the replication of other plasmids harboring a well defined origin (orip15A, oripSC101, and oriRK2 = oriV) in amino-acid-starved stringent and relaxed strains of Escherichia coli. We found differential replication of plasmids during stringent and relaxed response. Inhibition of DNA synthesis or amplification of plasmid DNA in amino acid-starved relA+ and relA- cells depends on the kind of replicon and, surprisingly, on the nature of deprived amino acid. We conclude that there are no general rules for stringent control of DNA replication and each replicon must be considered separately. There are, however, possible explanations for the differences shown between replicons in their response to stringent and relaxed conditions.

Amino Acids↗
PubMed1998

The structural gene module in Streptococcus thermophilus bacteriophage phi Sfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts.

The structural gene cluster and the lysis module from lytic group II Streptococcus thermophilus bacteriophage phi Sfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. phi Sfi11 differed from the temperate S. thermophilus bacteriophage phi O1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, phi Sfi11 and the lytic group 1 S. thermophilus phi Sfi19 shared regions with variable degrees of similarity. Orf 1291 from phi Sfi19 was replaced by four genes in phi Sfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with phi Sfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between phi Sfi11 and phi Sfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of phi Sfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between phi Sfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G + C group of gram-positive bacteria is derived from a common ancestor.

Biological Evolution↗
PubMed1999

Transcription of the genome of the filamentous bacteriophage cf from both plus and minus DNA strands.

The filamentous bacteriophage cf infects the bacterium Xanthomonas campestris pv. citri. Northern blot analysis with probes derived from various restriction fragments of cf replicative form (RF) DNA has revealed the presence of five major phage-specific transcripts in infected cells. Four of these transcripts were shown to be derived from the region of the cf genome extending from gene II to gene VIII and are consistent with the cascade model of transcription proposed for Ff coliphages. These transcripts overlap with each other and terminate upstream of an efficient Rho-independent transcription terminator. Unlike the well-characterized Ff phages, in which only the minus strand of viral DNA serves as a transcription template, both strands of the RF DNA of phage cf appeared to be transcribed. Thus one of the five major cf transcripts was shown to be derived from a region of the viral minus strand that contains an open reading frame encoding a putative polypeptide of 165 amino acids. Primer extension analysis mapped the transcriptional initiation site of this RNA to a cytosine residue at position 870. A partial transcription map of phage cf revealed two independent regions of transcriptional activity. The region with the highest activity coincides with that encoding the polypeptides required in the largest amounts during the cf infection cycle.

5' Untranslated Regions↗
PubMed2000

Characterization of the lysogenic repressor (c) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112.

Bacteriophage D3112 is a Mu-like temperate transposable phage of Pseudomonas aeruginosa. Genetic mapping and DNA sequence analysis have identified the left end of the phage genome as encoding the transposase enzyme (A) and the lysogenic (c) repressor. The c open reading frame (ORF), located at the leftmost end of the phage genome and transcribed from right to left, has four possible GTG initiation codons. Using site-directed mutagenesis, each of the four GTG codons was modified to GTA, which cannot serve as an initiation codon. Plasmids were constructed expressing either the wild-type repressor ORF or the ORFs containing the mutated GTA codons. When introduced into Pseudomonas aeruginosa, no immunity to superinfection by D3112 was observed when the second GTG had been mutated. Northern blotting analysis demonstrated that the D3112 c repressor is transcribed as a 900-nt mRNA. The promoter region was defined by transcriptional lacZ fusions and primer extension analyses to bp 972-940 from the left end of the phage genome. When the D3112 c repressor was overexpressed and purified as a fusion protein with a C-terminal six-histidine extension (cts15-His6), it showed high affinity for a 261-bp PvuII fragment localized directly upstream of the c repressor ORF. Our results indicate that although D3112 c shows higher amino acid similarity to the lambda family of repressors than it does to those of Mu and D108, it appears that its structure and function more accurately reflect an evolutionary ancestry with those from transposable coliphages Mu and D108.

Amino Acid Sequence↗
PubMed1981

Enzymatic synthesis and function of folylpolyglutamates.

Derivatives of folic acid occur in nature predominantly as poly (gamma-glutamyl) derivatives containing 2-8 glutamate residues. The data regarding the function of these derivatives, and their biosynthesis by eucaryotic and procaryotic folylpolyglutamate synthetases, is reviewed. The most universal functions of folylpolyglutamates appear to be (a) as the actual cofactors in vivo for folate dependent enzymes, (b) as inhibitors of folate dependent enzymes for which they are not substrates, and (c) to increase retention of folates after they are transported into cells as monoglutamates. Folylpolyglutamates also have numerous specialized functions in specific organisms, e.g. as structural components of some coliphage, and as allosteric regulators in Neurospora crassa. A single enzyme appears responsible for synthesis of all polyglutamate derivatives, regardless of length. With the recent introduction of sensitive assays this folylpolyglutamate synthetase has begun to be characterized. Although procaryotic and eucaryotic synthetases have many dissimilar properties, both types catalyze the ATP-dependent addition of L-glutamate to the gamma-carboxyl of the glutamate present in the folate. Both types also require a monovalent cation and relatively high pH. The most significant differences between the two types are in their folate substrate specificity and the product lengths derived from various folates.

Animals↗
PubMed1980

Induction of prophage lambda without amplification of recA protein.

The requirement for amplified synthesis of recA protein in the UV-promoted induction of coliphage lambda was studied. We confirmed that a low concentration of rifampicin inhibited specifically the increased synthesis of recA protein after an inducing treatment (Satta and Pardee, 1978). Under these conditions, using an optimal dose of UV, E. coli lysogens were induced, producing active phage. The drug delayed the onset of induction and with increasing concentrations affected the yield of phage, but all the cells lysed. The results established that induction can proceed without amplification of recA protein synthesis.

Bacteriophage lambda↗