Studies on the bacteriophage MS2. The untranslated 5'-terminal nucleotide sequence preceding the first cistron

Molecular detection and genotyping of male-specific coliphages by reverse transcription-PCR and reverse line blot hybridization

In recent years, there has been increased interest in the use of male-specific or F+ coliphages as indicators of microbial inputs to source waters. Sero- or genotyping of these coliphages can also be used for microbial source tracking (MST). Among the male-specific coliphages, the F+ RNA (FRNA) viruses are well studied, while little is known about the F+ DNA (FDNA) viruses. We have developed a reverse line blot hybridization (RLB) assay which allows for the simultaneous detection and genotyping of both FRNA as well as FDNA coliphages. These assays included a novel generic duplex reverse transcription-PCR (RT-PCR) assay for FRNA viruses as well as a generic PCR for FDNA viruses. The RT-PCR assays were validated by using 190 field and prototype strains. Subsequent DNA sequencing and phylogenetic analyses of RT-PCR products revealed the classification of six different FRNA clusters, including the well-established subgroups I through IV, and three different FDNA clusters, including one (CH) not previously described. Within the leviviruses, a potentially new subgroup (called JS) including strains having more than 40% nucleotide sequence diversity with the known levivirus subgroups (MS2 and GA) was identified. We designed subgroup-specific oligonucleotides that were able to genotype all nine (six FRNA, three FDNA) different clusters. Application of the method to a panel of 351 enriched phage samples from animal feces and wastewater, including known prototype strains (MS2, GA, Q beta, M11, FI, and SP for FRNA and M13, f1, and fd for FDNA), resulted in successful genotyping of 348 (99%) of the samples. In summary, we developed a novel method for standardized genotyping of F+ coliphages as a useful tool for large-scale MST studies.

Nucleotide sequence and secondary structure of VSV leader RNA and homologous DNA involved in inhibition of DNA-dependent transcription

We have analyzed the nucleotide sequences and secondary structure required for the transcriptional inhibitory activity of the plus-strand leader RNA of vesicular stomatitis virus (VSV) in a reconstituted HeLa cell transcription system using the adenovirus-2 late promoter (LP) and virus-associated (VA) genes as templates. The New Jersey serotype (VSVNJ) leader and the leader of the Indiana serotype (VSVInd) both contain cleavage sites for the double-strand-specific ribonuclease V1, and these sites are consistent with the presence of a predicted AU-rich stem-loop structure. Studies in which the secondary structure was perturbed with the intercalating agent proflavin suggested that a stem-loop structure enhances the efficiency of transcription inhibition in the VSVNJ leader. Experiments using leader RNA fragments, a VSVInd cDNA derived from the 3' end of the genome, and synthetic oligodeoxynucleotide homologous to regions of the VSV leader indicated that the AU(AT)-rich center region of the VSV leader molecule is sufficient to inhibit DNA-dependent transcription directed by both polymerase II and III, but flanking nucleotide sequences are important for more efficient inhibition of transcription.

5-Methylcytosine depletion during tumour development: an extension of the miscoding concept

We propose a general model for neoplastic development which postulates that the loss of methyl groups from 5-methylcytosines (5-mC) involved in the control of gene expression may initiate neoplastic transformation and give rise to the aberrant phenotype of the transformed cell. Interference with normal patterns of methylation can be envisioned to occur by a number of mechanisms: as a result of carcinogen-induced G:C leads to A:T transition leading to a loss of potentially methylatable cytosines; by mutations or chromosome rearrangement which disrupt the integrity of active DNA methylase genes; by separating methylated repressor regions of the genome from the genes they control; by direct interference with DNA methylation, as proposed for ethionine and 5-azacytidine; by spontaneous deamination of 5-mC to thymine, leading to accumulation of 5-mC:G leads to T:A transitions, by virus-induced perturbations in host cell methylation patterns; and by activation of DNA demethylases.

Stable hairpin structure within the 5'-terminal 85 nucleotides of poliovirus RNA

The primary sequence of a 5'-terminal fragment of poliovirus type 1 RNA, generated by digestion with RNase III, has been determined. This sequence reveals the presence of a stable hairpin structure beginning nine nucleotides from the terminally linked protein VPg. The sequence does not contain (i) the initiation codons AUG or GUG or (ii) the putative ribosome-binding sequence complementary to the 3' end of eucaryotic ribosomal 18S RNA. The stem-and-loop structure identified can be drawn in either plus or minus RNA strands. It is unclear to which strand functional significance (if any) can be assigned. It is possible that the hairpin structure is involved in ribosomal recognition and translation or in RNA synthesis by interacting with replicase molecules.

Nucleotide sequence of the simian virus 40 HindII + III restriction fragment I (fourth part of the T antigen gene)

The HindII + III restriction fragment I (Hind-I) from simian virus 40 DNA represents 4.96% of the genome and maps in the early transcription region. Hind-I is an internal segment of the A gene and its information is expressed as part of the early 19-S mRNA, which codes for T antigen. We report here the nucleotide sequence of the 259-base-pair Hind-I fragment. The sequence was determined and confirmed by RNA and DNA sequencing methods: by analysis of oligonucleotides resulting from T1 and pancreatic RNase digestion of labeled RNA transcribed from SV40 DNA with Escherichia coli DNA-dependent RNA polymerase, by partial degradation of RNA transcripts with snake venom phosphodiesterase, and by base-specific chemical degradation of 5'-end-labeled subfragments of Hind-I according to the procedure of Maxam and Gilbert. Multiple triplets corresponding to termination codons occur in two of the three reading frames of the DNA strand that has the same polarity as early mRNA. The open reading frame connects in phase with the one of the Hind fragments flanking Hind-I, and the amino acid sequence specified by Hind-I lies in the middle part of the large-T antigen. Some features of the primary nucleotide sequence and of early transcription are discussed.

Secondary structure of mRNA and efficiency of translation initiation

A series of recombinant plasmids, containing the cro gene of phage lambda, exhibit strikingly different levels of expression depending apparently only on the nucleotide sequence of the untranslated 5' mRNA (Roberts et al., 1979). We postulate that initiation of translation involves interaction between an activated 30S ribosomal subunit and the 5'-terminal region of a messenger RNA already folded in a specific secondary structure. The observed variation in cro synthesis can then adequately be explained by secondary structure models which were derived for the different mRNAs. To maximize expression, it appears necessary that the initiation codon and, although less important, the ribosome interaction site are accessible.

Secondary structure of the 5' end of bacteriophage MS2 RNA Methoxyamine and kethoxal modification

To refine the secondary structure model of the 5' end of the bacteriophage MS2 genome, 32P-labeled MS2 RNA was partially digested with T1 RNase or with Cm-RNase and the 5'-end fragment was isolated, renatured and submitted to treatment with methoxyamine or kethoxal. The resulting modified RNA was digested with T1 RNase and the products were separated by minifingerprinting. Methoxyamine-induced modification of exposed cytidines was detected by differential mobility of modified oligonucleotides, while kethoxal-induced alteration of exposed guanosines was monitored by resistance to T1 ribonuclease digestion. The positions of the modified residues are discussed in terms of an improved secondary structure model proposed for the 5' end of the viral RNA. The structure itself is discussed in relation to sequence conservation and biological function.

Towards an experimental analysis of molecular self-organization and precellular Darwinian evolution

An experimental system is described, which opens up a novel pathway towards a molecular understanding of the origin of life. The systemic conditions for the evolution of biological macromolecules are investigated in detail.

Nucleotide sequence of the simian virus 40 Hind-K restriction fragment

The restriction fragment Hind-K represents 4.2% of the genome of Simian virus 40 (SV40) and is located near the middle of the late region. Its nucleotide sequence is reported here. It was mainly established by analysis of transcription products, synthesized by means of Escherichia coli RNA polymerase and nucleoside triphosphates, one of which was (alpha-32P)-labeled. Strand assignment was possible by hybridization of asymmetric, labeled transcripts of total SV40 DNA to filter-bound Hind-K fragment. Further information and unambiguous confirmation of the sequence was obtained by the use of direct DNA-sequencing methods. For this purpose the fragment was labeled at the 5' ends by means of polynucleotide kinase and [gamma-32P]ATP and redigested with a suitable restriction enzyme. The separated products were then either partially digested with snake venom diesterase for analysis by the 'wandering spot' method or partially degraded with the base-specific reagents dimethylsulphate or hydrazine for direct sequence analysis on gel. The Hind-K sequence is 219 base pairs long. The message strand is particularly rich in adenosine (39%) and purines. The nucleotide sequence cna unambiguously be translated into an amino acid sequence and the N-terminal codon of the viral protein VP1 gene could be identified. The amino-terminal part of VP1 is rich in proline and lysine. The nucleotide sequence of Hind-K codes also for the carboxyl-terminal part of the viral protein VP2 and VP3 genes, which partly overlap the VP1 gene.

On the possible modulating role of the isoleucine AUA-codon in bacteriophage MS2 RNA

A set of MS2 mutants were shown to have an additional silent mutation met --> ile at position 108 of the coat protein. As transitions are more frequent than transversions one would have expected an AUA codon in this position in the mutant RNAs. As the AUA codon is one of the best candidates for a modulation role in the control of translation in E. coli, the presence of this AUA in the gene for the protein made in major amounts upon viral infection would impose serious doubt on the theory of modulation. We have directly proven by minifinger-printing of mutant RNA and further analysis of the relevant spots that, in fact, the isoleucine residue at position 108 of the coat protein gene is specified by the non-rate-limiting AUU codon, in agreement with a modulation type of control of protein synthesis.

Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene

Bacteriophage MS2 RNA is 3,569 nucleotides long. The nucleotide sequence has been established for the third and last gene, which codes for the replicase protein. A secondary structure model has also been proposed. Biological properties, such as ribosome binding and codon interactions can now be discussed on a molecular basis. As the sequences for the other regions of this RNA have been published already, the complete, primary chemical structure of a viral genome has now been established.

In vitro site-directed mutagenesis: generation and properties of an infectious extracistronic mutant of bacteriophage Qbeta

An infectious extracistronic mutant of phage Qbeta has been prepared by site-directed mutagenesis. Qbeta RNA minus strands containing the mutagenic base analog N4-hydroxy-CMP instead of UMP at position 39 from the 5' end were synthesized in vitro and used as template for Qbeta replicase to synthesize one generation of plus strands. E. coli spheroplasts were infected with the newly synthesized plus strands and phage recovered from single plaques. RNA sequence analysis revealed that four out of the eighteen phage clones analyzed contained RNA with an A leads to G transition at position 40 from the 3' end (which corresponds to position 39 of the minus strand). Thus, the viability of phage Qbeta does not depend on a unique nucleotide sequence in the 3'-extracistronic RNA segment. Upon in vivo propagation of mutant 40, spontaneous true revertants arose with high frequency and overgrew the parental clone within about 10 passages, indicating a selective disadvantage of the extracistronic mutant. Replication of mixtures of wild type and mutant RNA in vitro resulted in a decrease of the proportion of mutated RNA in the progeny plus strands. The fact that Qbeta RNA containing an A leads to G transition in nucleotide--40 of Qbeta RNA is less efficiently replicated in vitro may explain the selective disadvantage of the mutant phage in vivo. The preparation of an infectious mutated RNA by site-directed mutagenesis shows that the method is suitable to produce specific nucleotide exchanges without impairing the biological competence of the RNA.

Polyamines in bacteriophage R17 and its RNA

Bacteriophage R17 and its RNA were found to contain significant amounts of spermidine but not of putrescine. When isolated at 0.01 M KCl, up to 1,000 molecules of spermidine were associated with the virion. The phage RNA isolated with phenol plus sodium lauryl sulfate contained approximately 70 to 90 molecules of spermidine. The association appeared to be ionic because the bound spermidine could be dissociated by KCl, MgCl2, or both. Effects of polyamines on in vitro translation were studied using both poly(U) and phage R17-RNA as mRNA. Addition of spermidine to the system at suboptimal concentrations of Mg2+ resulted in marked stimulations of the rate of protein synthesis. Putrescine alone had no effect but stimulated the incorporation in the presence of suboptimal concentrations of spermidine plus Mg2+. The isolated amino acid-incorporating system contained suboptimal soluble and bound polyamines. A comparison of incorporation was made in this system using R17-RNA with and without bound spermidine. No effects of these bound cations were detected on the rate or extent of incorporation of valine. The ratio of incorporation of histidine (present in non-coat proteins) to valine (total protein) revealed little difference as a functions of cation in the system or a function of the spermidine present in R17-RNA.

3'-Terminal nucletide sequence (n equals 361) of bacteriophage MS2 RNA

32P-Labeled MS2 RNA was partially digested with ribonuclease T1 (guanyloribonuclease; ribonucleate 3'-guanylo-oligonucleotidohydrolase; EC 3.1.4.8) or with epilson-carboxymethyl-lysine-41 pancreatic ribonuclease A (ribonucleate 3'-pyrimidino-oligonucleotidohydrolase; EC 3.1.4.22). A series of overlapping fragments was obtained which allowed the reconstruction of a 361-nucleotide-long 3'-terminal sequence. A unique reading frame could be deduced, which indicated that the replicase gene ends with a U-A-G termination signal and is followed by a 174-nucleotide-long untranslated segment.

Minimal requirements for template recognition by bacteriophage Qbeta replicase: approach to general RNA-dependent RNA synthesis

Any oligo- or polynucleotide able to offer a C-C-C-sequence at the 3'-terminus and a second C-C-C-sequence in a defined steric position to Qbeta replicase is an efficient template. Corresponding chemical modifications convert non-template RNAs to template RNAs.

Doublet frequencies in sequenced nucleic acids

A doublet frequency count (set of frequencies of the 16 possible two-base sequences) can be calculated from the experimentally determined overall sequence of a nucleic acid. In this paper, a statistical methodology is developed for comparing such counts with random, with others of the same type or with doublet proportions found in whole DNAs. The methods are applied to two major categories of sequenced RNAs. It is found that vertebrate ribosomal and transfer RNAs show significant differences from the overall vertebrate DNA pattern, especially in the frequency of the doublet CG. Bacterial rRNA and tRNA, on the other hand, show less dissimilarity from total DNA. In the RNA of the small bacteriophage MS2, the doublet frequencies of the translated regions of the genome resemble those in the host E. coli, whereas those in the intercistronic regions differ substantially. All these findings are discussed in relation to the origin, evolution and selection of the nucleic acids concerned.

Determinant of cistron specificity in bacterial ribosomes

The sequence of the 3'-terminus of 16S RNA from different bacteria has been determined. Complementarity relationships between this sequence and a purine-rich tract in the ribosome binding site of different bacterial mRNAs suggest that the 3'-end of 16S RNA determines the intrinsic capacity of ribosomes to translate a particular cistron.

tRNA nucleotidyltransferase-catalyzed incorporation of CMP and AMP into RNA-bacteriophage genome fragments

Fragments of bacteriophage RNAs R17, MS2 and Qbeta obtained by incubation with commercial snake venom phosphodiesterase become substrates of the Escherichia coli tRNA nucleotidyltransferase. The transferase adds back CMP and AMP in conditions in which it remains highly specific of CCA-deprived tRNAs. The results suggest that the fragment from the 3' end of the viral genome and/or possibly one or more internal fragment(s) are recognized by the transferase. These observations might indicate that bacteriophage RNAs contain certain features probably present in all tRNAs and which are recognized by the transferase.

Two-dimensional polyacrylamide-gel electrophoresis for purification of small RNAs specified by virulent coliphages T4, T5, T7 and BF23

RNAs synthesized in Escherichia coli infected with virulent phages T4, T5, T7 and BF23 were labelled with 32PO4 3- after phage infection. [32P]RNAs of low molecular weight were separated by two-dimensional polyacrylamide gel electrophoresis, in which electrophoresis was carried out in two dimensions at different concentrations of acrylamide. The fractionated RNAs were characterized by RNA-fingerprint patterns made after T1 ribonuclease digestion. The two-dimensional gel of 10% yields 20% acrylamide was suitable for RNA of less than 200 nucleotides, while that of 5% yields 10% was preferred for RNAs of about 150--400 nucleotides. With T4 phage, 16 RNA species were separable on a single slab gel. Among those, 11 were identified as the known RNA species, including eight T4 tRNAs, one tRNA precursor and two non-tRNA molecules. In the case of T5 and BF23, more than 20 RNA species were separated on a slab gel; 15 or more RNAs were found in the 4-S RNA region, and several in 5-S and 6-S region. The RNA-fingerprint patterns of many BF23 RNAs were very similar to those of corresponding RNAs of T5. Pseudouridine and ribosylthymidine, minor nucleosides generally present in tRNA, were found in several BF23 4-S RNAs tested. Possibility of those BF23 4-S RNAs as tRNAs is discussed. With phage T7, three RNAs were detected, two of which were much smaller than tRNAs.

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

With a stepwise degradation and terminal labeling procedure the 3'-terminal sequence of E. coli 16S ribosomal RNA is shown to be Pyd-A-C-C-U-C-C-U-U-A(OH). It is suggested that this region of the RNA is able to interact with mRNA and that the 3'-terminal U-U-A(OH) is involved in the termination of protein synthesis through base-pairing with terminator codons. The sequence A-C-C-U-C-C could recognize a conserved sequence found in the ribosome binding sites of various coliphage mRNAs; it may thus be involved in the formation of the mRNA.30S subunit complex.

Polyamine synthesis and accumulation in Escherichia coli infected with bacteriophage R17

We have studied the biosynthesis of polyamines during the multiplication of the RNA bacteriophage R17. R17-sensitive strains of Escherichia coli were derived from the stringent CP78 and the relaxed mutant derivative CP79. The cells were infected with R17 in the presence or absence of arginine, a required amino acid, and both the RNA and polyamine contents of the bacteria were determined before and after the infection. The uninfected CP79 rel derivative accumulated RNA and spermidine in the absence of arginine, unlike the stringent organism that accumulated neither under these conditions. After R17 infection, the stringent strain accumulated RNA and spermidine in the presence or absence of arginine. The data indicate a close correlation between the synthesis of RNA and spermidine, suggesting a significant role for this polyamine in the multiplication of phage R17.