J van Duin's research while affiliated with Leiden University and other places

Publications (58)

Article
The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two gene...
Article
The potential of the RNA phage MS2 to accommodate extra amino acids in its major coat protein has been examined. Accordingly, a pentapeptide was encoded in the genome as an N-terminal extension. In the MS2 crystal structure, this part of the coat protein forms a loop that extends from the outer surface of the icosahedral virion. At the RNA level, t...
Article
A puzzling aspect of replication of bacteriophage Qbeta RNA has always been that replicase binds at an internal segment, the M-site, some 1450 nt away from the 3' end. Here, we report on the existence of a long-range pseudoknot, base-pairing eight nt in the loop of the 3' terminal hairpin to a single-stranded interdomain sequence located about 1200...
Article
The genome of the positive strand RNA bacteriophage Qbeta folds into a number of structural domains, defined by long-distance interactions. The RNA within each domain is ordered in arrays of three- and four-way junctions that confer rigidity to the chain. One such domain, RD2, is about 1,000-nt long and covers most of the replicase gene. Its downst...
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In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies o...
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The secondary structure of the RNA from the single-stranded RNA bacteriophages, like MS2 and Qβ, has evolved to serve a variety of functions such as controlling gene expression, exposing binding sites for the replicase and capsid proteins, allowing strand separation and so forth. On the other hand, all of these foldings have to perform in bacterial...
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Alcaligenes faecalis penicillin G acylase is more stable than the Escherichia coli enzyme. The activity of the A. faecalis enzyme was not affected by incubation at 50 degrees C for 20 min, whereas more than 50% of the E. coli enzyme was irreversibly inactivated by the same treatment. To study the molecular basis of this higher stability, the A. fae...
Article
We have introduced 13 base substitutions into the coat protein gene of RNA bacteriophage MS2. The mutations, which are clustered ahead of the overlapping lysis cistron, do not change the amino acid sequence of the coat protein, but they disrupt a local hairpin, which is needed to control translation of the lysis gene. The mutations decreased the ph...
Article
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To examine the function of the central pseudoknot in 16S rRNA, we have studied Escherichia coli 30S subunits with the A18 mutation in this structure element. Previously, this mutation, which changes the central base pair of helix 2, C18-G917, to an A18×G917 mismatch, was shown to inhibit translation in vivo and a defect in initiation was suggested....
Article
The intercistronic region between the maturation and coat-protein genes of RNA phage MS2 contains important regulatory and structural information. The sequence participates in two adjacent stem-loop structures, one of which, the coat-initiator hairpin, controls coat-gene translation and is thus under strong selection pressure. We have removed 19 ou...
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We have monitored the evolution of insertions in two MS2 RNA regions of known secondary structure where coding pressure is negligible or absent. Base changes and shortening of the inserts proceed until the excessive nucleotides can be accommodated in the original structure. The stems of hairpins can be dramatically extended but the loops cannot, re...
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F-specific RNA phages can be used as model organisms for enteric viruses to monitor the effectiveness of sewage treatment, and to assess the potential contamination of surface water with these viruses. In this paper a method is described which identifies RNA phages quantitatively by a plaque hybridization assay. Oligonucleotide probes were develope...
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F-specific (F+) RNA coliphages are prevalent in sewage and other fecal wastes of humans and animals. There are four antigenically distinct serogroups of F+ RNA coliphages, and those predominating in humans (groups II and III) differ from those predominating in animals (groups I and IV). Hence, it may be possible to distinguish between human and ani...
Article
The expression of the gene encoding Escherichia coli threonyl-tRNA synthetase is negatively autoregulated at the translational level. The negative feedback is due to the binding of the synthetase to an operator site on its own mRNA located upstream of the initiation codon. The present work describes the characterisation of operator mutants that hav...
Article
We have determined the nucleotide sequence of three positive single-stranded RNA coliphages and have used this information, together with the known sequences of the related phages Qβ and SP, to construct a secondary structure model for the two distal domains of Qβ RNA. The 3′ terminal domain, which is about 100 nucleotides long, contains most of th...
Article
The gene for the maturation (A) protein of the single-stranded RNA coliphage MS2 is preceded by an untranslated leader of 130 nt. Secondary structure of the leader was deduced by phylogenetic comparison and by probing with enzymes and chemicals. The RNA folds into a cloverleaf, i.e., three stem-loop structures enclosed by a long-distance interactio...
Article
The initiation region of the coat-protein gene of RNA bacteriophage MS2 adopts a well-defined hairpin structure with the start codon occupying the loop position, while the Shine-Dalgarno (SD) sequence is part of the stem. In a previous study, we introduced mutations in this hairpin that changed its thermodynamic stability. The resulting phages evol...
Article
Full-text available
We report the complete nucleotide sequence of the single-stranded RNA phage PP7 from Pseudomonas aeruginosa. There are three open reading frames which code for apparent protein homologues of the single-stranded RNA coliphages, i.e., maturation protein, coat protein, and replicase. A fourth overlapping reading frame exists that probably encodes a ly...
Article
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The start of the coat protein gene of RNA phage MS2 adopts a well-defined hairpin structure of 12 bp (including one mismatch) in which the start codon occupies the loop position. An earlier expression study using partial MS2 cDNA clones had indicated that the stability of this hairpin is important for gene expression. For every -1.4 kcal/mol increa...
Article
Translational efficiency in Escherichia coli is in part determined by the Shine-Dalgarno (SD) interaction, i.e. the base-pairing of the 3' end of 16S ribosomal RNA to a stretch of complementary nucleotides in the messenger, located just upstream of the initiation codon. Although a large number of mutations in SD sequences have been produced and ana...
Article
One of the two mechanisms that regulate expression of the repllcase clstron In the single stranded RNA collphages is translatlonal coupling. This mechanism prevents rlbosomes from binding at the start of the repllcase clstron unless the upstream coat clstron Is being translated. Genetic analysis had identified a maximal region of 132 nucleotides In...
Article
We have quantitatively analyzed the relationship between translational efficiency and the mRNA secondary structure in the initiation region. The stability of a defined hairpin structure containing a ribosome binding site was varied over 12 kcal/mol (1 cal = 4.184 J) by site-directed mutagenesis and the effects on protein yields were analyzed in viv...
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Arginine is coded for by CGN (N = G, A, U, C), AGA and AGG. In Escherichia coli there is little tRNA for AGA and AGG and the use of these codons is strongly avoided in virtually all genes. Recently, we demonstrated that the presence of tandem AGA or AGG codons in mRNA causes frameshifts with high frequency. Here, we show that phaseshifts can be sup...
Article
The RNA of the Escherichia coli RNA phages is highly structured with 75% of the nucleotides estimated to take part in base-pairing. We have used enzymatic and chemical sensitivity of nucleotides, phylogenetic sequence comparison and the phenotypes of constructed mutants to develop a secondary structure model for the central region (900 nucleotides)...
Article
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Bacterial lysis induced by the expression of the cloned lysis gene of the RNA bacteriophage MS2 in Escherichia coli was shown to be under the same regulatory control mechanisms as penicillin-induced lysis. It was controlled by the stringent response and showed the phenomenon of tolerance when E. coli was grown at pH 5. Changes in the fine structure...
Article
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We have inserted the sequence 5'-AAG-GAGGU-3', which is complementary to the 3' terminus of Escherichia coli 16S rRNA, in a reading frame and analyzed its effect on the accuracy and overall rate of translation in vivo. Translation over the sequence yields a 50% ribosomal frameshift if the reading phase is A-AGG-AGG-U. The other two possible frames...
Article
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The RNA phage MS2 encodes a protein, 75 amino acids long, that is necessary and sufficient for lysis of the host cell. DNA deletion analysis has shown that the lytic activity is confined to the C-terminal half of the protein. We have examined the effects of a synthetic peptide, covering the C-terminal 25 amino acids of the lysis protein, on the ele...
Article
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Expression of the cloned lysis protein of phage MS2, which is sufficient to lyse wild type Escherichia coli, does not cause lysis of mutants lacking the osmoregulatory membrane-derived oligosaccharides (MDO). The lysis gene product normally found in the membrane fraction was not stably inserted into the membranes of a mdoA mutant; rather degradatio...
Article
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We have asked whether genetic overlaps only evolve to provide extra coding capacity in genomes of restricted size. As a model system we have used the lysis gene of the RNA bacteriophage MS2. This gene overlaps with the distal part of the coat protein gene and with the proximal part of the replicase gene. Using recombinant DNA procedures we have det...
Article
In overlapping reading frames of prokaryotic mRNA, the ribosome-binding site (RBS) of the downstream cistron is part of the coding sequence of the upstream message. We have examined whether the rate of translation in Escherichia coli can be sufficiently high to preclude the use of an RBS in initiation of protein synthesis when it is part of an acti...
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We have tested a putative base-paired interaction between the conserved GT psi C sequence of tRNA and the conserved GAAC47 sequence of 5 S ribosomal RNA by in vitro protein synthesis using ribosomes containing deletions in this region of 5 S rRNA. Ribosomes reconstituted with 5 S rRNA possessing a single break between residues 41 and 42, deletion o...
Article
In prokaryotes gene expression is mainly regulated at the levels of transcription and translation. An important form of translational control operates at the initiation of protein synthesis. For instance the translation of an existing mRNA can be prevented by features in the mRNA structure that prohibit binding of ribosomes. This type of control is...
Article
The translational efficiency of the coat protein gene of phage MS2 has been examined in vivo with respect to neighbouring sequences. The cloned MS2 DNA has been gradually shortened starting at the 5' or 3' terminus, and its effect on coat protein synthesis monitored. Removal of the 3'-terminal sequences had little influence. In contrast, the gradua...
Article
Translation of the lysis cistron of MS2 RNA requires a frameshift of ribosomes reading the upstream coat protein mRNA. The out-of-phase fraction of ribosomes terminates at either one of two nonsense codons just preceding the lysis cistron. Termination is followed by initiation at the start codon of the lysis protein message.
Article
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The deoxyoctanucleotide 5′d(AAGGAGGT) which is complementary to the 3′ terminus of 16S RNA has been used as a probe to measure the potential of this rRNA region to engage in intermolecular basepairing. The site specific binding of the octanucleotide is shown by labeling 16S RNA in situ at its 3′ end with [32P]pCp and T4 RNA ligase (EC 6.5.1.3.). Th...
Article
The effect of cloacin DF13 cleavage on several functional properties of the ribosome has been studied in a translational system in vitro. Cleaved ribosomes synthesize relatively shorter polypeptide chains on synthetic and natural templates. Their translational specificity is, however, unchanged as judged by the read-out of MS2 RNA. Here, cleaved as...
Article
An Escherichia coli cell-free translational system, deprived of initiation factor IF-3, has been used to study the role of the factor in protein synthesis. In this system, 30-S ribosomal subunits are preincubated together with MS2 phage RNA in a small volume in the presence of 10 mM Mg(Ac)2; the missing components required for protein synthesis are...
Article
Using an in vitro preparation for protein synthesis, we have studied the effect of the ribosomal protein S1 from Escherichia coli on the synthesis of the coat protein of the RNA-containing phages Qbeta and MS2, on that of an "early" and a "late" enzyme encoded by the DNA containing phage T7, and on that of anthranilate synthetase, an enzyme encoded...
Article
The previously reported requirement of ribosomal protein S1 for translation of phage RNA is now shown to be related to the involvement of the protein in initiation complex formation. The structure of the messenger RNA appears to be uniquely related to S1 function, since translation and initiation and midly unfolded phage RNA (by modification with f...
Article
The effect of Escherichia coli ribosomal protein S1 on translation has been studied in S1-depleted systems programmed with poly(U), poly(A) and MS2 RNA‡. The translation of the phage RNA depends strictly on the presence of S1. Optimum poly(U)-directed polyphenylalanine synthesis and poly(A)-programmed polylysine synthesis also require S1. Excess S1...
Article
Poly(U)-dependent polyphenylalanine synthesis is completely dependent on the presence of ribosomal protein S1. Polysomes generated under the direction of poly(U) contain approximately one molecule of S1 per ribosome. Isolation of 30 S ribosomes from poly(U)-generated polysomes by a procedure requiring a low concentration of Mg2+ (0·25 mM) results i...
Article
Native 30S ribosomal subunits fromEscherichia coli are deficient in fractional protein S21, which is present on the monosome and polysome-derived 30S subunits. The presence of S21 prevents the binding of Fmet-tRNA if and only if 50S subunits are present. In contrast, proteins S2, S3 and S14 stimulate the binding of Fmet-tRNA. These results have bee...
Article
1Mg2+-dependent dissociation of Escherichia coli ribosomes has been studied at various Mg2+ concentrations ranging from 10 to 0.5 mM. The extent of dissociation was determined by sucrose gradient centrifugation.2Of all 70 S ribosomes present in standard iS30 extracts about 50% dissociate in a relatively narrow range of Mg2+ concentration (between 4...
Article
When 30S ribosomal subunits from E. coli are incubated with poly U, two separable components are recovered by zonal centrifugation of the incubation mixture. The faster sedimenting component is an aggregate of 30S subunits and poly U, while the slower one corresponds to the 30S ribosomal subunit. One ribosomal protein, protein 30S-1 is predominantl...
Article
RNA derived from turnip yellow mosaic virus (TYMV) associates with washed Escherichia coli ribosomes at 0° with the formation of complexes, which sediment much faster than single 70-S ribosomes during centrifugation in the ultra-centrifuge. Under comparable conditions such complexes could not be detected when ribosomes were mixed with RNA from toba...
Article
Turnip yellow mosaic virus (TYMV) has been treated at alkaline pH (10.5–11.0) and high ionic strength (1.0 M KCl) at 30° for 8 minutes. According to Kaper and Halperin (1965) such a treatment causes in situ breakage of the viral RNA chain, yielding fragments of uniform size (about 5 S). In the present paper it is demonstrated that in situ fragmenta...
Article
1. Association of turnip yellow mosaic virus ribonucleic acid and varying numbers of isolated 70-S ribosomes from Escherichia coli occurs at 0° under appropriate ionic conditions and in the absence of soluble enzymes and cofactors required for protein synthesis.2. This association leads to the formation of polysomal aggregates of varying sizes up t...
Article
This 5-wave study among 397 adolescents examined the longitudinal associations between the development of adolescents’ relationships with parents and peers and commitment to the romantic partner. Data were collected annually from adolescents who completed self-report questionnaires on relationship quality with both parents and best friend at all me...
Article
In deze thesis is onderzoek gedaan naar het borgingsplan gedrag van Toekomst VBG. De hoofdvraag die centraal stond is: Op welke elementen is er theoretische ondersteuning voor het borgingsplan van de pijler gedrag van ‘Toekomst VBG’ om het beoogde gedrag van het VBG-mt binnen ‘Toekomst VBG’ te bewerkstelligen en welke betekenis geven de betrokkenen...

Citations

... Another prominent model phage is MS2, which has very small virions (27 nm in diameter) with a symmetric icosahedral capsid containing 180 copies of the coat protein [25]. Unlike the ssDNA-containing filamentous phages, MS2 phages contain a single-stranded RNA genome (family Leviviridae), making genetic engineering less straightforward [26]. However, MS2 capsids have 32 pores that allow access to the inside of the capsid [27], enabling chemical modification of the interior as well as exterior surfaces. ...
... Experimental Validation: MS2 Phage RNA Mutants. MS2 phage RNA (135 nucleotides) regulates the expression rate of phage MS2 maturation protein [20,33] at the translational level. It works as a regulator only when a specific subsequence (the SD sequence) is open (i.e., does not form base-pair contacts). ...
... Considerable dissociation of S21 protein from reassembled subunits is likely to be due to its peculiar properties. It is known that 30-S subunits usually contain significantly less than one molecule of this protein per particle [19]. The data of Table 1 show that practically all reassembled subunits contain an iodinat- ed S21 molecule, Therefore partial loss of this protein during sedimentation does not seem to be unexpected. ...
... It was synthesized at very low rates in vitro, absent in early coat gene amber mutants, and never appeared until the coat protein was made. These findings were explained by evidence that the lysis gene ribosome binding site is not directly accessible to initiating ribosomes, and requires passage of elongating ribosomes along the upstream coat gene to open the inhibitory secondary structure (Kastelein et al., 1983). The locus encoding a lysis function (S) in phage l also displayed a complex arrangement, with two in-frame AUGs (AUGAAGAUG) preceded by Shine-Dalgarno sequences. ...
... Furthermore, our results suggest a direct competition for the 3′ end between the replicase and IF3 because increasing concentrations of either the replicase or the substrate RNA compensated for the inhibitory effect of IF3. Notably, MS2 gene expression was also shown to be completely independent from IF3, unlike for E. coli host proteins 53 . Thus, replication and translation of MS2 genomes seem to be well adapted to conditions under which IF3 levels are minimal, such as it was reported for E. coli cells that have reached stationary phase 54 . ...
... The translationally nonspecific genera have G+C contents of 50% or more and, in addition, the ribosomes of these genera contain a protein equivalent to ribosomal protein S1, whereas none of the translationally specific genera contain S1. S1 has been shown to be necessary for translation in E. coli (33). ...
... By providing a more flexible binding platform in the A site, E3-mediated cleavage may lower both the stabilization of near-cognate and cognate aa-tRNA in the codon-recognition complex. This could lead to the loss of a relatively high proportion of cognate aa-tRNA during proofreading and might explain why ribosomes with cleaved 16S rRNA were found to be hyper-accurate and able to offset the effect of the error-inducing antibiotic streptomycin 37,38 . These in turn could lead to a slowly translating ribosome that would also arrest the following ribosomes in a polysome array. ...
... Such a function has also been proposed for IF3 and ribosomal protein S1 acting in conjunction (8). On the other hand, it is just as reasonable to propose that IF3 alters the 30S subunit conformation so as to favor mRNA:rRNA basepairing, without direct IF3/mRNA interaction (9,10). IF3 has been crosslinked to the 3' terminus of 16S RNA Nucleic Acids Research in 30S subunits (11), and to several 30S subunit proteins (12)(13)(14)(15) which, like the 3' terminus (16)(17)(18), are located in the cleft of the 30S subunit. ...
... The closed conformation (Fig. 2B), on the other hand, would represent the state of a 30S particle which in conjunction with the 50S particle is involved in the elongation and termination process of mRNA translation in which interaction with fortuitous mRNA binding sites has to be avoided. It is also tempting to speculate that initiation factor IF3, which is known to interact with the 3'-terminal region of bacterial 16S rRNA (26,27) stabilizes the open form of the free 30S subunit or even actively causes a switch from the closed to the open form by melting out specifically the helix between the two RNA ends. ...
... Ideally, in-vitro RNA replication is exponentially amplified in an autocatalytic manner [88,90]. With its wellcharacterized structure and function, Qβ replicase has been used in various studies, including Qβ replicase-mediated "template-free" RNA synthesis [91], the discovery of spontaneous recombination of RNA molecules [92], the ability of Qβ replicase to recognize specific templates [93], and the discovery of new functions of ribosomal protein S1 [94]. These studies laid the groundwork for the application of RNA replication both in vitro and in vivo. ...